diff --git a/DESCRIPTION b/DESCRIPTION index ecca64cf..6a6ad190 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -56,7 +56,8 @@ Suggests: colorspace, magrittr, vdiffr, - httptest + httptest, + rmdformats License: MIT + file LICENSE LazyData: true RoxygenNote: 7.3.1 diff --git a/NAMESPACE b/NAMESPACE index 67a5dfba..315ece05 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,7 +8,6 @@ export(tcplAddModel) export(tcplCode2CASN) export(tcplConf) export(tcplConfDefault) -export(tcplConfExample) export(tcplConfList) export(tcplConfLoad) export(tcplConfReset) diff --git a/R/assay_funcs.R b/R/assay_funcs.R index de69daae..f5c1020f 100644 --- a/R/assay_funcs.R +++ b/R/assay_funcs.R @@ -19,12 +19,7 @@ #' return the assay source ID (asid) and assay source name (asnm). #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' TCPLlite <- file.path(system.file(package = "tcpl"), "example") -#' tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite") -#' +#' \dontrun{ #' ## The load assay functions can be used without any parameters to list the #' ## full list of registered assay elements: #' tcplLoadAsid() @@ -43,9 +38,7 @@ #' a1 <- tcplLoadAeid(fld = "anm", val = "Steroidogenesis") #' a2 <- tcplLoadAeid(fld = "assay_name", val = "Steroidogenesis") #' identical(a1, a2) -#' -#' ## Reset configuration -#' options(conf_store) +#' } #' #' @return A data.table containing the ID, name, and any additional fields. NULL \ No newline at end of file diff --git a/R/config_funcs.R b/R/config_funcs.R index 2d33bd72..8bb755d4 100644 --- a/R/config_funcs.R +++ b/R/config_funcs.R @@ -14,8 +14,8 @@ #' @param ... Additional arguments that should be passed to dbConnect function #' #' @details -#' Currently, the tcpl package only supports the "MySQL" and "tcplLite" database -#' drivers. +#' Currently, the tcpl package supports the "MySQL", "example", and "API" +#' database drivers. #' #' The settings can be stored in a configuration file to make the using the #' package more user-friendly. To create the configuration file, the user must @@ -48,8 +48,7 @@ #' configuration file. #' #' \code{tcplConfDefault} changes the \code{options} to reflect the default -#' settings for the example tcplLite database, i.e. local directory, but does -#' not alter the configuration file. +#' settings for the API connection, but does not alter the configuration file. #' #' \code{tcplConfReset} is used to generate the initial configuration script, #' and can be used to reset or regenerate the configuration script by the user. diff --git a/R/data.R b/R/data.R index b5da029c..1c47e0b4 100644 --- a/R/data.R +++ b/R/data.R @@ -1,7 +1,7 @@ #' A subset of ToxCast data showing changes in transcription factor activity for multiple targets. #' #' The example dataset is used to illustrate how the user can pipeline single-concentration -#' data from chemical screening using tcplLite. +#' data from chemical screening using tcpl. #' #' @format A data frame with 320 rows and 10 variables: #' \describe{ @@ -22,7 +22,7 @@ #' A subset of ToxCast data showing changes in the activity of the intracellular estrogen receptor. #' #' The example dataset is used to illustrate how the user can pipeline multiple-concentration -#' data from chemical screening using tcplLite. +#' data from chemical screening using tcpl. #' #' @format A data frame with 14183 rows and 10 variables: #' \describe{ @@ -39,21 +39,6 @@ #' } #' @source ToxCast database "mcdat" -#' Chemical library of tested chemicals in the example datasets with the corresponding sample IDs. -#' -#' -#' @format A data frame with 6 rows and 6 variables: -#' \describe{ -#' \item{spid}{sample ID} -#' \item{casn}{Chemical Abstract Service(CAS) number} -#' \item{chnm}{chemical name} -#' \item{dsstox_substance_id}{chemical-specific DTXSID} -#' \item{code}{CAS number compressed into numeric string} -#' \item{chid}{unique chemical ID number for tcpl} -#' -#' } -#' @source ToxCast database -"chdat" #' List with multi-concentration data for the vignette diff --git a/R/mc2_mthds.R b/R/mc2_mthds.R index b0b647f0..7b11d330 100644 --- a/R/mc2_mthds.R +++ b/R/mc2_mthds.R @@ -62,7 +62,6 @@ #' \item{agg.percent.rep.spid}{Use for binary data. Aggregate technical replicates as percentage by taking the sum of rval (raw values) relative to total replicates per sample id (spid) and concentration index (cndx); \eqn{cval = (sum(rval)/.N)*100}{cval = (sum(rval)/.N)*100}.} #' \item{agg.percent.rep.spid.min1}{Use for binary data with variable number of replicates. Aggregate technical replicates as percentage by taking the sum of rval (raw values) relative to total replicates per per sample id (spid) and concentration index (cndx), where there is more than one replicate; \eqn{cval=(sum(rval)/.N)*100,~where~.N>1}{cval = (sum(rval)/.N)*100, where .N>1}.} Rvals are collapsed to one value per cndx.} #' } -#' } #' #' @note #' This function is not exported and is not intended to be used by the user. diff --git a/R/mc6.R b/R/mc6.R index 7c4ba0d9..9ebb774d 100644 --- a/R/mc6.R +++ b/R/mc6.R @@ -76,11 +76,7 @@ mc6 <- function(ae, wr = FALSE) { ## Load assay information to check for cell viability. Fill with 0 if unavailable. tbl <- "assay_component_endpoint" drvr = getOption("TCPL_DRVR") - if (drvr == "MySQL") { - flds <- tcplQuery(paste0("DESCRIBE ", tbl, ";"))$Field - } else if (drvr == "tcplLite") { - flds <- tcplQuery(paste0("PRAGMA table_info(", tbl, ");"),tbl=c(tbl))$name - } + flds <- tcplQuery(paste0("DESCRIBE ", tbl, ";"))$Field if("cell_viability_assay" %in% flds){ cell_viability <- tcplLoadAeid(fld = "aeid",val = ae,add.fld = "cell_viability_assay") diff --git a/R/mthd_funcs.R b/R/mthd_funcs.R index cc99d51d..a7f1729a 100644 --- a/R/mthd_funcs.R +++ b/R/mthd_funcs.R @@ -31,11 +31,7 @@ #' and the delete cascade are available in the package vignette. #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfDefault() -#' +#' \dontrun{ #' ## tcplListMthd allows the user to display the available methods for #' ## a given level and data type #' head(tcplMthdList(lvl = 2, type = "mc")) @@ -46,7 +42,6 @@ #' ## whether an ID exists before assigning/clearing methods. #' tcplMthdLoad(lvl = 2, id = 55, type = "mc") #' -#' \dontrun{ #' ## ACID 55 does not have any methods. Assign methods from the list above. #' tcplMthdAssign(lvl = 2, #' id = 55, @@ -63,6 +58,4 @@ #' ## Cleanup example method assigments #' tcplMthdClear(lvl = 2, id = 53:55, type = "mc") #' } -#' ## Reset configuration -#' options(conf_store) NULL diff --git a/R/query_funcs.R b/R/query_funcs.R index 5e91d0ca..449c5886 100644 --- a/R/query_funcs.R +++ b/R/query_funcs.R @@ -10,7 +10,7 @@ #' @inheritParams tcplConf #' #' @details -#' Currently, the tcpl package supports the "MySQL", "tcplLite", and "API" +#' Currently, the tcpl package supports the "MySQL", "example", and "API" #' database drivers. #' #' \code{tcplQuery} returns a data.table object with the query results. @@ -20,23 +20,13 @@ #' connected using "API" as driver. #' #' @examples -#' -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' TCPLlite <- file.path(system.file(package = "tcpl"), "example") -#' tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite") -#' +#' \dontrun{ +#' # only with MySQL driver #' tcplQuery("SELECT 'Hello World';") #' -#' ## When using tcplLite, name of table must be passed into tcplQuery -#' if (conf_store$TCPL_DRVR == 'MySQL') { -#' tcplQuery("SELECT * FROM assay;") -#' } else { -#' tcplQuery("SELECT * FROM assay;", tbl='assay') +#' # only with API driver +#' tcplConfDefault() +#' tcplQueryAPI(resource = "data", fld = "aeid", val = 2) #' } -#' -#' ## Reset configuration -#' options(conf_store) #' NULL \ No newline at end of file diff --git a/R/rgstr_funcs.R b/R/rgstr_funcs.R index b6a7a164..1ab1cff6 100644 --- a/R/rgstr_funcs.R +++ b/R/rgstr_funcs.R @@ -39,13 +39,7 @@ #' the registration process and all of the fields is available in the vignette. #' #' @examples -#' #' \dontrun{ -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfDefault() -#' #' ## Load current ASID information #' tcplLoadAsid() #' @@ -66,17 +60,6 @@ #' #' ## Remove the created ASID. Note: Manually deleting primary keys can cause #' ## serious database problems and should not generally be done. -#' -#' ## If using the tcplLite DRVR, must specify table name -#' if (conf_store$TCPL_DRVR == 'MySQL') { -#' tcplSendQuery(paste0("DELETE FROM assay_source WHERE asid = ", i1, ";")) -#' } else { -#' qy <- paste0("SELECT * FROM assay_source WHERE NOT asid = ", i1, ";") -#' tcplSendQuery(qy, tbl='assay_source', delete=TRUE) -#' } -#' -#' ## Reset configuration -#' options(conf_store) #' } #' NULL \ No newline at end of file diff --git a/R/tcplAppend.R b/R/tcplAppend.R index 40604070..3f75de12 100644 --- a/R/tcplAppend.R +++ b/R/tcplAppend.R @@ -28,6 +28,9 @@ tcplAppend <- function(dat, tbl, db, lvl=NULL) { db_pars <- NULL + if (getOption("TCPL_DRVR") == "API") { + stop("'API' driver not supported in tcplAppend.") + } if (getOption("TCPL_DRVR") == "MySQL") { @@ -66,63 +69,6 @@ tcplAppend <- function(dat, tbl, db, lvl=NULL) { } - if (getOption("TCPL_DRVR") == "tcplLite") { - # Rather than write to db, write to appropriate csv in db dir - db_pars <- db - fpath <- paste(db, tbl, sep='/') # Stitch together the dir path and the level table we're working on - fpath <- paste(fpath, 'csv', sep='.') - - tbl_cols <- colnames(read.table(fpath, header=T, sep=',', fill=T)) - if (length(setdiff(tbl_cols,names(dat)))>0){ - setDT(dat)[, setdiff(tbl_cols, names(dat)) := NA] - }else{ - setDT(dat) - } - - setcolorder(dat, tbl_cols) - - - # Need to set the "id" column. Don't have the luxury of the sql auto increment schema - autoFlag <- T - if (!is.null(lvl)) { - if (lvl %in% 0L:6L) { - if (startsWith(tbl, "mc")) { - autoIncr <- paste0("m",lvl,"id") - } else if (startsWith(tbl, "sc")) { - autoIncr <- paste0("s", lvl, "id") - } - } else if (lvl == "acid") { - autoIncr <- "acid" - } else if (lvl == "aeid") { - autoIncr <- "aeid" - } else if (lvl == "aid") { - autoIncr <- "aid" - } else if (lvl == "asid") { - autoIncr <- "asid" - } else { - autoFlag <- F - } - - if (autoFlag == T){ - temp_dt <- read.csv(fpath, sep=',', header=T) - if (length(temp_dt[,eval(autoIncr)]) == 0) { - start = 1 - } else { - start = tail(temp_dt[,eval(autoIncr)], 1) + 1 - } - - end <- nrow(dat)+start-1 - dat[, eval(autoIncr)] <- seq.int(start,end) - } - } - - - - write.table(dat, file=fpath, append=T, row.names=F, sep=',', col.names=F) - - return(TRUE) - } - if (is.null(db_pars)) { stop(getOption("TCPL_DRVR"), " is not a supported database system. See ", diff --git a/R/tcplConf.R b/R/tcplConf.R index 8c6071c4..6a95d64c 100644 --- a/R/tcplConf.R +++ b/R/tcplConf.R @@ -10,11 +10,6 @@ tcplConf <- function (drvr = NULL, user = NULL, pass = NULL, host = NULL, db = NULL,...) { #tcplConf(user='_dataminer', pass='pass', host='au.epa.gov', drvr = 'MySQL',db = 'invitrodb') - # Notes for tcplLite - # ================== - # Allow drvr='tcplLite' for writing flat files for each level of analysis - # db= - # Notes for example # ================== # Allow drvr='example' for loading example data from data directory in tcpl package @@ -47,9 +42,9 @@ tcplConf <- function (drvr = NULL, user = NULL, pass = NULL, host = NULL, if (!is.null(drvr)) { - if (!drvr %in% c( "MySQL", "tcplLite", "example", "API")) { + if (!drvr %in% c( "MySQL", "example", "API")) { stop(drvr, " is not a supported database driver. Must be ", - "'MySQL', 'tcplLite', 'API' or 'example'.") + "'MySQL', 'API', or 'example'.") } if (drvr == "example"){ @@ -67,11 +62,6 @@ tcplConf <- function (drvr = NULL, user = NULL, pass = NULL, host = NULL, } } - if (drvr == "tcplLite") { - tcplLiteInit() - options("TCPL_DRVR" = "tcplLite") - } - if (drvr == "API") { options("TCPL_DRVR" = "API") if (is.null(pass)) stop("'API' driver requires an API-key, supply it to ", diff --git a/R/tcplConfExample.R b/R/tcplConfExample.R deleted file mode 100644 index 8e03d1bd..00000000 --- a/R/tcplConfExample.R +++ /dev/null @@ -1,15 +0,0 @@ -#------------------------------------------------------------------------------- -# tcplConfExample: Generate default example location -#------------------------------------------------------------------------------- - -#' @rdname config_funcs -#' @export - -tcplConfExample <- function () { - - TCPLlite <- file.path(system.file(package = "tcpl"), "example") - tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite") - -} - -#------------------------------------------------------------------------------- diff --git a/R/tcplConfReset.R b/R/tcplConfReset.R index 17a482b3..5ba2c61d 100644 --- a/R/tcplConfReset.R +++ b/R/tcplConfReset.R @@ -14,12 +14,11 @@ tcplConfReset <- function () { "## Detailed information about this file available in the help file for", "## tcplConf (?tcplConf).", "", - "DRVR <- \"tcplLite\"", + "DRVR <- \"API\"", "HOST <- NA_character_", "USER <- NA_character_", - "PASS <- NA_character_", - "DB <- file.path(system.file(package = \"tcpl\"),", - " \"csv\")", + "PASS <- \"01cbaf22-904f-11ee-954e-325096b39f47\"", + "DB <- NA_character_", "", "###################################################################", sep = "\n", diff --git a/R/tcplConfSave.R b/R/tcplConfSave.R index b001d565..83e88c5d 100644 --- a/R/tcplConfSave.R +++ b/R/tcplConfSave.R @@ -16,8 +16,8 @@ tcplConfSave <- function () { } drvr <- getOption("TCPL_DRVR") - if (!drvr %in% c("MySQL", "tcplLite")) { - stop(drvr, " is not a supported database driver. Must be 'tcplLite' or ", + if (!drvr %in% c("MySQL", "API")) { + stop(drvr, " is not a supported database driver. Must be 'API' or ", "'MySQL'.") } drvr <- shQuote(drvr) diff --git a/R/tcplCytoPt.R b/R/tcplCytoPt.R index 83cceacb..76035874 100644 --- a/R/tcplCytoPt.R +++ b/R/tcplCytoPt.R @@ -72,11 +72,7 @@ #' #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfDefault() -#' +#' \dontrun{ #' ## Can only calculate the cytotox burst if using the MySQL database and #' ## TCPL_DRVR == 'MySQL' #' @@ -99,9 +95,7 @@ #' ## Changing 'default.pt' will change cyto_pt in the resulting data.table #' tcplCytoPt(aeid = 1:2, default.pt = 6) #' } -#' -#' ## Reset configuration -#' options(conf_store) +#' } #' #' @return A data.table with the cytotoxicity distribution for each chemical. #' The definition of the field names are listed under "details." diff --git a/R/tcplDelete.R b/R/tcplDelete.R index 5b6749cc..8538834b 100644 --- a/R/tcplDelete.R +++ b/R/tcplDelete.R @@ -26,14 +26,9 @@ tcplDelete <- function(tbl, fld, val, db) { if (length(tbl) != 1 || !is(tbl,"character")) { stop("The input 'tbl' must be a character of length one.") } - - if (getOption("TCPL_DRVR") == "tcplLite") { - qformat <- paste("SELECT * FROM", tbl, "WHERE NOT ") - qformat <- paste0(qformat, "( ", paste( fld, "IN (%s)", collapse = " AND "), ")") - } else { - qformat <- paste("DELETE FROM", tbl, "WHERE") - qformat <- paste0(qformat, " ", paste(fld, "IN (%s)", collapse = " AND ")) - } + + qformat <- paste("DELETE FROM", tbl, "WHERE") + qformat <- paste0(qformat, " ", paste(fld, "IN (%s)", collapse = " AND ")) qformat <- paste0(qformat, ";") diff --git a/R/tcplGetAeid.R b/R/tcplGetAeid.R index 03cba1aa..504db244 100644 --- a/R/tcplGetAeid.R +++ b/R/tcplGetAeid.R @@ -12,17 +12,11 @@ #' @param name A string that will be matched to the assay component endpoint name #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' ## Search for aenm (assay name) case insensitive #' tcplGetAeid("TOX21") #' tcplGetAeid("tox21") -#' -#' ## Reset configuration -#' options(conf_store) +#' } #' #' @export diff --git a/R/tcplListFlds.R b/R/tcplListFlds.R index fb5d5da0..853397c3 100644 --- a/R/tcplListFlds.R +++ b/R/tcplListFlds.R @@ -14,8 +14,10 @@ #' tcplLoad- functions. #' #' @examples +#' \dontrun{ #' ## Gives the fields in the mc1 table #' tcplListFlds("mc1") +#' } #' #' @return A string of field names for the given table. #' @@ -28,6 +30,9 @@ tcplListFlds <- function(tbl, db = getOption("TCPL_DB")) { ## Variable-binding to pass R CMD Check name <- COLUMN_NAME <- NULL + if (getOption("TCPL_DRVR") == "API") { + stop("'API' driver not supported in tcplListFlds.") + } if (length(tbl) > 1 | length(db) > 1) { stop("tbl and db must both be of length 1.") } @@ -51,16 +56,6 @@ tcplListFlds <- function(tbl, db = getOption("TCPL_DB")) { } - if (getOption("TCPL_DRVR") == "tcplLite") { - # return the data table by reading the file. No need to run tcplQuery, simply return data.table columns here - fpath <- paste(db, tbl, sep='/') - fpath <- paste(fpath, 'csv', sep='.') - DT <- read.table(fpath, header=T, sep=',', fill=T) - return(colnames(DT)) - - - } - stop(getOption("TCPL_DRVR"), " is not a supported database system. See ", "?tcplConf for more details.") diff --git a/R/tcplLiteInit.R b/R/tcplLiteInit.R deleted file mode 100644 index 35ccbeea..00000000 --- a/R/tcplLiteInit.R +++ /dev/null @@ -1,71 +0,0 @@ -tcplLiteInit <- function () { - # Create initial flat files with appropriate fields - db = getOption("TCPL_DB") - all_files <- list('assay_source'= c('asid', 'assay_source_name', 'assay_source_long_name', 'assay_source_desc'), - 'assay'= c('aid', 'asid', 'assay_name', 'assay_desc', 'timepoint_hr', 'organism_id', 'organism', 'tissue', 'cell_format', 'cell_free_component_source', 'cell_short_name', 'cell_growth_mode', 'assay_footprint', 'assay_format_type', 'assay_format_type_sub', 'content_readout_type', 'dilution_solvent', 'dilution_solvent_percent_max'), - 'assay_component'= c('acid', 'aid', 'assay_component_name', 'assay_component_desc', 'assay_component_target_desc', 'parameter_readout_type', 'assay_design_type', 'assay_design_type_sub', 'biological_process_target', 'detection_technology_type', 'detection_technology_type_sub', 'detection_technology', 'signal_direction_type', 'key_assay_reagent_type', 'key_assay_reagent', 'technological_target_type', 'technological_target_type_sub'), - 'assay_component_endpoint'=c('aeid', 'acid', 'assay_component_endpoint_name', 'export_ready', 'internal_ready', 'assay_component_endpoint_desc', 'assay_function_type', 'normalized_data_type', 'analysis_direction', 'burst_assay', 'key_positive_control', 'signal_direction', 'intended_target_type', 'intended_target_type_sub', 'intended_target_family', 'intended_target_family_sub', 'fit_all', 'cell_viability_assay', 'data_usability'), - 'assay_component_map'= c('acid', 'acsn'), - 'sample'= c('spid', 'chid', 'stkc', 'stkc_unit', 'tested_conc_unit', 'spid_legacy'), - 'chemical_library'= c('chid', 'clib'), - 'chemical' = c('chid', 'casn', 'chnm', 'dsstox_substance_id', 'code'), - - 'mc0'= c('m0id', 'acid', 'spid', 'apid', 'rowi', 'coli', 'wllt', 'wllq', 'conc', 'rval', 'srcf', 'created_date', 'modified_date', 'modified_by'), - 'mc1' = c('m1id', 'm0id', 'acid', 'cndx', 'repi', 'created_date', 'modified_date', 'modified_by'), - 'mc2' = c('m2id', 'm0id', 'acid', 'm1id', 'cval', 'created_date', 'modified_date', 'modified_by'), - - 'mc3' = c('m3id', 'aeid', 'm0id', 'acid', 'm1id', 'm2id', 'bval', 'pval', 'logc', 'resp', 'created_date', 'modified_date', 'modified_by'), - 'mc4' = c('m4id', 'aeid', 'spid', 'bmad', 'resp_max', 'resp_min', 'max_mean', 'max_mean_conc', 'max_med', 'max_med_conc', 'logc_max', 'logc_min', 'cnst', 'hill', 'hcov', 'gnls', 'gcov', 'cnst_er', 'cnst_aic', 'cnst_rmse', 'cnst_prob', 'hill_tp', 'hill_tp_sd', 'hill_ga', 'hill_ga_sd', 'hill_gw', 'hill_gw_sd', 'hill_er', 'hill_er_sd', 'hill_aic', 'hill_rmse', 'hill_prob', 'gnls_tp', 'gnls_tp_sd', 'gnls_ga', 'gnls_ga_sd', 'gnls_gw', 'gnls_gw_sd', 'gnls_la', 'gnls_la_sd', 'gnls_lw', 'gnls_lw_sd', 'gnls_er', 'gnls_er_sd', 'gnls_aic', 'gnls_rmse', 'gnls_prob', 'nconc', 'npts', 'nrep', 'nmed_gtbl', 'tmpi', 'created_date', 'modified_date', 'modified_by'), - 'mc4_agg' = c('aeid', 'm0id', 'm1id', 'm2id', 'm3id', 'm4id'), - 'mc5' = c('m5id', 'm4id', 'aeid', 'modl', 'hitc', 'fitc', 'coff', 'actp', 'modl_er', 'modl_tp', 'modl_ga', 'modl_gw', 'modl_la', 'modl_lw', 'modl_prob', 'modl_rmse', 'modl_acc', 'modl_acb', 'modl_ac10', 'model_type', 'created_date', 'modified_date', 'modified_by'), - 'mc6' = c('m6id', 'm5id', 'm4id', 'aeid', 'mc6_mthd_id', 'flag', 'fval', 'fval_unit', 'created_date', 'modified_date', 'modified_by'), - - 'mc2_acid' = c('mc2_mthd_id', 'acid', 'exec_ordr', 'created_date', 'modified_date', 'modified_by'), - 'mc3_aeid' = c('mc3_mthd_id', 'aeid', 'exec_ordr', 'created_date', 'modified_date', 'modified_by'), - 'mc4_aeid' = c('mc4_mthd_id', 'aeid', 'created_date', 'modified_date', 'modified_by'), - 'mc5_aeid' = c('aeid', 'mc5_mthd_id', 'created_date', 'modified_date', 'modified_by'), - 'mc6_aeid' = c('aeid', 'mc6_mthd_id', 'created_date', 'modified_date', 'modified_by'), - - 'sc0' = c('s0id', 'acid', 'spid', 'apid', 'rowi', 'coli', 'wllt', 'wllq', 'conc', 'rval', 'srcf', 'created_date', 'modified_date', 'modified_by'), - 'sc1' = c('s1id', 's0id', 'acid', 'aeid', 'logc', 'bval', 'pval', 'resp', 'created_date', 'modified_date', 'modified_by'), - 'sc2' = c('s2id', 'aeid', 'spid', 'bmad', 'max_med', 'coff', 'hitc', 'tmpi', 'created_date', 'modified_date', 'modified_by'), - 'sc2_agg' = c('aeid', 's0id', 's1id', 's2id'), - 'sc1_aeid' = c('sc1_mthd_id', 'aeid', 'exec_ordr', 'created_date', 'modified_date', 'modified_by'), - 'sc2_aeid' = c('sc2_mthd_id', 'aeid', 'created_date', 'modified_date', 'modified_by') - ) - for (k in names(all_files)) { - v = all_files[[k]] - fpath <- paste(db, k, sep='/') - fpath <- paste(fpath, 'csv', sep='.') - if (!file.exists(fpath)) { - df <- data.frame(matrix(ncol=length(v), nrow=0)) - colnames(df) <- v - print(sprintf("Writing local %s table for future referencing.", k)) - write.table(df, file=fpath, append=F, row.names=F, sep=',', col.names=T) - } - } - - methods = c("mc2_methods", "mc3_methods","mc4_methods", "mc5_methods","mc5_fit_categories", "mc6_methods", "sc1_methods", "sc2_methods")#, "chemical") - - for (m in methods) { - tcpl_fpath <- file.path(system.file(package = "tcpl"), "csv") - tcpl_fpath <- paste(tcpl_fpath, m, sep='/') - tcpl_fpath <- paste(tcpl_fpath, 'csv', sep='.') - fpath <- paste(db, m, sep='/') - fpath <- paste(fpath, 'csv', sep='.') - if (!file.exists(fpath)) { - print(sprintf("Writing local %s table for future referencing.", m)) - file.copy(tcpl_fpath, db) - } - - - } - - - - - - - - -} \ No newline at end of file diff --git a/R/tcplLoadChem.R b/R/tcplLoadChem.R index 7b50a7ab..3a7d2c28 100644 --- a/R/tcplLoadChem.R +++ b/R/tcplLoadChem.R @@ -25,11 +25,7 @@ #' the string in 'val' to an RLIKE statement within the MySQL query. #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' ## Passing no parameters gives all of the registered chemicals with their #' ## sample IDs #' tcplLoadChem() @@ -43,9 +39,7 @@ #' ## Other examples: #' tcplLoadChem(field = "chnm", val = "Bisphenol A") #' tcplLoadChem(field = "chid", val = 20182) -#' -#' ## Reset configuration -#' options(conf_store) +#' } #' #' @return A data.table with the chemical information for the given parameters #' diff --git a/R/tcplLoadChemList.R b/R/tcplLoadChemList.R index 9ee02288..06e288a3 100644 --- a/R/tcplLoadChemList.R +++ b/R/tcplLoadChemList.R @@ -23,11 +23,7 @@ #' multiple times (one for each distinct list). #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' ## Passing no parameters gives all of the chemical IDs that have a chemical #' ## list registered #' clist <- tcplLoadChemList() @@ -47,9 +43,7 @@ #' tcplLoadChemList(field = "list_acronym", val = "CPDBAS") #' tcplLoadChemList(field = "chid", val = 20182) #' tcplLoadChemList(field = "dsstox_substance_id", val = "DTXSID7020182") -#' -#' ## Reset configuration -#' options(conf_store) +#' } #' #' @return A data.table with the chemical list information for the given #' parameters. diff --git a/R/tcplLoadData.R b/R/tcplLoadData.R index c510cb57..3f62268f 100644 --- a/R/tcplLoadData.R +++ b/R/tcplLoadData.R @@ -56,11 +56,7 @@ #' } #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' ## Load all of level 0 for multiple-concentration data, note 'mc' is the #' ## default value for type #' tcplLoadData(lvl = 0) @@ -75,9 +71,7 @@ #' ## Load level 0 data where the well type is "t" and the concentration #' ## index is 3 or 4 #' tcplLoadData(lvl = 1, fld = c("wllt", "cndx"), val = list("t", c(3:4))) -#' -#' ## Reset configuration -#' options(conf_store) +#' } #' @return A data.table containing data for the given fields. #' #' @seealso \code{\link{tcplQuery}}, \code{\link{data.table}} diff --git a/R/tcplLvlCount.R b/R/tcplLvlCount.R index d97c83d9..8d4139f5 100644 --- a/R/tcplLvlCount.R +++ b/R/tcplLvlCount.R @@ -20,16 +20,10 @@ #' #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' TCPLlite <- file.path(system.file(package = "tcpl"), "example") -#' tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite") -#' +#' \dontrun{ #' ## Get all counts for level 1 for multiple-concentration #' tcplLvlCount(lvls = 1) #' -#' \dontrun{ #' ## Get all counts for levels 4 through 7 for multiple-concentration #' tcplLvlCount(lvls = 4:7) #' @@ -37,9 +31,6 @@ #' ## default value for type #' tcplLvlCount() #' } -#' -#' ## Reset configuration -#' options(conf_store) #' #' @return A data.table containing data for the given fields. #' diff --git a/R/tcplPlot.R b/R/tcplPlot.R index a7a44cdc..3c2a0ba1 100644 --- a/R/tcplPlot.R +++ b/R/tcplPlot.R @@ -54,15 +54,9 @@ #' @export #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' tcplPlot(fld = "m4id", val = c(18609966)) ## Create a level 4 plot -#' -#' ## Reset configuration -#' options(conf_store) +#' } tcplPlot <- function(dat = NULL, type = "mc", fld = "m4id", val = NULL, compare.val = NULL, by = NULL, output = c("console", "pdf", "png", "jpg", "svg", "tiff"), fileprefix = paste0("tcplPlot_", Sys.Date()), multi = NULL, verbose = FALSE, nrow = NULL, ncol = NULL, dpi = 600, flags = FALSE, yuniform = FALSE, yrange=c(NA,NA)) { #variable binding conc_unit <- bmd <- resp <- compare.dat <- NULL diff --git a/R/tcplPlotFits.R b/R/tcplPlotFits.R index 906aaf14..fd703539 100644 --- a/R/tcplPlotFits.R +++ b/R/tcplPlotFits.R @@ -31,12 +31,7 @@ #' endpoint ID. #' #' @examples -#' -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfDefault() -#' +#' \dontrun{ #' ## tcplPlotFits needs data.tables supplying the concentration/response #' ## data stored in mc4_agg, as well as the fit information from mc4 or mc5. #' ## Additionally, tcplPlotFits can take level 6 data from mc6 and add the @@ -47,11 +42,9 @@ #' l5 <- tcplLoadData(lvl = 5, fld = "m4id", val = 18609966) #' l4_agg <- tcplLoadData(lvl = "agg", fld = "m4id", val = 18609966) #' -#' \dontrun{ #' pdf(file = "tcplPlotFits.pdf", height = 6, width = 10, pointsize = 10) #' tcplPlotFits(dat = l5, agg = l4_agg) #' graphics.off() -#' } #' #' ## While it is most likely the user will want to just save all of the plots #' ## to view in a PDF, the 'browse' parameter can be used to quickly view @@ -61,14 +54,10 @@ #' ## a subset of the data. This browse function is admittedly clunky. #' bpa <- tcplLoadChem(field = "chnm", val = "Bisphenol A")[ , spid] #' l5_sub <- l5[spid %in% bpa] -#' \dontrun{ #' tcplPlotFits(dat = l5_sub, #' agg = l4_agg[m4id %in% l5_sub$m4id], #' browse = TRUE) #' } -#' -#' ## Reset configuration -#' options(conf_store) #' #' @import data.table #' @export diff --git a/R/tcplPlotLoadData.R b/R/tcplPlotLoadData.R index 8563f362..17054e7a 100644 --- a/R/tcplPlotLoadData.R +++ b/R/tcplPlotLoadData.R @@ -28,11 +28,7 @@ #' 'sc' for single concentration data. #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' ## load mc plot data for an entire endpoint #' dat <- tcplPlotLoadData(fld = "aeid", val = 703) #' @@ -56,9 +52,8 @@ #' output = "pdf", #' flags = TRUE, #' fileprefix="example") -#' -#' ## Reset configuration -#' options(conf_store) +#' } +#' #' @return A data.table containing plot-ready data for the given fields. #' #' @seealso \code{\link{tcplPlot}} diff --git a/R/tcplPlotM4ID.R b/R/tcplPlotM4ID.R index 5bff6a39..f5c09dd4 100644 --- a/R/tcplPlotM4ID.R +++ b/R/tcplPlotM4ID.R @@ -27,17 +27,11 @@ #' the AC50 confidence interval and hit percentage information from bootstrapping. #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' tcplPlotM4ID(m4id = 18609966, lvl = 4) ## Create a level 4 plot #' tcplPlotM4ID(m4id = 18609966, lvl = 5) ## Create a level 5 plot #' tcplPlotM4ID(m4id = 18609966, lvl = 6) ## Create a level 6 plot -#' -#' #' ## Reset configuration -#' options(conf_store) +#' } #' #' @seealso \code{\link{tcplPlotFits}}, \code{\link{tcplMakeAeidPlts}} #' @import data.table diff --git a/R/tcplPlotPlate.R b/R/tcplPlotPlate.R index 22569846..39b7470f 100644 --- a/R/tcplPlotPlate.R +++ b/R/tcplPlotPlate.R @@ -35,19 +35,10 @@ #' pointsize = 10, units = "in" #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfDefault() -#' -#' d1 <- tcplLoadData(lvl = 1, fld = "acid", val = 1) #' \dontrun{ +#' d1 <- tcplLoadData(lvl = 1, fld = "acid", val = 1) #' tcplPlotPlate(dat = d1, apid = "09Apr2014.Plate.17") #' } -#' -#' ## Reset configuration -#' options(conf_store) -#' #' @import data.table #' @importFrom stats quantile #' @export diff --git a/R/tcplPrepOtpt.R b/R/tcplPrepOtpt.R index d8b9249c..95bb22eb 100644 --- a/R/tcplPrepOtpt.R +++ b/R/tcplPrepOtpt.R @@ -21,12 +21,7 @@ #' function will only attempt to map the ID fields given by 'ids.' #' #' @examples -#' -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' ## Load some example data #' d1 <- tcplLoadData(1) #' @@ -42,10 +37,7 @@ #' d3 <- tcplPrepOtpt(d1, ids = "spid") #' "chnm" %in% names(d3) ## TRUE #' "acnm" %in% names(d3) ## FALSE -#' -#' ## Reset configuration -#' options(conf_store) -#' +#' } #' #' @return The given data.table with chemical and assay information mapped #' @export diff --git a/R/tcplQuery.R b/R/tcplQuery.R index 01cb8a2b..653249ed 100644 --- a/R/tcplQuery.R +++ b/R/tcplQuery.R @@ -17,6 +17,9 @@ tcplQuery <- function(query, db = getOption("TCPL_DB"), if (is.null(drvr)) drvr <- getOption("TCPL_DRVR") #Check for valid inputs + if (drvr == "API") { + stop("'API' driver not supported in tcplQuery.") + } if (length(query) != 1 || !is(query, "character")) { stop("The input 'query' must be a character of length one.") } @@ -45,20 +48,6 @@ tcplQuery <- function(query, db = getOption("TCPL_DB"), } - if (drvr == "tcplLite") { - #query <- "SELECT spid,chemical.chid,casn,chnm FROM sample LEFT JOIN chemical ON chemical.chid=sample.chid WHERE sample.chid is NULL " - db_pars <- "Just running tcplLite, we're OK" - for (t in tbl) { - fpath <- paste(db, t, sep='/') - fpath <- paste(fpath, 'csv', sep='.') - assign(t, read.table(fpath, header=T, sep=',')) - } - - result <- as.data.table(sqldf(query, stringsAsFactors=F)) - - - } - if (is.null(db_pars)) { stop(getOption("TCPL_DRVR"), " is not a supported database system. See ", diff --git a/R/tcplSendQuery.R b/R/tcplSendQuery.R index e19e3bb6..11e6e083 100644 --- a/R/tcplSendQuery.R +++ b/R/tcplSendQuery.R @@ -18,6 +18,9 @@ tcplSendQuery <- function(query, db = getOption("TCPL_DB"), drvr = getOption("TCPL_DRVR"), tbl=NULL, delete=F) { #Check for valid inputs + if (getOption("TCPL_DRVR") == "API") { + stop("'API' driver not supported in tcplSendQuery.") + } if (length(query) != 1 || !is(query,"character")) { stop("The input 'query' must be a character of length one.") } @@ -47,28 +50,6 @@ tcplSendQuery <- function(query, db = getOption("TCPL_DB"), } - if (getOption("TCPL_DRVR") == "tcplLite") { - db_pars <- "Just running tcplLite, we're OK" - - for (t in tbl) { - fpath <- paste(db, t, sep='/') - fpath <- paste(fpath, 'csv', sep='.') - assign(t, read.table(fpath, header=T, sep=',')) - } - - temp <- as.data.table(sqldf(query, stringsAsFactors=F)) - - if (delete == T) { - if (length(tbl) > 1) { - stop("Can't execute delete on more that one table") - } - db_pars <- db - fpath <- paste(db, tbl, sep='/') - fpath <- paste(fpath, 'csv', sep='.') - write.table(temp, file=fpath, append=F, row.names=F, sep=',', col.names=T) # Need to rewrite whole table - } - } - if (is.null(db_pars)) { stop(getOption("TCPL_DRVR"), " is not a supported database system. See ", diff --git a/R/tcplSubsetChid.R b/R/tcplSubsetChid.R index 67625320..d71365d1 100644 --- a/R/tcplSubsetChid.R +++ b/R/tcplSubsetChid.R @@ -32,11 +32,7 @@ #' considering any flags. #' #' @examples -#' ## Store the current config settings, so they can be reloaded at the end -#' ## of the examples -#' conf_store <- tcplConfList() -#' tcplConfExample() -#' +#' \dontrun{ #' ## Load the example level 5 data #' d1 <- tcplLoadData(lvl = 5, fld = "aeid", val = 797) #' d1 <- tcplPrepOtpt(d1) @@ -49,9 +45,7 @@ #' ## all equal. Therefore, if the flags are ignored, the selected sample will #' ## be the sample with the lowest modl_ga. #' tcplSubsetChid(dat = d2, flag = FALSE)[, list(m4id, modl_ga)] -#' -#' ## Reset configuration -#' options(conf_store) +#' } #' #' @return A data.table with a single sample for every given chemical-assay #' pair. diff --git a/R/tcpldbStats.R b/R/tcpldbStats.R index 891d03ba..3457b5ea 100644 --- a/R/tcpldbStats.R +++ b/R/tcpldbStats.R @@ -5,7 +5,7 @@ #' @title Get summary statistics for the database #' #' @description -#' \code{tcpldbStats} takes a string(type) and an optional parameter(val) to return the summary statistics on the entire tcplLite database +#' \code{tcpldbStats} takes a string(type) and an optional parameter(val) to return the summary statistics on the entire tcpl database #' When type = "all" the val is ignored. the function returns the number of distinct spid and aeids in the database at each level #' When type = "aeid", the val parameter has to be a valid aeid in the database. The function returns a #' table consisting of the number of distinct spids at each level of processing for the aeid given in 'val' diff --git a/data/chdat.rda b/data/chdat.rda deleted file mode 100644 index d9c01594..00000000 Binary files a/data/chdat.rda and /dev/null differ diff --git a/inst/csv/assay.csv b/inst/csv/assay.csv deleted file mode 100644 index 98672b2b..00000000 --- a/inst/csv/assay.csv +++ /dev/null @@ -1 +0,0 @@ -"aid","asid","assay_name","assay_desc","timepoint_hr","organism_id","organism","tissue","cell_format","cell_free_component_source","cell_short_name","cell_growth_mode","assay_footprint","assay_format_type","assay_format_type_sub","content_readout_type","dilution_solvent","dilution_solvent_percent_max" diff --git a/inst/csv/assay_component.csv b/inst/csv/assay_component.csv deleted file mode 100644 index 5ce3f51e..00000000 --- a/inst/csv/assay_component.csv +++ /dev/null @@ -1 +0,0 @@ -"acid","aid","assay_component_name","assay_component_desc","assay_component_target_desc","parameter_readout_type","assay_design_type","assay_design_type_sub","biological_process_target","detection_technology_type","detection_technology_type_sub","detection_technology","signal_direction_type","key_assay_reagent_type","key_assay_reagent","technological_target_type","technological_target_type_sub" diff --git a/inst/csv/assay_component_endpoint.csv b/inst/csv/assay_component_endpoint.csv deleted file mode 100644 index 8a73250b..00000000 --- a/inst/csv/assay_component_endpoint.csv +++ /dev/null @@ -1 +0,0 @@ -"aeid","acid","assay_component_endpoint_name","export_ready","internal_ready","assay_component_endpoint_desc","assay_function_type","normalized_data_type","analysis_direction","burst_assay","key_positive_control","signal_direction","intended_target_type","intended_target_type_sub","intended_target_family","intended_target_family_sub","fit_all" diff --git a/inst/csv/assay_component_map.csv b/inst/csv/assay_component_map.csv deleted file mode 100644 index 8a4dc485..00000000 --- a/inst/csv/assay_component_map.csv +++ /dev/null @@ -1 +0,0 @@ -"acid","acsn" diff --git a/inst/csv/assay_reagent.csv b/inst/csv/assay_reagent.csv deleted file mode 100644 index 2b80d31f..00000000 --- a/inst/csv/assay_reagent.csv +++ /dev/null @@ -1 +0,0 @@ -arid,aid,reagent_name_value,reagent_name_value_type,culture_or_assay diff --git a/inst/csv/assay_source.csv b/inst/csv/assay_source.csv deleted file mode 100644 index 956cca34..00000000 --- a/inst/csv/assay_source.csv +++ /dev/null @@ -1 +0,0 @@ -"asid","assay_source_name","assay_source_long_name","assay_source_desc" diff --git a/inst/csv/chemical.csv b/inst/csv/chemical.csv deleted file mode 100644 index 6156b732..00000000 --- a/inst/csv/chemical.csv +++ /dev/null @@ -1,7 +0,0 @@ -"chid","casn","chnm","dsstox_substance_id","code" -"20182","80-05-7","Bisphenol A","DTXSID7020182","C80057" -"22364","521-18-6","5alpha-Dihydrotestosterone","DTXSID9022364","C521186" -"23463","150-30-1","Phenylalanine","DTXSID9023463","C150301" -"24102","22224-92-6","Fenamiphos","DTXSID3024102","C22224926" -"21735","67-68-5","Dimethyl sulfoxide","DTXSID2021735","C67685" -"20283","95-83-0","4-Chloro-1,2-diaminobenzene","DTXSID5020283","C95830" diff --git a/inst/csv/chemical_library.csv b/inst/csv/chemical_library.csv deleted file mode 100644 index 4c5cbed0..00000000 --- a/inst/csv/chemical_library.csv +++ /dev/null @@ -1 +0,0 @@ -chid,clib diff --git a/inst/csv/mc0.csv b/inst/csv/mc0.csv deleted file mode 100644 index 0472dd5a..00000000 --- a/inst/csv/mc0.csv +++ /dev/null @@ -1 +0,0 @@ -"m0id","acid","spid","apid","rowi","coli","wllt","wllq","conc","rval","srcf","created_date","modified_date","modified_by" diff --git a/inst/csv/mc1.csv b/inst/csv/mc1.csv deleted file mode 100644 index e1fce207..00000000 --- a/inst/csv/mc1.csv +++ /dev/null @@ -1 +0,0 @@ -"m1id","m0id","acid","cndx","repi","created_date","modified_date","modified_by" diff --git a/inst/csv/mc2.csv b/inst/csv/mc2.csv deleted file mode 100644 index 0ab7ae5e..00000000 --- a/inst/csv/mc2.csv +++ /dev/null @@ -1 +0,0 @@ -"m2id","m0id","acid","m1id","cval","created_date","modified_date","modified_by" diff --git a/inst/csv/mc2_acid.csv b/inst/csv/mc2_acid.csv deleted file mode 100644 index a95bcb82..00000000 --- a/inst/csv/mc2_acid.csv +++ /dev/null @@ -1,3 +0,0 @@ -"mc2_mthd_id","acid","exec_ordr","created_date","modified_date","modified_by" -1,1,1,NA,NA,"mshobair.mshobair.mshobair" -1,1,1,NA,NA,"mshobair.mshobair.mshobair" diff --git a/inst/csv/mc2_methods.csv b/inst/csv/mc2_methods.csv deleted file mode 100644 index 3f2667ac..00000000 --- a/inst/csv/mc2_methods.csv +++ /dev/null @@ -1,13 +0,0 @@ -mc2_mthd_id,mc2_mthd,desc,created_date,modified_date,modified_by -1,none,"apply no level 2 method","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -2,log2,"log2 all raw data","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -3,rmneg,"remove negative values prior to logging values","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -4,rmzero,"remove 0 values prior to logging values","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -5,mult25,"multiply values by 25","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -7,mult100,"multiply values by 100","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -10,log10,"log10 the raw data","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -11,negshift,"Shifts all data to be positive (new min=1)","2014-10-06 14:47:15","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 -12,mult2.5,"multiply values by 2.5","2014-11-06 10:36:15","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 -13,mult3,"multiply values by 3","2014-11-06 10:36:34","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 -14,mult6,"multiply values by 6","2014-11-06 15:53:33","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 -17,sub100,"100 minus cval (centers data around zero if prenormalized starting at 100 and going down to zero)","2015-10-05 12:42:21","0000-00-00 00:00:00","mmarti02.mmarti02.mmarti02" diff --git a/inst/csv/mc3.csv b/inst/csv/mc3.csv deleted file mode 100644 index 200acfdd..00000000 --- a/inst/csv/mc3.csv +++ /dev/null @@ -1 +0,0 @@ -"m3id","aeid","m0id","acid","m1id","m2id","bval","pval","logc","resp","created_date","modified_date","modified_by" diff --git a/inst/csv/mc3_aeid.csv b/inst/csv/mc3_aeid.csv deleted file mode 100644 index 805ba2ba..00000000 --- a/inst/csv/mc3_aeid.csv +++ /dev/null @@ -1,13 +0,0 @@ -"mc3_mthd_id","aeid","exec_ordr","created_date","modified_date","modified_by" -17,1,1,NA,NA,"mshobair.mshobair.mshobair" -17,2,1,NA,NA,"mshobair.mshobair.mshobair" -9,1,2,NA,NA,"mshobair.mshobair.mshobair" -9,2,2,NA,NA,"mshobair.mshobair.mshobair" -7,1,3,NA,NA,"mshobair.mshobair.mshobair" -7,2,3,NA,NA,"mshobair.mshobair.mshobair" -17,1,1,NA,NA,"mshobair.mshobair.mshobair" -17,2,1,NA,NA,"mshobair.mshobair.mshobair" -9,1,2,NA,NA,"mshobair.mshobair.mshobair" -9,2,2,NA,NA,"mshobair.mshobair.mshobair" -7,1,3,NA,NA,"mshobair.mshobair.mshobair" -7,2,3,NA,NA,"mshobair.mshobair.mshobair" diff --git a/inst/csv/mc3_methods.csv b/inst/csv/mc3_methods.csv deleted file mode 100644 index 40dd8873..00000000 --- a/inst/csv/mc3_methods.csv +++ /dev/null @@ -1,38 +0,0 @@ -mc3_mthd_id,mc3_mthd,desc,created_date,modified_date,modified_by -1,none,apply no level 3 method,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,bval.apid.lowconc.med,plate-wise baseline based on low conc median value,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,pval.apid.medpcbyconc.max,plate-wise median response of positive control (max),0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,pval.apid.medpcbyconc.min,plate-wise median response of positive control (min),0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,resp.pc,response percent activity,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,resp.multneg1,multiply the response by -1,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,resp.log2,take the log base 2 of the response,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,resp.mult25,multiply the response by 25,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -9,resp.fc,calculate response as fold-change,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -11,bval.apid.nwlls.med,plate-wise baseline based on neutral ctrl median value,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -12,bval.spid.lowconc.med,sample-wise baseline based on low conc median value,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -13,pval.apid.pwlls.med,"plate-wise meidan based on positive control, single dose",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -14,pval.apid.mwlls.med,"plate-wise meidan based on negative control, single dose",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -15,pval.apid.medncbyconc.min,"plate-wise meidan based on negative control, (min)",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -16,bval.apid.twlls.med,"Take the median cval of the t wells, by apid",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -17,bval.apid.nwllslowconc.med,"Take the median cval of the n wells and the first two concentrations, by apid",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -18,resp.shiftneg.3bmad,Make values below baseline zero.,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -19,resp.blineshift.3bmad.repi,"Do baseline correction by repi, with a window of 3*bmad",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -20,resp.blineshift.50.repi,"Do baseline correction by repi, with a window of 50",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -21,resp.blineshift.50.spid,"Do baseline correction by spid, with a window of 50",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -23,resp.blineshift.3bmad.spid,"Do baseline correction by repi, with a window of 3*bmad",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -24,bval.apid.tn.med,"Take the median cval of the t and n wells, by apid",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -25,pval.apid.pmv.min,"Calculate the median p, m, and v values by concentration, then take the minimum by apid.",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -26,pval.apid.pmv.max,"Calculate the median p, m, and v values by concentration, then take the maximum by apid.",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -27,pval.apid.f.max,"Calculate the median of f values by concentration, then take the maximum by apid",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -28,pval.apid.f.min,"Calculate the median of f values by concentration, then take the minimum by apid",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -29,pval.apid.p.min,"Calculate the median of p values by concentration, then take the minimum by apid",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -30,pval.apid.p.max,"Calculate the median of p values by concentration, then take the maximum by apid",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -31,pval.apid.v.min,"Calculate the median of v values by concentration, then take the minimum by apid",0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -32,pval.zero,Set pval to 0.,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -33,resp.shiftneg.6bmad,Shift response values falling below -6 * bmad to 0.,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -34,resp.shiftneg.10bmad,Shift response values falling below -10 * bmad to 0.,0000-00-00 00:00:00,0000-00-00 00:00:00,dfiler.dfiler.dfiler -35,resp.logfc,Calculate the response as a fold change over baseline for logged values,2014-10-02 14:18:40,0000-00-00 00:00:00,dfiler.dfiler.dfiler -36,resp.scale.mad.log2fc,Scale the resp data by the ratio of log2(1.2) over 3* baseline mad of the unscaled resp values,2015-02-23 13:58:52,0000-00-00 00:00:00, -37,resp.scale.quant.log2fc,Scale resp such that 20% of the maximum resp equals log2(1.2),2015-03-13 16:44:05,0000-00-00 00:00:00,dfiler.dfiler.dfiler -38,bval.apid.nwllstcwllslowconc.med,plate-wise baseline based on neutral and t and c well low conc,2015-09-16 15:22:54,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 -39,resp.pc.pval.cor,response percent activity using previously corrected pval,2018-09-05 09:38:32,0000-00-00 00:00:01,tzurlind.tzurlind.tzurlind diff --git a/inst/csv/mc4.csv b/inst/csv/mc4.csv deleted file mode 100644 index 91838497..00000000 --- a/inst/csv/mc4.csv +++ /dev/null @@ -1 +0,0 @@ -"m4id","aeid","spid","bmad","resp_max","resp_min","max_mean","max_mean_conc","max_med","max_med_conc","logc_max","logc_min","cnst","hill","hcov","gnls","gcov","cnst_er","cnst_aic","cnst_rmse","cnst_prob","hill_tp","hill_tp_sd","hill_ga","hill_ga_sd","hill_gw","hill_gw_sd","hill_er","hill_er_sd","hill_aic","hill_rmse","hill_prob","gnls_tp","gnls_tp_sd","gnls_ga","gnls_ga_sd","gnls_gw","gnls_gw_sd","gnls_la","gnls_la_sd","gnls_lw","gnls_lw_sd","gnls_er","gnls_er_sd","gnls_aic","gnls_rmse","gnls_prob","nconc","npts","nrep","nmed_gtbl","tmpi","created_date","modified_date","modified_by" diff --git a/inst/csv/mc4_aeid.csv b/inst/csv/mc4_aeid.csv deleted file mode 100644 index 34b70204..00000000 --- a/inst/csv/mc4_aeid.csv +++ /dev/null @@ -1,9 +0,0 @@ -"mc4_mthd_id","aeid","created_date","modified_date","modified_by" -1,1,NA,NA,"mshobair.mshobair.mshobair" -1,2,NA,NA,"mshobair.mshobair.mshobair" -2,1,NA,NA,"mshobair.mshobair.mshobair" -2,2,NA,NA,"mshobair.mshobair.mshobair" -1,1,NA,NA,"mshobair.mshobair.mshobair" -1,2,NA,NA,"mshobair.mshobair.mshobair" -2,1,NA,NA,"mshobair.mshobair.mshobair" -2,2,NA,NA,"mshobair.mshobair.mshobair" diff --git a/inst/csv/mc4_agg.csv b/inst/csv/mc4_agg.csv deleted file mode 100644 index 14104e8b..00000000 --- a/inst/csv/mc4_agg.csv +++ /dev/null @@ -1 +0,0 @@ -"aeid","m0id","m1id","m2id","m3id","m4id" diff --git a/inst/csv/mc4_methods.csv b/inst/csv/mc4_methods.csv deleted file mode 100644 index 71aa9e90..00000000 --- a/inst/csv/mc4_methods.csv +++ /dev/null @@ -1,3 +0,0 @@ -mc4_mthd_id,mc4_mthd,desc,created_date,modified_date,modified_by -1,bmad.aeid.lowconc.twells,bmad based on two lowest concentration of treatment wells,0000-00-00 00:00:01,0000-00-00 00:00:00,spendse.scitovation -2,bmad.aeid.lowconc.nwells,bmad based on two lowest concentration of nwells,0000-00-00 00:00:00,0000-00-00 00:00:00,spendse.scitovation diff --git a/inst/csv/mc5.csv b/inst/csv/mc5.csv deleted file mode 100644 index a1e00f8b..00000000 --- a/inst/csv/mc5.csv +++ /dev/null @@ -1 +0,0 @@ -m5id,m4id,aeid,modl,hitc,fitc,coff,actp,modl_er,modl_tp,modl_ga,modl_gw,modl_la,modl_lw,modl_prob,modl_rmse,modl_acc,modl_acb,modl_ac10,model_type,created_date,modified_date,modified_by diff --git a/inst/csv/mc5_aeid.csv b/inst/csv/mc5_aeid.csv deleted file mode 100644 index 16b7d08a..00000000 --- a/inst/csv/mc5_aeid.csv +++ /dev/null @@ -1,5 +0,0 @@ -"aeid","mc5_mthd_id","created_date","modified_date","modified_by" -1,6,NA,NA,"mshobair.mshobair.mshobair" -2,6,NA,NA,"mshobair.mshobair.mshobair" -1,6,NA,NA,"mshobair.mshobair.mshobair" -2,6,NA,NA,"mshobair.mshobair.mshobair" diff --git a/inst/csv/mc5_chid.csv b/inst/csv/mc5_chid.csv deleted file mode 100644 index aae71025..00000000 --- a/inst/csv/mc5_chid.csv +++ /dev/null @@ -1 +0,0 @@ -m5id,chid_rep diff --git a/inst/csv/mc5_fit_categories.csv b/inst/csv/mc5_fit_categories.csv deleted file mode 100644 index 2900872d..00000000 --- a/inst/csv/mc5_fit_categories.csv +++ /dev/null @@ -1,56 +0,0 @@ -"fitc","parent_fitc","name","xloc","yloc" -"1","NULL","01: ALL DOSE RESPONSE",1110,756.5 -"2","1","02: CANNOT DETERMINE",977.7455523765,611.9831921304 -"3","1","03: INACTIVE",1022.9653320313,924.2873535156 -"4","3","04: RESP < BLINE",1271.6083984375,974.8182373047 -"5","3","05: RESP >= BLINE",996.8209228516,1127.5755004883 -"6","5","06: CNST",666,1251.5 -"7","6","07: NOTP >= 0.8(COFF)",761.8584594727,1333.5216674805 -"8","6","08: ANYTP >= 0.8(COFF)",507.3630981445,1333.6228027344 -"9","8","09: NOTP >= COFF",337.4776000977,1263.4637451172 -"10","8","10: ANYTP >= COFF",450.4357910156,1397.3994140625 -"11","5","11: HILL",1189.7768554688,1209.4105834961 -"12","11","12: TP < 0.8(COFF)",1149.2390136719,1317.5518188477 -"13","12","13: GNLS < 0.8(COFF)",992.1193237305,1394.7369384766 -"14","12","14: GNLS >= 0.8(COFF)",1246.0364990234,1386.9293518066 -"15","14","15: GNLS < COFF",1218.9203491211,1496.1217041016 -"16","14","16: GNLS >= COFF",1361.9873046875,1443.5811157227 -"17","11","17: TP >= 0.8(COFF)",1460.6746826172,1119.6658935547 -"18","17","18: GNLS < 0.8(COFF)",1539.3952956084,1228.8681030273 -"19","17","19: GNLS >= 0.8(COFF)",1623.3784179688,1043.5646362305 -"20","19","20: GNLS < COFF",1876.1442871094,1040.0154418945 -"21","19","21: GNLS >= COFF",1849.7615966797,948.6744995117 -"22","5","22: GNLS",794.5350952148,1043.2316894531 -"23","22","23: TP < 0.8(COFF)",632.9550857544,936.3232232708 -"24","23","24: HILL < 0.8(COFF)",803.6691931111,753.821326896 -"25","23","25: HILL >= 0.8(COFF)",542.0636749268,831.3344537395 -"26","25","26: HILL < COFF",478.504219532,698.9990045207 -"27","25","27: HILL >= COFF",359.5413589478,763.8884088176 -"28","22","28: TP >= 0.8(COFF)",491.8406066895,1063.1170043945 -"29","28","29: HILL < 0.8(COFF)",446.9388122559,1132.0888671875 -"30","28","30: HILL >= 0.8(COFF)",371.3406066895,956.1169433594 -"31","30","31: HILL < COFF",288.3405761719,853.1170654297 -"32","30","32: HILL >= COFF",107.8862915039,948.5189208984 -"33","1","33: ACTIVE",1276.5,563.5 -"34","33","34: HILL",1190.094543457,462.0799560547 -"35","34","35: TP <= 1.2(COFF)",991.5,302.5 -"36","35","36: AC50 <=",764.6481933594,350.3658447266 -"37","35","37: AC50 ==",749.6301269531,254.4168701172 -"38","35","38: AC50 >=",966.6704101563,183.7718505859 -"39","34","39: TP > 1.2(COFF)",1310.6741943359,263.3843994141 -"40","39","40: AC50 <=",1134.5294799805,105.1185302734 -"41","39","41: AC50 ==",1412.8084716797,121.1416015625 -"42","39","42: AC50 >=",1578.5758056641,187.1433105469 -"43","33","43: GNLS",1558.3104248047,570.28125 -"44","43","44: TP <= 1.2(COFF)",1639.5,451.5 -"45","44","45: AC50 <=",1811.0447998047,377.1083984375 -"46","44","46: AC50 ==",1905.2620849609,445.5483398437 -"47","44","47: AC50 >=",1659.5,320.5 -"48","43","48: TP > 1.2(COFF)",1647.5,685.5 -"49","48","49: AC50 <=",1704.5,806.5 -"50","48","50: AC50 ==",1873.9647216797,741.5611572266 -"51","48","51: AC50 >=",1926.5576171875,671.6712646484 -"52","23","52: HILL DNC",890.4145965576,837.0693170207 -"53","28","53: HILL DNC",155.8844682354,1077.1187744141 -"54","12","54: GNLS DNC",1463.7992844698,1325.916809082 -"55","17","55: GNLS DNC",1774.73046875,1155.2709031221 diff --git a/inst/csv/mc5_methods.csv b/inst/csv/mc5_methods.csv deleted file mode 100644 index 8598257f..00000000 --- a/inst/csv/mc5_methods.csv +++ /dev/null @@ -1,13 +0,0 @@ -mc5_mthd_id,mc5_mthd,desc,created_date,modified_date,modified_by -1,bmad3,Add a cutoff value of 3*bmad.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,pc20,Add a cutoff value of 20.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,log2_1.2,Add a cutoff value of log2(1.2).,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,log10_1.2,Add a cutoff value of log10(1.2).,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,bmad5,Add a cutoff value of 5*bmad.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,bmad6,Add a cutoff value of 6*bmad.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,bmad10,Add a cutoff value of 10*bmad.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,maxmed20pct,Add a cutoff value of 20% of the max of max_med,2015-05-06 09:08:50,0000-00-00 00:00:00,kconnors.kconnors.kconnors -9,pc70,70% cutoff,2015-07-28 15:06:35,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 -10,pc50,50% cutoff,2015-07-28 15:08:01,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 -11,log2_2,log2 of 2 fold change cutoff,2015-07-28 15:08:01,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 -12,log10_2,log10 of 2 fold change cutoff,2015-07-28 15:08:01,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 diff --git a/inst/csv/mc6.csv b/inst/csv/mc6.csv deleted file mode 100644 index a9256b01..00000000 --- a/inst/csv/mc6.csv +++ /dev/null @@ -1 +0,0 @@ -"m6id","m5id","m4id","aeid","mc6_mthd_id","flag","fval","fval_unit","created_date","modified_date","modified_by" diff --git a/inst/csv/mc6_aeid.csv b/inst/csv/mc6_aeid.csv deleted file mode 100644 index f06a14e4..00000000 --- a/inst/csv/mc6_aeid.csv +++ /dev/null @@ -1,17 +0,0 @@ -"aeid","mc6_mthd_id","created_date","modified_date","modified_by" -1,6,NA,NA,"mshobair.mshobair.mshobair" -2,6,NA,NA,"mshobair.mshobair.mshobair" -1,7,NA,NA,"mshobair.mshobair.mshobair" -2,7,NA,NA,"mshobair.mshobair.mshobair" -1,8,NA,NA,"mshobair.mshobair.mshobair" -2,8,NA,NA,"mshobair.mshobair.mshobair" -1,10,NA,NA,"mshobair.mshobair.mshobair" -2,10,NA,NA,"mshobair.mshobair.mshobair" -1,11,NA,NA,"mshobair.mshobair.mshobair" -2,11,NA,NA,"mshobair.mshobair.mshobair" -1,12,NA,NA,"mshobair.mshobair.mshobair" -2,12,NA,NA,"mshobair.mshobair.mshobair" -1,15,NA,NA,"mshobair.mshobair.mshobair" -2,15,NA,NA,"mshobair.mshobair.mshobair" -1,16,NA,NA,"mshobair.mshobair.mshobair" -2,16,NA,NA,"mshobair.mshobair.mshobair" diff --git a/inst/csv/mc6_methods.csv b/inst/csv/mc6_methods.csv deleted file mode 100644 index 2b15f3d9..00000000 --- a/inst/csv/mc6_methods.csv +++ /dev/null @@ -1,19 +0,0 @@ -mc6_mthd_id,mc6_mthd,desc,nddr,created_date,modified_date,modified_by -1,row.dev.up,"Look for row-wise plate effects, increase",1,2014-07-28 14:03:41,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,row.dev.dn,"Look for row-wise plate effects, decrease",1,2014-07-28 14:03:54,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,col.dev.dn,"Look for column-wise plate effects, decrease",1,2014-07-28 14:04:08,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,col.dev.up,"Look for column-wise plate effects, increase",1,2014-07-28 14:04:17,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,plate.flare,Look for plate flare effects,1,2014-07-28 14:04:27,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,singlept.hit.high,Look for single point hits with activity only at the highest conc tested,0,2014-07-28 14:06:05,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,singlept.hit.mid,Look for signle point hits with activity not at highest conc tested,0,2014-07-28 14:06:51,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,multipoint.neg,Look for inactives with multiple medians above baseline,0,2014-07-28 14:08:42,0000-00-00 00:00:00,dfiler.dfiler.dfiler -9,pintool,Look for pintool carryover issues,1,2014-07-28 14:09:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -10,noise,"Look for noisy curves, relative to the assay",0,2014-07-28 14:09:41,0000-00-00 00:00:00,dfiler.dfiler.dfiler -11,border.hit,Look for actives with borderline activity,0,2014-07-28 14:10:14,0000-00-00 00:00:00,dfiler.dfiler.dfiler -12,border.miss,Look for inactives with borderline activity,0,2014-07-28 14:10:21,0000-00-00 00:00:00,dfiler.dfiler.dfiler -13,plate.interlace,Look for interlaced chemical-plate effects,1,2014-08-21 12:13:26,0000-00-00 00:00:00,dfiler.dfiler.dfiler -14,rep.mismatch,Look for mismatched techinal replicates,1,2014-08-21 12:16:44,0000-00-00 00:00:00,dfiler.dfiler.dfiler -15,gnls.lowconc,Look for low concentration gnls winners,0,2014-08-21 12:21:32,0000-00-00 00:00:00,dfiler.dfiler.dfiler -16,overfit.hit,Flag hit-calls that would get changed after doing the small N correction to the aic values.,0,2014-09-16 11:51:14,0000-00-00 00:00:00,dfiler.dfiler.dfiler -17,efficacy.50,Flag hit-calls with efficacy values less than 50% -- intended for biochemical assays.,0,2014-09-16 11:51:58,0000-00-00 00:00:00,dfiler.dfiler.dfiler -19,viability.gnls,Flag hit-calls with cell viability assay that are fit with gnls winning model,0,03/26/19 10:53 AM,, diff --git a/inst/csv/sample.csv b/inst/csv/sample.csv deleted file mode 100644 index 8420dae4..00000000 --- a/inst/csv/sample.csv +++ /dev/null @@ -1,7 +0,0 @@ -"spid","chid","stkc","stkc_unit","tested_conc_unit","spid_legacy" -"Tox21_400088","20182","","","","" -"Tox21_303655","22364","","","","" -"Tox21_110011","23463","","","","" -"Tox21_400081","24102","","","","" -"DMSO","21735","","","","" -"Tox21_400037","20283","","","","" diff --git a/inst/csv/sc0.csv b/inst/csv/sc0.csv deleted file mode 100644 index 6adac25a..00000000 --- a/inst/csv/sc0.csv +++ /dev/null @@ -1,2 +0,0 @@ -s0id,acid,spid,apid,rowi,coli,wllt,wllq,conc,rval,srcf,created_date,modified_date,modified_by - diff --git a/inst/csv/sc1.csv b/inst/csv/sc1.csv deleted file mode 100644 index 2d54ea07..00000000 --- a/inst/csv/sc1.csv +++ /dev/null @@ -1 +0,0 @@ -s1id,s0id,acid,aeid,logc,bval,pval,resp,created_date,modified_date,modified_by diff --git a/inst/csv/sc1_aeid.csv b/inst/csv/sc1_aeid.csv deleted file mode 100644 index db1ea033..00000000 --- a/inst/csv/sc1_aeid.csv +++ /dev/null @@ -1 +0,0 @@ -sc1_mthd_id,aeid,exec_ordr,created_date,modified_date,modified_by diff --git a/inst/csv/sc1_methods.csv b/inst/csv/sc1_methods.csv deleted file mode 100644 index 0a300039..00000000 --- a/inst/csv/sc1_methods.csv +++ /dev/null @@ -1,17 +0,0 @@ -sc1_mthd_id,sc1_mthd,desc,created_date,modified_date,modified_by -1,bval.apid.nwlls.med,plate-wise baseline based on neutral ctrl median value,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,bval.apid.twlls.med,"Take the median cval of the t wells, by apid",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,bval.apid.tn.med,"Take the median cval of the t and n wells, by apid",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,pval.apid.pwlls.med,"plate-wise meidan based on positive control, single dose",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,pval.apid.mwlls.med,"plate-wise meidan based on negative control, single dose",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,pval.apid.medpcbyconc.max,plate-wise median response of positive control (max),2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,pval.apid.medpcbyconc.min,plate-wise median response of positive control (min),2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,pval.apid.medncbyconc.min,"plate-wise meidan based on negative control, (min)",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -9,pval.zero,Set pval to 0.,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -10,resp.pc,response percent activity,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -11,resp.fc,calculate response as fold-change,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -12,resp.logfc,Calculate the response as a fold change over baseline for logged values,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -13,resp.log2,take the log base 2 of the response,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -14,none,apply no level 2 method,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -16,resp.multneg1,multiply response values by negative 1,2015-05-29 10:27:45,0000-00-00 00:00:00,Akarmaus.Akarmaus.Akarmaus -17,pval.apid.or.aeid.pwlls.med,calculates pval first based on p wells by plate and then for any plates missing p wells it calculates a pval by median of pval for all other plates,2015-09-30 14:43:40,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 diff --git a/inst/csv/sc2.csv b/inst/csv/sc2.csv deleted file mode 100644 index 1fa7efb8..00000000 --- a/inst/csv/sc2.csv +++ /dev/null @@ -1 +0,0 @@ -s2id,aeid,spid,bmad,max_med,coff,hitc,tmpi,created_date,modified_date,modified_by diff --git a/inst/csv/sc2_aeid.csv b/inst/csv/sc2_aeid.csv deleted file mode 100644 index df7cc430..00000000 --- a/inst/csv/sc2_aeid.csv +++ /dev/null @@ -1 +0,0 @@ -sc2_mthd_id,aeid,exec_ordr,created_date,modified_date,modified_by diff --git a/inst/csv/sc2_agg.csv b/inst/csv/sc2_agg.csv deleted file mode 100644 index db0d02fd..00000000 --- a/inst/csv/sc2_agg.csv +++ /dev/null @@ -1 +0,0 @@ -aeid,s0id,s1id,s2id diff --git a/inst/csv/sc2_methods.csv b/inst/csv/sc2_methods.csv deleted file mode 100644 index c79bb628..00000000 --- a/inst/csv/sc2_methods.csv +++ /dev/null @@ -1,11 +0,0 @@ -sc2_mthd_id,sc2_mthd,desc,created_date,modified_date,modified_by -1,bmad3,Add a cutoff value of 3*bmad.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,pc20,Add a cutoff value of 20.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,log2_1.2,Add a cutoff value of log2(1.2).,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,log10_1.2,Add a cutoff value of log10(1.2).,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,bmad5,Add a cutoff value of 5*bmad.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,bmad6,Add a cutoff value of 6*bmad.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,bmad10,Add a cutoff value of 10*bmad.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,pc30orbmad3,"Add a cutoff value of either 30 or 3*bmad, whichever is less.",2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -9,pc0.88,Add a cutoff value of 0.88.,2015-05-14 13:25:38,0000-00-00 00:00:00,dfiler.dfiler.dfiler -10,log2_1.5,Add a cutoff value of log2(1.5).,2015-05-14 13:25:38,0000-00-00 00:00:00,dfiler.dfiler.dfiler diff --git a/inst/example/assay.csv b/inst/example/assay.csv deleted file mode 100644 index 98672b2b..00000000 --- a/inst/example/assay.csv +++ /dev/null @@ -1 +0,0 @@ -"aid","asid","assay_name","assay_desc","timepoint_hr","organism_id","organism","tissue","cell_format","cell_free_component_source","cell_short_name","cell_growth_mode","assay_footprint","assay_format_type","assay_format_type_sub","content_readout_type","dilution_solvent","dilution_solvent_percent_max" diff --git a/inst/example/assay_component.csv b/inst/example/assay_component.csv deleted file mode 100644 index 5ce3f51e..00000000 --- a/inst/example/assay_component.csv +++ /dev/null @@ -1 +0,0 @@ -"acid","aid","assay_component_name","assay_component_desc","assay_component_target_desc","parameter_readout_type","assay_design_type","assay_design_type_sub","biological_process_target","detection_technology_type","detection_technology_type_sub","detection_technology","signal_direction_type","key_assay_reagent_type","key_assay_reagent","technological_target_type","technological_target_type_sub" diff --git a/inst/example/assay_component_endpoint.csv b/inst/example/assay_component_endpoint.csv deleted file mode 100644 index 7d12e3fe..00000000 --- a/inst/example/assay_component_endpoint.csv +++ /dev/null @@ -1,5 +0,0 @@ -"aeid","acid","assay_component_endpoint_name","export_ready","internal_ready","assay_component_endpoint_desc","assay_function_type","normalized_data_type","analysis_direction","burst_assay","key_positive_control","signal_direction","intended_target_type","intended_target_type_sub","intended_target_family","intended_target_family_sub","fit_all" -797,534,"TOX21_MMP_ratio_down",1,1,"Data from the assay component Tox21_MMP_ratio was analyzed into 2 assay endpoints. This assay endpoint, Tox21_MMP_ratio, was analyzed in the positive fitting direction relative to DMSO as the negative control and baseline of activity. -Using a type of 6 membrane potential reporter, gain-of-signal activity can be used to understand changes in the signaling. -Furthermore, this assay endpoint can be referred to as a primary readout, because this assay has produced multiple assay endpoints where this one serves a signaling function. -To generalize the intended target to other relatable targets, this assay endpoint is annotated to the cell morphology intended target family, where the subfamily is organelle conformation.","signaling","percent_activity","positive",0,"FCCP","loss","cellular","mitochondria","cell morphology","organelle conformation",0 diff --git a/inst/example/assay_component_map.csv b/inst/example/assay_component_map.csv deleted file mode 100644 index 8a4dc485..00000000 --- a/inst/example/assay_component_map.csv +++ /dev/null @@ -1 +0,0 @@ -"acid","acsn" diff --git a/inst/example/assay_source.csv b/inst/example/assay_source.csv deleted file mode 100644 index 956cca34..00000000 --- a/inst/example/assay_source.csv +++ /dev/null @@ -1 +0,0 @@ -"asid","assay_source_name","assay_source_long_name","assay_source_desc" diff --git a/inst/example/chemical.csv b/inst/example/chemical.csv deleted file mode 100644 index c4e45594..00000000 --- a/inst/example/chemical.csv +++ /dev/null @@ -1,2 +0,0 @@ -chid,casn,chnm,dsstox_substance_id,code -20182,80-05-7,Bisphenol A,DTXSID7020182,C80057 diff --git a/inst/example/chemical_library.csv b/inst/example/chemical_library.csv deleted file mode 100644 index 02616e4c..00000000 --- a/inst/example/chemical_library.csv +++ /dev/null @@ -1,8 +0,0 @@ -"chid","clib" -20182,"TOX21SL" -20182,"TOXCAST" -20182,"TOXCAST_EPATox21" -20182,"TOXCAST_ph1v2" -20182,"TOXCAST_PhaseI" -20182,"TOXCAST_PhaseII" -20182,"TOXCAST_PhaseIII" diff --git a/inst/example/mc0.csv b/inst/example/mc0.csv deleted file mode 100644 index e42a25c1..00000000 --- a/inst/example/mc0.csv +++ /dev/null @@ -1,45 +0,0 @@ -"m0id","acid","spid","apid","rowi","coli","wllt","wllq","conc","rval","srcf","created_date","modified_date","modified_by" -430748046,534,"Tox21_202992","T5397033",7,17,"t",1,3.65161290322581,-25.8516680725,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430752654,534,"Tox21_202992","T5397035",7,17,"t",1,1.63305093580645,-12.808278967,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430764942,534,"Tox21_202992","T5397037",7,17,"t",1,0.730322580645161,-7.7695268125,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430754190,534,"Tox21_202992","T5397039",7,17,"t",1,0.326610187142857,-3.0309182114,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430761870,534,"Tox21_202992","T5397041",7,17,"t",1,0.146064516129032,0.6320821129,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430763406,534,"Tox21_202992","T5397043",7,17,"t",1,0.0653220374193548,0.2937049989,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430746510,534,"Tox21_202992","T5397047",7,17,"t",1,0.0292129032258065,4.8854945307,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430744974,534,"Tox21_202992","T5397049",7,17,"t",1,0.0130644074654378,0.6047468531,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430751118,534,"Tox21_202992","T5397051",7,17,"t",1,0.00584258064516129,0.3394452023,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430758798,534,"Tox21_202992","T5397053",7,17,"t",1,0.00261288147465438,1.0971752187,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430755726,534,"Tox21_202992","T5397067",7,17,"t",1,0.00116851612903226,5.1009273696,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430766478,534,"Tox21_202992","T5397071",7,17,"t",1,8.16525467912442,-27.4639329578,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430749582,534,"Tox21_202992","T5397073",7,17,"t",1,18.258064516129,-56.1735755773,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430757262,534,"Tox21_202992","T5397077",7,17,"t",1,40.8262733956221,-72.2783059098,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430760334,534,"Tox21_202992","T5397079",7,17,"t",1,91.2903225806452,-90.5887455377,"tox21-mitotox-p1.txt","2017-06-09 07:56:25","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430377914,534,"Tox21_202992","T5397607",8,17,"t",1,0.146064516129032,4.9452627381,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430385594,534,"Tox21_202992","T5397609",8,17,"t",1,0.0653220374193548,19.7403169424,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430422415,534,"Tox21_202992","T5397611",7,18,"t",1,0.00116851612903226,20.6084942663,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430388666,534,"Tox21_202992","T5397617",8,17,"t",1,91.2903225806452,-94.4253640904,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430393274,534,"Tox21_202992","T5397619",8,17,"t",1,40.8262733956221,-77.3032971548,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430391738,534,"Tox21_202992","T5397621",8,17,"t",1,18.258064516129,-58.5190729633,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430387130,534,"Tox21_202992","T5397625",8,17,"t",1,8.16525467912442,-50.0178492903,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430384058,534,"Tox21_202992","T5397627",8,17,"t",1,3.65161290322581,-44.5386085275,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430382522,534,"Tox21_202992","T5397629",8,17,"t",1,1.63305093580645,-24.2872869162,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430425487,534,"Tox21_202992","T5400075",7,18,"t",1,0.00584258064516129,9.6191813961,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430423951,534,"Tox21_202992","T5400077",7,18,"t",1,0.00261288147465438,-0.1189863227,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430440847,534,"Tox21_202992","T5400009",7,18,"t",1,91.2903225806452,-109.5033957167,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430433167,534,"Tox21_202992","T5400071",7,18,"t",1,0.0292129032258065,12.7991460404,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430436239,534,"Tox21_202992","T5400073",7,18,"t",1,0.0130644074654378,3.6750887039,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430396346,534,"Tox21_202992","T5400079",8,17,"t",1,0.326610187142857,-6.2171842637,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430430095,534,"Tox21_202992","T5400069",7,18,"t",1,0.0653220374193548,4.2768491029,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430376378,534,"Tox21_202992","T5400081",8,17,"t",1,0.0292129032258065,16.0491804873,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430434703,534,"Tox21_202992","T5400083",7,18,"t",1,0.730322580645161,-12.5694069267,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430442383,534,"Tox21_202992","T5400087",7,18,"t",1,0.326610187142857,-5.5464142931,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430437775,534,"Tox21_202992","T5400089",7,18,"t",1,0.146064516129032,7.7790889947,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430443919,534,"Tox21_202992","T5400091",7,18,"t",1,40.8262733956221,-108.1864438838,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430428559,534,"Tox21_202992","T5400093",7,18,"t",1,18.258064516129,-78.5294105576,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430431631,534,"Tox21_202992","T5400095",7,18,"t",1,8.16525467912442,-41.5760993818,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430427023,534,"Tox21_202992","T5400097",7,18,"t",1,3.65161290322581,-29.8191354153,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430439311,534,"Tox21_202992","T5400099",7,18,"t",1,1.63305093580645,-5.7325549136,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430380986,534,"Tox21_202992","T5400111",8,17,"t",1,0.0130644074654378,7.0767484891,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430394810,534,"Tox21_202992","T5400113",8,17,"t",1,0.00584258064516129,-9.2539696563,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430397882,534,"Tox21_202992","T5400115",8,17,"t",1,0.00261288147465438,-9.1805107616,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -430390202,534,"Tox21_202992","T5400117",8,17,"t",1,0.00116851612903226,-3.4352984691,"tox21-mitotox-p1.txt","2017-06-09 07:54:27","0000-00-00 00:00:00","rjudson.rjudson.rjudson" diff --git a/inst/example/mc1.csv b/inst/example/mc1.csv deleted file mode 100644 index 73118131..00000000 --- a/inst/example/mc1.csv +++ /dev/null @@ -1,45 +0,0 @@ -"m1id","m0id","acid","cndx","repi","created_date","modified_date","modified_by" -449243302,430748046,534,11,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243303,430752654,534,10,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243304,430764942,534,9,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243305,430754190,534,8,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243306,430761870,534,7,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243307,430763406,534,6,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243308,430746510,534,5,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243309,430744974,534,4,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243310,430751118,534,3,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243311,430758798,534,2,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243312,430755726,534,1,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243313,430766478,534,12,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243314,430749582,534,13,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243315,430757262,534,14,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243316,430760334,534,15,1,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243317,430377914,534,7,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243318,430385594,534,6,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243319,430422415,534,1,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243320,430388666,534,15,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243321,430393274,534,14,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243322,430391738,534,13,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243323,430387130,534,12,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243324,430384058,534,11,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243325,430382522,534,10,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243330,430425487,534,3,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243331,430423951,534,2,2,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243334,430440847,534,15,3,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243341,430433167,534,5,3,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243342,430436239,534,4,3,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243343,430396346,534,8,3,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243348,430430095,534,6,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243349,430376378,534,5,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243350,430434703,534,9,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243351,430442383,534,8,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243352,430437775,534,7,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243353,430443919,534,14,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243354,430428559,534,13,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243355,430431631,534,12,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243356,430427023,534,11,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243357,430439311,534,10,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243358,430380986,534,4,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243359,430394810,534,3,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243360,430397882,534,2,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -449243361,430390202,534,1,4,"2017-06-10 01:44:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" diff --git a/inst/example/mc2.csv b/inst/example/mc2.csv deleted file mode 100644 index 26913820..00000000 --- a/inst/example/mc2.csv +++ /dev/null @@ -1,45 +0,0 @@ -"m2id","m0id","acid","m1id","cval","created_date","modified_date","modified_by" -424939723,430748046,534,449243302,-25.8516680725,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939722,430752654,534,449243303,-12.808278967,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939721,430764942,534,449243304,-7.7695268125,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939720,430754190,534,449243305,-3.0309182114,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939719,430761870,534,449243306,0.6320821129,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939718,430763406,534,449243307,0.2937049989,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939717,430746510,534,449243308,4.8854945307,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939716,430744974,534,449243309,0.6047468531,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939715,430751118,534,449243310,0.3394452023,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939714,430758798,534,449243311,1.0971752187,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939713,430755726,534,449243312,5.1009273696,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939712,430766478,534,449243313,-27.4639329578,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939711,430749582,534,449243314,-56.1735755773,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939710,430757262,534,449243315,-72.2783059098,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939709,430760334,534,449243316,-90.5887455377,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939708,430377914,534,449243317,4.9452627381,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939707,430385594,534,449243318,19.7403169424,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939706,430422415,534,449243319,20.6084942663,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939705,430388666,534,449243320,-94.4253640904,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939704,430393274,534,449243321,-77.3032971548,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939703,430391738,534,449243322,-58.5190729633,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939702,430387130,534,449243323,-50.0178492903,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939701,430384058,534,449243324,-44.5386085275,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939700,430382522,534,449243325,-24.2872869162,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939699,430425487,534,449243330,9.6191813961,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939698,430423951,534,449243331,-0.1189863227,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939697,430440847,534,449243334,-109.5033957167,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939696,430433167,534,449243341,12.7991460404,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939695,430436239,534,449243342,3.6750887039,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939694,430396346,534,449243343,-6.2171842637,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939693,430430095,534,449243348,4.2768491029,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939692,430376378,534,449243349,16.0491804873,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939691,430434703,534,449243350,-12.5694069267,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939690,430442383,534,449243351,-5.5464142931,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939689,430437775,534,449243352,7.7790889947,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939688,430443919,534,449243353,-108.1864438838,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939687,430428559,534,449243354,-78.5294105576,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939686,430431631,534,449243355,-41.5760993818,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939685,430427023,534,449243356,-29.8191354153,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939684,430439311,534,449243357,-5.7325549136,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939683,430380986,534,449243358,7.0767484891,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939682,430394810,534,449243359,-9.2539696563,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939681,430397882,534,449243360,-9.1805107616,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -424939680,430390202,534,449243361,-3.4352984691,"2017-06-10 01:45:15","0000-00-00 00:00:00","rjudson.rjudson.rjudson" diff --git a/inst/example/mc2_acid.csv b/inst/example/mc2_acid.csv deleted file mode 100644 index 4eeb2ffc..00000000 --- a/inst/example/mc2_acid.csv +++ /dev/null @@ -1 +0,0 @@ -"mc2_mthd_id","acid","exec_ordr","created_date","modified_date","modified_by" diff --git a/inst/example/mc2_methods.csv b/inst/example/mc2_methods.csv deleted file mode 100644 index 3f2667ac..00000000 --- a/inst/example/mc2_methods.csv +++ /dev/null @@ -1,13 +0,0 @@ -mc2_mthd_id,mc2_mthd,desc,created_date,modified_date,modified_by -1,none,"apply no level 2 method","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -2,log2,"log2 all raw data","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -3,rmneg,"remove negative values prior to logging values","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -4,rmzero,"remove 0 values prior to logging values","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -5,mult25,"multiply values by 25","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -7,mult100,"multiply values by 100","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -10,log10,"log10 the raw data","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -11,negshift,"Shifts all data to be positive (new min=1)","2014-10-06 14:47:15","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 -12,mult2.5,"multiply values by 2.5","2014-11-06 10:36:15","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 -13,mult3,"multiply values by 3","2014-11-06 10:36:34","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 -14,mult6,"multiply values by 6","2014-11-06 15:53:33","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 -17,sub100,"100 minus cval (centers data around zero if prenormalized starting at 100 and going down to zero)","2015-10-05 12:42:21","0000-00-00 00:00:00","mmarti02.mmarti02.mmarti02" diff --git a/inst/example/mc3.csv b/inst/example/mc3.csv deleted file mode 100644 index 4cb95056..00000000 --- a/inst/example/mc3.csv +++ /dev/null @@ -1,45 +0,0 @@ -"m3id","aeid","m0id","acid","m1id","m2id","bval","pval","logc","resp","created_date","modified_date","modified_by" -482775747,797,430748046,534,449243302,424939723,NA,NA,0.602059991327962,25.8516680725,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775748,797,430752654,534,449243303,424939722,NA,NA,0.301029995663981,12.808278967,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775749,797,430764942,534,449243304,424939721,NA,NA,-0.154901959985743,7.7695268125,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775750,797,430754190,534,449243305,424939720,NA,NA,-0.522878745280338,3.0309182114,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775751,797,430761870,534,449243306,424939719,NA,NA,-1,-0.6320821129,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775752,797,430763406,534,449243307,424939718,NA,NA,-1.15490195998574,-0.2937049989,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775753,797,430746510,534,449243308,424939717,NA,NA,-1.52287874528034,-4.8854945307,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775754,797,430744974,534,449243309,424939716,NA,NA,-2,-0.6047468531,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775755,797,430751118,534,449243310,424939715,NA,NA,-2.22184874961636,-0.3394452023,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775756,797,430758798,534,449243311,424939714,NA,NA,-2.52287874528034,-1.0971752187,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775757,797,430755726,534,449243312,424939713,NA,NA,-3,-5.1009273696,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775758,797,430766478,534,449243313,424939712,NA,NA,0.903089986991944,27.4639329578,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775759,797,430749582,534,449243314,424939711,NA,NA,1.30102999566398,56.1735755773,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775760,797,430757262,534,449243315,424939710,NA,NA,1.60205999132796,72.2783059098,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775761,797,430760334,534,449243316,424939709,NA,NA,1.95424250943932,90.5887455377,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775762,797,430377914,534,449243317,424939708,NA,NA,-1,-4.9452627381,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775763,797,430385594,534,449243318,424939707,NA,NA,-1.15490195998574,-19.7403169424,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775764,797,430422415,534,449243319,424939706,NA,NA,-3,-20.6084942663,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775765,797,430388666,534,449243320,424939705,NA,NA,1.95424250943932,94.4253640904,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775766,797,430393274,534,449243321,424939704,NA,NA,1.60205999132796,77.3032971548,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775767,797,430391738,534,449243322,424939703,NA,NA,1.30102999566398,58.5190729633,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775768,797,430387130,534,449243323,424939702,NA,NA,0.903089986991944,50.0178492903,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775769,797,430384058,534,449243324,424939701,NA,NA,0.602059991327962,44.5386085275,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775770,797,430382522,534,449243325,424939700,NA,NA,0.301029995663981,24.2872869162,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775771,797,430425487,534,449243330,424939699,NA,NA,-2.22184874961636,-9.6191813961,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775772,797,430423951,534,449243331,424939698,NA,NA,-2.52287874528034,0.1189863227,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775773,797,430440847,534,449243334,424939697,NA,NA,1.95424250943932,109.5033957167,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775774,797,430433167,534,449243341,424939696,NA,NA,-1.52287874528034,-12.7991460404,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775775,797,430436239,534,449243342,424939695,NA,NA,-2,-3.6750887039,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775776,797,430396346,534,449243343,424939694,NA,NA,-0.522878745280338,6.2171842637,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775777,797,430430095,534,449243348,424939693,NA,NA,-1.15490195998574,-4.2768491029,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775778,797,430376378,534,449243349,424939692,NA,NA,-1.52287874528034,-16.0491804873,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775779,797,430434703,534,449243350,424939691,NA,NA,-0.154901959985743,12.5694069267,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775780,797,430442383,534,449243351,424939690,NA,NA,-0.522878745280338,5.5464142931,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775781,797,430437775,534,449243352,424939689,NA,NA,-1,-7.7790889947,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775782,797,430443919,534,449243353,424939688,NA,NA,1.60205999132796,108.1864438838,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775783,797,430428559,534,449243354,424939687,NA,NA,1.30102999566398,78.5294105576,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775784,797,430431631,534,449243355,424939686,NA,NA,0.903089986991944,41.5760993818,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775785,797,430427023,534,449243356,424939685,NA,NA,0.602059991327962,29.8191354153,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775786,797,430439311,534,449243357,424939684,NA,NA,0.301029995663981,5.7325549136,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775787,797,430380986,534,449243358,424939683,NA,NA,-2,-7.0767484891,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775788,797,430394810,534,449243359,424939682,NA,NA,-2.22184874961636,9.2539696563,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775789,797,430397882,534,449243360,424939681,NA,NA,-2.52287874528034,9.1805107616,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -482775790,797,430390202,534,449243361,424939680,NA,NA,-3,3.4352984691,"2017-06-10 01:49:02","0000-00-00 00:00:00","rjudson.rjudson.rjudson" diff --git a/inst/example/mc3_aeid.csv b/inst/example/mc3_aeid.csv deleted file mode 100644 index 91fe04a8..00000000 --- a/inst/example/mc3_aeid.csv +++ /dev/null @@ -1 +0,0 @@ -"mc3_mthd_id","aeid","exec_ordr","created_date","modified_date","modified_by" diff --git a/inst/example/mc3_methods.csv b/inst/example/mc3_methods.csv deleted file mode 100644 index 4561cd21..00000000 --- a/inst/example/mc3_methods.csv +++ /dev/null @@ -1,37 +0,0 @@ -mc3_mthd_id,mc3_mthd,desc,created_date,modified_date,modified_by -1,none,"apply no level 3 method","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -2,bval.apid.lowconc.med,"plate-wise baseline based on low conc median value","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -3,pval.apid.medpcbyconc.max,"plate-wise median response of positive control (max)","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -4,pval.apid.medpcbyconc.min,"plate-wise median response of positive control (min)","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -5,resp.pc,"response percent activity","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -6,resp.multneg1,"multiply the response by -1","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -7,resp.log2,"take the log base 2 of the response","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -8,resp.mult25,"multiply the response by 25","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -9,resp.fc,"calculate response as fold-change","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -11,bval.apid.nwlls.med,"plate-wise baseline based on neutral ctrl median value","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -12,bval.spid.lowconc.med,"sample-wise baseline based on low conc median value","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -13,pval.apid.pwlls.med,"plate-wise meidan based on positive control, single dose","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -14,pval.apid.mwlls.med,"plate-wise meidan based on negative control, single dose","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -15,pval.apid.medncbyconc.min,"plate-wise meidan based on negative control, (min)","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -16,bval.apid.twlls.med,"Take the median cval of the t wells, by apid","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -17,bval.apid.nwllslowconc.med,"Take the median cval of the n wells and the first two concentrations, by apid","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -18,resp.shiftneg.3bmad,"Make values below baseline zero.","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -19,resp.blineshift.3bmad.repi,"Do baseline correction by repi, with a window of 3*bmad","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -20,resp.blineshift.50.repi,"Do baseline correction by repi, with a window of 50","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -21,resp.blineshift.50.spid,"Do baseline correction by spid, with a window of 50","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -23,resp.blineshift.3bmad.spid,"Do baseline correction by repi, with a window of 3*bmad","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -24,bval.apid.tn.med,"Take the median cval of the t and n wells, by apid","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -25,pval.apid.pmv.min,"Calculate the median p, m, and v values by concentration, then take the minimum by apid.","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -26,pval.apid.pmv.max,"Calculate the median p, m, and v values by concentration, then take the maximum by apid.","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -27,pval.apid.f.max,"Calculate the median of f values by concentration, then take the maximum by apid","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -28,pval.apid.f.min,"Calculate the median of f values by concentration, then take the minimum by apid","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -29,pval.apid.p.min,"Calculate the median of p values by concentration, then take the minimum by apid","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -30,pval.apid.p.max,"Calculate the median of p values by concentration, then take the maximum by apid","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -31,pval.apid.v.min,"Calculate the median of v values by concentration, then take the minimum by apid","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -32,pval.zero,"Set pval to 0.","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -33,resp.shiftneg.6bmad,"Shift response values falling below -6 * bmad to 0.","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -34,resp.shiftneg.10bmad,"Shift response values falling below -10 * bmad to 0.","0000-00-00 00:00:00","0000-00-00 00:00:00",dfiler.dfiler.dfiler -35,resp.logfc,"Calculate the response as a fold change over baseline for logged values","2014-10-02 14:18:40","0000-00-00 00:00:00",dfiler.dfiler.dfiler -36,resp.scale.mad.log2fc,"Scale the resp data by the ratio of log2(1.2) over 3* baseline mad of the unscaled resp values","2015-02-23 13:58:52","0000-00-00 00:00:00", -37,resp.scale.quant.log2fc,"Scale resp such that 20% of the maximum resp equals log2(1.2)","2015-03-13 16:44:05","0000-00-00 00:00:00",dfiler.dfiler.dfiler -38,bval.apid.nwllstcwllslowconc.med,"plate-wise baseline based on neutral and t and c well low conc","2015-09-16 15:22:54","0000-00-00 00:00:00",mmarti02.mmarti02.mmarti02 diff --git a/inst/example/mc4.csv b/inst/example/mc4.csv deleted file mode 100644 index 2c41f5c8..00000000 --- a/inst/example/mc4.csv +++ /dev/null @@ -1,3 +0,0 @@ -"m4id","aeid","spid","bmad","resp_max","resp_min","max_mean","max_mean_conc","max_med","max_med_conc","logc_max","logc_min","cnst","hill","hcov","gnls","gcov","cnst_er","cnst_aic","cnst_rmse","cnst_prob","hill_tp","hill_tp_sd","hill_ga","hill_ga_sd","hill_gw","hill_gw_sd","hill_er","hill_er_sd","hill_aic","hill_rmse","hill_prob","gnls_tp","gnls_tp_sd","gnls_ga","gnls_ga_sd","gnls_gw","gnls_gw_sd","gnls_la","gnls_la_sd","gnls_lw","gnls_lw_sd","gnls_er","gnls_er_sd","gnls_aic","gnls_rmse","gnls_prob","nconc","npts","nrep","nmed_gtbl","tmpi","created_date","modified_date","modified_by" -18609966,797,"Tox21_202992",6.44391923052108,109.5033957167,-20.6084942663,98.1725017816,1.95424250943932,94.4253640904,1.95424250943932,1.95424250943932,-3,1,1,1,1,1,3.30736588007509,448.319915469051,41.5886357915789,3.35489346740589e-26,117.394184254973,17.4784180417536,1.21619689238089,0.200620880158924,0.854051897308764,0.141503541025264,2.00693525091024,0.143926067618168,331.260186646208,9.63076046108619,0.880797096613293,117.393199211778,17.4776426213293,1.21617912878982,0.200614786833848,0.854055545558882,0.141499853761845,2.61425477137428,262.04321448648,11.362237550244,4508.98837634178,2.00693352306279,0.143925899094951,335.26018700119,9.63073734439273,0.119202903386706,15,44,3,5,1638,"2017-06-10 02:09:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" -18610151,797,"Tox21_400088",6.44391923052108,117.540528361,-37.3394224506,100.465424800569,1.95424250943932,100.3208208064,1.95424250943932,1.95424250943932,-3,1,1,1,1,1,3.33501313432901,6821.79750955702,41.9662055992013,0,133.708893343495,6.41773553786922,1.31680522530087,0.0665611981171054,0.743424361310043,0.0334320778614389,1.96352280443088,0.0360049761129623,4868.6694563213,9.32970302693295,0.880797093510943,133.711503236814,6.41799605183265,1.31683434789418,0.0665631490577626,0.74340794366297,0.0334305924702818,2.59988218062917,283.579662805397,13.0554747440897,5724.33660767495,1.96351586178074,0.0360048976725412,4872.66945661719,9.32970719208977,0.119202906489057,15,670,45,6,1823,"2017-06-10 02:09:36","0000-00-00 00:00:00","rjudson.rjudson.rjudson" diff --git a/inst/example/mc4_aeid.csv b/inst/example/mc4_aeid.csv deleted file mode 100644 index 3d9062b3..00000000 --- a/inst/example/mc4_aeid.csv +++ /dev/null @@ -1 +0,0 @@ -"mc4_mthd_id","aeid","created_date","modified_date","modified_by" diff --git a/inst/example/mc4_agg.csv b/inst/example/mc4_agg.csv deleted file mode 100644 index f55d3ae6..00000000 --- a/inst/example/mc4_agg.csv +++ /dev/null @@ -1,45 +0,0 @@ -"aeid","m0id","m1id","m2id","m3id","m4id" -797,430748046,449243302,424939723,482775747,18609966 -797,430752654,449243303,424939722,482775748,18609966 -797,430764942,449243304,424939721,482775749,18609966 -797,430754190,449243305,424939720,482775750,18609966 -797,430761870,449243306,424939719,482775751,18609966 -797,430763406,449243307,424939718,482775752,18609966 -797,430746510,449243308,424939717,482775753,18609966 -797,430744974,449243309,424939716,482775754,18609966 -797,430751118,449243310,424939715,482775755,18609966 -797,430758798,449243311,424939714,482775756,18609966 -797,430755726,449243312,424939713,482775757,18609966 -797,430766478,449243313,424939712,482775758,18609966 -797,430749582,449243314,424939711,482775759,18609966 -797,430757262,449243315,424939710,482775760,18609966 -797,430760334,449243316,424939709,482775761,18609966 -797,430377914,449243317,424939708,482775762,18609966 -797,430385594,449243318,424939707,482775763,18609966 -797,430422415,449243319,424939706,482775764,18609966 -797,430388666,449243320,424939705,482775765,18609966 -797,430393274,449243321,424939704,482775766,18609966 -797,430391738,449243322,424939703,482775767,18609966 -797,430387130,449243323,424939702,482775768,18609966 -797,430384058,449243324,424939701,482775769,18609966 -797,430382522,449243325,424939700,482775770,18609966 -797,430425487,449243330,424939699,482775771,18609966 -797,430423951,449243331,424939698,482775772,18609966 -797,430440847,449243334,424939697,482775773,18609966 -797,430433167,449243341,424939696,482775774,18609966 -797,430436239,449243342,424939695,482775775,18609966 -797,430396346,449243343,424939694,482775776,18609966 -797,430430095,449243348,424939693,482775777,18609966 -797,430376378,449243349,424939692,482775778,18609966 -797,430434703,449243350,424939691,482775779,18609966 -797,430442383,449243351,424939690,482775780,18609966 -797,430437775,449243352,424939689,482775781,18609966 -797,430443919,449243353,424939688,482775782,18609966 -797,430428559,449243354,424939687,482775783,18609966 -797,430431631,449243355,424939686,482775784,18609966 -797,430427023,449243356,424939685,482775785,18609966 -797,430439311,449243357,424939684,482775786,18609966 -797,430380986,449243358,424939683,482775787,18609966 -797,430394810,449243359,424939682,482775788,18609966 -797,430397882,449243360,424939681,482775789,18609966 -797,430390202,449243361,424939680,482775790,18609966 diff --git a/inst/example/mc4_methods.csv b/inst/example/mc4_methods.csv deleted file mode 100644 index 71aa9e90..00000000 --- a/inst/example/mc4_methods.csv +++ /dev/null @@ -1,3 +0,0 @@ -mc4_mthd_id,mc4_mthd,desc,created_date,modified_date,modified_by -1,bmad.aeid.lowconc.twells,bmad based on two lowest concentration of treatment wells,0000-00-00 00:00:01,0000-00-00 00:00:00,spendse.scitovation -2,bmad.aeid.lowconc.nwells,bmad based on two lowest concentration of nwells,0000-00-00 00:00:00,0000-00-00 00:00:00,spendse.scitovation diff --git a/inst/example/mc5.csv b/inst/example/mc5.csv deleted file mode 100644 index 0e6bf2aa..00000000 --- a/inst/example/mc5.csv +++ /dev/null @@ -1,3 +0,0 @@ -m5id,m4id,aeid,modl,hitc,fitc,coff,actp,modl_er,modl_tp,modl_ga,modl_gw,modl_la,modl_lw,modl_prob,modl_rmse,modl_acc,modl_acb,modl_ac10,model_type,created_date,modified_date,modified_by -19428453,18609966,797,hill,1,42,38.6635153831265,1,2.00693525091024,117.394184254973,1.21619689238089,0.854051897308764,NA,NA,0.880797096613293,9.63076046108619,0.854576476290224,0.390449306126648,0.098884803447799,0,2017-06-10 02:10:13,0000-00-00 00:00:00,rjudson.rjudson.rjudson -19428267,18610151,797,hill,1,42,38.6635153831265,1,1.96352280443088,133.708893343495,1.31680522530087,0.743424361310043,NA,NA,0.880797093510943,9.32970302693295,0.79135881305226,0.278276070856458,0.033228093448769,0,2017-06-10 02:10:13,0000-00-00 00:00:00,rjudson.rjudson.rjudson diff --git a/inst/example/mc5_aeid.csv b/inst/example/mc5_aeid.csv deleted file mode 100644 index 0cc5ff7f..00000000 --- a/inst/example/mc5_aeid.csv +++ /dev/null @@ -1 +0,0 @@ -"aeid","mc5_mthd_id","created_date","modified_date","modified_by" diff --git a/inst/example/mc5_fit_categories.csv b/inst/example/mc5_fit_categories.csv deleted file mode 100644 index 2900872d..00000000 --- a/inst/example/mc5_fit_categories.csv +++ /dev/null @@ -1,56 +0,0 @@ -"fitc","parent_fitc","name","xloc","yloc" -"1","NULL","01: ALL DOSE RESPONSE",1110,756.5 -"2","1","02: CANNOT DETERMINE",977.7455523765,611.9831921304 -"3","1","03: INACTIVE",1022.9653320313,924.2873535156 -"4","3","04: RESP < BLINE",1271.6083984375,974.8182373047 -"5","3","05: RESP >= BLINE",996.8209228516,1127.5755004883 -"6","5","06: CNST",666,1251.5 -"7","6","07: NOTP >= 0.8(COFF)",761.8584594727,1333.5216674805 -"8","6","08: ANYTP >= 0.8(COFF)",507.3630981445,1333.6228027344 -"9","8","09: NOTP >= COFF",337.4776000977,1263.4637451172 -"10","8","10: ANYTP >= COFF",450.4357910156,1397.3994140625 -"11","5","11: HILL",1189.7768554688,1209.4105834961 -"12","11","12: TP < 0.8(COFF)",1149.2390136719,1317.5518188477 -"13","12","13: GNLS < 0.8(COFF)",992.1193237305,1394.7369384766 -"14","12","14: GNLS >= 0.8(COFF)",1246.0364990234,1386.9293518066 -"15","14","15: GNLS < COFF",1218.9203491211,1496.1217041016 -"16","14","16: GNLS >= COFF",1361.9873046875,1443.5811157227 -"17","11","17: TP >= 0.8(COFF)",1460.6746826172,1119.6658935547 -"18","17","18: GNLS < 0.8(COFF)",1539.3952956084,1228.8681030273 -"19","17","19: GNLS >= 0.8(COFF)",1623.3784179688,1043.5646362305 -"20","19","20: GNLS < COFF",1876.1442871094,1040.0154418945 -"21","19","21: GNLS >= COFF",1849.7615966797,948.6744995117 -"22","5","22: GNLS",794.5350952148,1043.2316894531 -"23","22","23: TP < 0.8(COFF)",632.9550857544,936.3232232708 -"24","23","24: HILL < 0.8(COFF)",803.6691931111,753.821326896 -"25","23","25: HILL >= 0.8(COFF)",542.0636749268,831.3344537395 -"26","25","26: HILL < COFF",478.504219532,698.9990045207 -"27","25","27: HILL >= COFF",359.5413589478,763.8884088176 -"28","22","28: TP >= 0.8(COFF)",491.8406066895,1063.1170043945 -"29","28","29: HILL < 0.8(COFF)",446.9388122559,1132.0888671875 -"30","28","30: HILL >= 0.8(COFF)",371.3406066895,956.1169433594 -"31","30","31: HILL < COFF",288.3405761719,853.1170654297 -"32","30","32: HILL >= COFF",107.8862915039,948.5189208984 -"33","1","33: ACTIVE",1276.5,563.5 -"34","33","34: HILL",1190.094543457,462.0799560547 -"35","34","35: TP <= 1.2(COFF)",991.5,302.5 -"36","35","36: AC50 <=",764.6481933594,350.3658447266 -"37","35","37: AC50 ==",749.6301269531,254.4168701172 -"38","35","38: AC50 >=",966.6704101563,183.7718505859 -"39","34","39: TP > 1.2(COFF)",1310.6741943359,263.3843994141 -"40","39","40: AC50 <=",1134.5294799805,105.1185302734 -"41","39","41: AC50 ==",1412.8084716797,121.1416015625 -"42","39","42: AC50 >=",1578.5758056641,187.1433105469 -"43","33","43: GNLS",1558.3104248047,570.28125 -"44","43","44: TP <= 1.2(COFF)",1639.5,451.5 -"45","44","45: AC50 <=",1811.0447998047,377.1083984375 -"46","44","46: AC50 ==",1905.2620849609,445.5483398437 -"47","44","47: AC50 >=",1659.5,320.5 -"48","43","48: TP > 1.2(COFF)",1647.5,685.5 -"49","48","49: AC50 <=",1704.5,806.5 -"50","48","50: AC50 ==",1873.9647216797,741.5611572266 -"51","48","51: AC50 >=",1926.5576171875,671.6712646484 -"52","23","52: HILL DNC",890.4145965576,837.0693170207 -"53","28","53: HILL DNC",155.8844682354,1077.1187744141 -"54","12","54: GNLS DNC",1463.7992844698,1325.916809082 -"55","17","55: GNLS DNC",1774.73046875,1155.2709031221 diff --git a/inst/example/mc5_methods.csv b/inst/example/mc5_methods.csv deleted file mode 100644 index 8598257f..00000000 --- a/inst/example/mc5_methods.csv +++ /dev/null @@ -1,13 +0,0 @@ -mc5_mthd_id,mc5_mthd,desc,created_date,modified_date,modified_by -1,bmad3,Add a cutoff value of 3*bmad.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,pc20,Add a cutoff value of 20.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,log2_1.2,Add a cutoff value of log2(1.2).,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,log10_1.2,Add a cutoff value of log10(1.2).,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,bmad5,Add a cutoff value of 5*bmad.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,bmad6,Add a cutoff value of 6*bmad.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,bmad10,Add a cutoff value of 10*bmad.,2015-05-04 12:03:49,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,maxmed20pct,Add a cutoff value of 20% of the max of max_med,2015-05-06 09:08:50,0000-00-00 00:00:00,kconnors.kconnors.kconnors -9,pc70,70% cutoff,2015-07-28 15:06:35,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 -10,pc50,50% cutoff,2015-07-28 15:08:01,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 -11,log2_2,log2 of 2 fold change cutoff,2015-07-28 15:08:01,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 -12,log10_2,log10 of 2 fold change cutoff,2015-07-28 15:08:01,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 diff --git a/inst/example/mc6.csv b/inst/example/mc6.csv deleted file mode 100644 index a9256b01..00000000 --- a/inst/example/mc6.csv +++ /dev/null @@ -1 +0,0 @@ -"m6id","m5id","m4id","aeid","mc6_mthd_id","flag","fval","fval_unit","created_date","modified_date","modified_by" diff --git a/inst/example/mc6_aeid.csv b/inst/example/mc6_aeid.csv deleted file mode 100644 index d2da162a..00000000 --- a/inst/example/mc6_aeid.csv +++ /dev/null @@ -1 +0,0 @@ -"aeid","mc6_mthd_id","created_date","modified_date","modified_by" diff --git a/inst/example/mc6_methods.csv b/inst/example/mc6_methods.csv deleted file mode 100644 index 2b15f3d9..00000000 --- a/inst/example/mc6_methods.csv +++ /dev/null @@ -1,19 +0,0 @@ -mc6_mthd_id,mc6_mthd,desc,nddr,created_date,modified_date,modified_by -1,row.dev.up,"Look for row-wise plate effects, increase",1,2014-07-28 14:03:41,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,row.dev.dn,"Look for row-wise plate effects, decrease",1,2014-07-28 14:03:54,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,col.dev.dn,"Look for column-wise plate effects, decrease",1,2014-07-28 14:04:08,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,col.dev.up,"Look for column-wise plate effects, increase",1,2014-07-28 14:04:17,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,plate.flare,Look for plate flare effects,1,2014-07-28 14:04:27,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,singlept.hit.high,Look for single point hits with activity only at the highest conc tested,0,2014-07-28 14:06:05,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,singlept.hit.mid,Look for signle point hits with activity not at highest conc tested,0,2014-07-28 14:06:51,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,multipoint.neg,Look for inactives with multiple medians above baseline,0,2014-07-28 14:08:42,0000-00-00 00:00:00,dfiler.dfiler.dfiler -9,pintool,Look for pintool carryover issues,1,2014-07-28 14:09:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -10,noise,"Look for noisy curves, relative to the assay",0,2014-07-28 14:09:41,0000-00-00 00:00:00,dfiler.dfiler.dfiler -11,border.hit,Look for actives with borderline activity,0,2014-07-28 14:10:14,0000-00-00 00:00:00,dfiler.dfiler.dfiler -12,border.miss,Look for inactives with borderline activity,0,2014-07-28 14:10:21,0000-00-00 00:00:00,dfiler.dfiler.dfiler -13,plate.interlace,Look for interlaced chemical-plate effects,1,2014-08-21 12:13:26,0000-00-00 00:00:00,dfiler.dfiler.dfiler -14,rep.mismatch,Look for mismatched techinal replicates,1,2014-08-21 12:16:44,0000-00-00 00:00:00,dfiler.dfiler.dfiler -15,gnls.lowconc,Look for low concentration gnls winners,0,2014-08-21 12:21:32,0000-00-00 00:00:00,dfiler.dfiler.dfiler -16,overfit.hit,Flag hit-calls that would get changed after doing the small N correction to the aic values.,0,2014-09-16 11:51:14,0000-00-00 00:00:00,dfiler.dfiler.dfiler -17,efficacy.50,Flag hit-calls with efficacy values less than 50% -- intended for biochemical assays.,0,2014-09-16 11:51:58,0000-00-00 00:00:00,dfiler.dfiler.dfiler -19,viability.gnls,Flag hit-calls with cell viability assay that are fit with gnls winning model,0,03/26/19 10:53 AM,, diff --git a/inst/example/sample.csv b/inst/example/sample.csv deleted file mode 100644 index 40880bf9..00000000 --- a/inst/example/sample.csv +++ /dev/null @@ -1,3 +0,0 @@ -"spid","chid","stkc","stkc_unit","tested_conc_unit","spid_legacy" -"Tox21_202992",20182,20,"mM","uM","Tox21_202992" -"Tox21_400088",20182,20,"mM","uM","Tox21_400088" diff --git a/inst/example/sc0.csv b/inst/example/sc0.csv deleted file mode 100644 index 79455906..00000000 --- a/inst/example/sc0.csv +++ /dev/null @@ -1,5 +0,0 @@ -"s0id","acid","spid","apid","rowi","coli","wllt","wllq","conc","rval","srcf","created_date","modified_date","modified_by" -13196766,201,"TP0000757A10","EPA13-A384-06",14,22,"t",1,10.2,25887,"400-0905-384-01-20111107.txt","2018-06-04 12:44:18","0000-00-00 00:00:00","nrush.nrush.nrush" -13196766,201,"TP0000757A10","EPA13-A384-06",14,22,"t",1,10.2,25887,"400-0905-384-01-20111107.txt","2018-06-04 12:44:18","0000-00-00 00:00:00","nrush.nrush.nrush" -13196765,201,"TP0000757A10","EPA13-A384-06",14,21,"t",1,10.2,26215,"400-0905-384-01-20111107.txt","2018-06-04 12:44:18","0000-00-00 00:00:00","nrush.nrush.nrush" -13196765,201,"TP0000757A10","EPA13-A384-06",14,21,"t",1,10.2,26215,"400-0905-384-01-20111107.txt","2018-06-04 12:44:18","0000-00-00 00:00:00","nrush.nrush.nrush" diff --git a/inst/example/sc1.csv b/inst/example/sc1.csv deleted file mode 100644 index b462e2cc..00000000 --- a/inst/example/sc1.csv +++ /dev/null @@ -1,5 +0,0 @@ -"s1id","s0id","acid","aeid","logc","bval","pval","resp","created_date","modified_date","modified_by" -10210785,13196766,201,320,1,26499,3970,-2.71649873496382,"2018-06-04 12:59:31","0000-00-00 00:00:00","nrush.nrush.nrush" -10205619,13196766,201,319,1,26499,3970,2.71649873496382,"2018-06-04 12:59:31","0000-00-00 00:00:00","nrush.nrush.nrush" -10210786,13196765,201,320,1,26499,3970,-1.26059745217275,"2018-06-04 12:59:31","0000-00-00 00:00:00","nrush.nrush.nrush" -10205620,13196765,201,319,1,26499,3970,1.26059745217275,"2018-06-04 12:59:31","0000-00-00 00:00:00","nrush.nrush.nrush" diff --git a/inst/example/sc1_aeid.csv b/inst/example/sc1_aeid.csv deleted file mode 100644 index feff4d15..00000000 --- a/inst/example/sc1_aeid.csv +++ /dev/null @@ -1 +0,0 @@ -"sc1_mthd_id","aeid","exec_ordr","created_date","modified_date","modified_by" diff --git a/inst/example/sc1_methods.csv b/inst/example/sc1_methods.csv deleted file mode 100644 index 0a300039..00000000 --- a/inst/example/sc1_methods.csv +++ /dev/null @@ -1,17 +0,0 @@ -sc1_mthd_id,sc1_mthd,desc,created_date,modified_date,modified_by -1,bval.apid.nwlls.med,plate-wise baseline based on neutral ctrl median value,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,bval.apid.twlls.med,"Take the median cval of the t wells, by apid",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,bval.apid.tn.med,"Take the median cval of the t and n wells, by apid",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,pval.apid.pwlls.med,"plate-wise meidan based on positive control, single dose",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,pval.apid.mwlls.med,"plate-wise meidan based on negative control, single dose",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,pval.apid.medpcbyconc.max,plate-wise median response of positive control (max),2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,pval.apid.medpcbyconc.min,plate-wise median response of positive control (min),2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,pval.apid.medncbyconc.min,"plate-wise meidan based on negative control, (min)",2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -9,pval.zero,Set pval to 0.,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -10,resp.pc,response percent activity,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -11,resp.fc,calculate response as fold-change,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -12,resp.logfc,Calculate the response as a fold change over baseline for logged values,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -13,resp.log2,take the log base 2 of the response,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -14,none,apply no level 2 method,2015-05-13 11:44:35,0000-00-00 00:00:00,dfiler.dfiler.dfiler -16,resp.multneg1,multiply response values by negative 1,2015-05-29 10:27:45,0000-00-00 00:00:00,Akarmaus.Akarmaus.Akarmaus -17,pval.apid.or.aeid.pwlls.med,calculates pval first based on p wells by plate and then for any plates missing p wells it calculates a pval by median of pval for all other plates,2015-09-30 14:43:40,0000-00-00 00:00:00,mmarti02.mmarti02.mmarti02 diff --git a/inst/example/sc2.csv b/inst/example/sc2.csv deleted file mode 100644 index aa92bfd3..00000000 --- a/inst/example/sc2.csv +++ /dev/null @@ -1 +0,0 @@ -"s2id","aeid","spid","bmad","max_med","coff","hitc","tmpi","created_date","modified_date","modified_by" diff --git a/inst/example/sc2_aeid.csv b/inst/example/sc2_aeid.csv deleted file mode 100644 index f471e380..00000000 --- a/inst/example/sc2_aeid.csv +++ /dev/null @@ -1 +0,0 @@ -"sc2_mthd_id","aeid","created_date","modified_date","modified_by" diff --git a/inst/example/sc2_agg.csv b/inst/example/sc2_agg.csv deleted file mode 100644 index 420ea93e..00000000 --- a/inst/example/sc2_agg.csv +++ /dev/null @@ -1 +0,0 @@ -"aeid","s0id","s1id","s2id" diff --git a/inst/example/sc2_methods.csv b/inst/example/sc2_methods.csv deleted file mode 100644 index c79bb628..00000000 --- a/inst/example/sc2_methods.csv +++ /dev/null @@ -1,11 +0,0 @@ -sc2_mthd_id,sc2_mthd,desc,created_date,modified_date,modified_by -1,bmad3,Add a cutoff value of 3*bmad.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -2,pc20,Add a cutoff value of 20.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -3,log2_1.2,Add a cutoff value of log2(1.2).,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -4,log10_1.2,Add a cutoff value of log10(1.2).,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -5,bmad5,Add a cutoff value of 5*bmad.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -6,bmad6,Add a cutoff value of 6*bmad.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -7,bmad10,Add a cutoff value of 10*bmad.,2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -8,pc30orbmad3,"Add a cutoff value of either 30 or 3*bmad, whichever is less.",2015-05-13 13:51:13,0000-00-00 00:00:00,dfiler.dfiler.dfiler -9,pc0.88,Add a cutoff value of 0.88.,2015-05-14 13:25:38,0000-00-00 00:00:00,dfiler.dfiler.dfiler -10,log2_1.5,Add a cutoff value of log2(1.5).,2015-05-14 13:25:38,0000-00-00 00:00:00,dfiler.dfiler.dfiler diff --git a/man/MC2_Methods.Rd b/man/MC2_Methods.Rd index f73165c5..55c27fed 100644 --- a/man/MC2_Methods.Rd +++ b/man/MC2_Methods.Rd @@ -40,7 +40,7 @@ available in the package vignette, "Data_processing." \item{rmneg}{Exclude wells with negative corrected response values (cval) and downgrading their well quality (wllq); if \eqn{cval<0, wllq=0}{cval<0, wllq=0}.} \item{rmzero}{Exclude wells with corrected response values (cval) equal to zero and - downgrading their well quality (wllq); if \eqn{cval=0, wllq=0}{cval=0, wllq=0}.} + downgrading their well quality (wllq); if \eqn{cval=0, wllq=0}{cval=0, wllq=0}.} \item{mult25}{Multiply corrected response value (cval) by 25; \eqn{25*cval}{25*cval}.} \item{mult100}{Multiply corrected response value (cval) by 100; \eqn{100*cval}{100*cval}.} \item{negshift}{Shift corrected response values (cval) by subtracting the minimum cval and @@ -49,15 +49,13 @@ available in the package vignette, "Data_processing." \item{mult3}{Multiply corrected response value (cval) by 3; \eqn{3*cval}{3*cval}.} \item{mult6}{Multiply corrected response value (cval) by 6; \eqn{6*cval}{6*cval}.} \item{sub100}{Center data around zero by subtracting the corrected response value (cval) from - 100; \eqn{100-cval}{100-cval}. Typically used if data was pre-normalized around 100 with - responses decreasing to 0.} + 100; \eqn{100-cval}{100-cval}. Typically used if data was pre-normalized around 100 with responses + decreasing to 0.} \item{zscore.npwlls}{Convert the corrected response value (cval) to an absolute Z-Score based - on the neutral and positive control wells (wllts = n and p), by assay plate ID (apid); - \eqn{cval=|(cval-mean(cval~for~wllt~=~n~and~p)/sd(cval~for~wllt~=~n~and~p)|}{cval= + on the neutral and positive control wells (wllts = n and p), by assay plate ID (apid); eqn{cval=|(cval-mean(cval~for~wllt~=~n~and~p)/sd(cval~for~wllt~=~n~and~p)|}{cval= |(cval-mean(cval for wllt = n and p)/sd(cval for wllt = n and p)|}.} \item{sub1}{Center data around zero by subtracting the corrected response value (cval) from 1; - \eqn{1-cval}{1-cval}. Typically used if data was pre-normalized around 1 with responses - decreasing to 0.} + \eqn{1-cval}{1-cval}. Typically used if data was pre-normalized around 1 with responses decreasing to 0.} } } @@ -65,22 +63,10 @@ available in the package vignette, "Data_processing." \describe{ \item{agg.mean.rep.apid}{Aggregate technical test replicates (wllt=t) by taking the plate-wise mean per sample id (spid), assay plate (apid), and concentration index (cndx).} \item{agg.median.rep.apid}{Aggregate technical test replicates (wllt=t) by taking the plate-wise median per sample id (spid), assay plate (apid), and concentration index (cndx).} - \item{agg.percent.rep.spid}{Use for binary data. Aggregate technical replicates as percentage by taking the sum of hits relative to total replicates per sample id (spid) and concentration index (cndx); cval = (sum(rval)/.N)*100.} - \item{agg.percent.rep.spid.min1}{Use for binary data. Aggregate technical replicates as percentage by taking the sum of hits relative to total replicates per per sample id (spid) and concentration index (cndx), where there is more than one replicate; cval = (sum(rval)/.N)*100, where .N>1.} - \item{agg.mean.rep.apid}{Aggregate technical replicates by taking the plate-wise mean per - sample id (spid), assay plate (apid), and concentration index (cndx).} - \item{agg.median.rep.apid}{Aggregate technical replicates by taking the plate-wise median per - sample id (spid), assay plate (apid), and concentration index (cndx).} - \item{agg.percent.rep.spid}{Use for binary data. Aggregate technical replicates as percentage - by taking the sum of hits relative to total replicates per sample id (spid) and concentration - index (cndx); \eqn{cval = (sum(rval)/.N)*100}{cval = (sum(rval)/.N)*100}.} - \item{agg.percent.rep.spid.min1}{Use for binary data. Aggregate technical replicates as - percentage by taking the sum of hits relative to total replicates per per sample id (spid) and - concentration index (cndx), where there is more than one replicate; - \eqn{cval=(sum(rval)/.N)*100,~where~.N>1}{cval = (sum(rval)/.N)*100, where .N>1}.} + \item{agg.percent.rep.spid}{Use for binary data. Aggregate technical replicates as percentage by taking the sum of rval (raw values) relative to total replicates per sample id (spid) and concentration index (cndx); \eqn{cval = (sum(rval)/.N)*100}{cval = (sum(rval)/.N)*100}.} + \item{agg.percent.rep.spid.min1}{Use for binary data with variable number of replicates. Aggregate technical replicates as percentage by taking the sum of rval (raw values) relative to total replicates per per sample id (spid) and concentration index (cndx), where there is more than one replicate; \eqn{cval=(sum(rval)/.N)*100,~where~.N>1}{cval = (sum(rval)/.N)*100, where .N>1}.} Rvals are collapsed to one value per cndx.} } } -} \seealso{ \code{\link{mc2}}, \code{\link{Method functions}} to query what diff --git a/man/MC4_Methods.Rd b/man/MC4_Methods.Rd index 2f6290aa..05b65458 100644 --- a/man/MC4_Methods.Rd +++ b/man/MC4_Methods.Rd @@ -39,16 +39,14 @@ available in the package vignette, "Data_processing." \describe{ \item{bmad.aeid.lowconc.twells}{Calculate the baseline median absolute value (bmad) as the - median absolute deviation of normalized response values (rep) for test compound wells - (wllt = t) with concentration index (cndx) equal to 1 or 2.} + median absolute deviation of normalized response values (rep) for test compound wells (wllt = t) + with concentration index (cndx) equal to 1 or 2. Calculate one standard deviation of the normalized + response for test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2; + onesd = sqrt(sum((resp - mean resp)^2)/sample size - 1). Onesd is used to establish BMR and therefore required for tcplfit2 processing.} \item{bmad.aeid.lowconc.nwells}{Calculate the baseline median absolute value (bmad) as the - median absolute deviation of normalized response values (resp) for neutral control wells - (wllt = n).} - \item{onesd.aeid.lowconc.twells}{Calculate one standard deviation of the normalized response - for test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2; - \eqn{onesd=\sqrt{\sum{(resp-mean(resp))^{2}}/(n-1)}}{onesd = sqrt(sum((resp - mean - resp)^2)/sample size - 1)}. Used to establish BMR and therefore required for tcplfit2 - processing.} + median absolute deviation of normalized response values (resp) for neutral control wells (wllt = n). + Calculate one standard deviation of the normalized response for neutral control wells (wllt = n); + onesd = sqrt(sum((resp - mean resp)^2)/sample size - 1). Onesd is used to establish BMR and therefore required for tcplfit2 processing.} \item{bidirectional.false}{Limits bidirectional fitting and processes data in positive analysis direction only. Use for gain-of-signal or inverted data.} \item{bmad5.onesd16.static}{Replace baseline median absolute deviation @@ -56,6 +54,7 @@ available in the package vignette, "Data_processing." for test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2 with 16. Typically used for binary data where values would otherwise be 0; non-zero values are required for tcplfit2 processing.} + \item{no.unbounded.models}{Exclude unbounded models and only fit data to bounded models (hill, gnls, exp4 and exp5).} } } diff --git a/man/MC6_Methods.Rd b/man/MC6_Methods.Rd index 001debeb..39718d3c 100644 --- a/man/MC6_Methods.Rd +++ b/man/MC6_Methods.Rd @@ -68,8 +68,9 @@ available in the package vignette, "Data_processing." viability assay with winning model is gain-loss (gnls); if hitc >= 0.9, modl = "gnls" and cell_viability_assay = 1, then flag.} \item{no.med.gt.3bmad}{Flag series where no median response values are greater than baseline as - defined by 3 times the baseline median absolute deviation (bmad); nmed_gtbl = 0, where - nmed_gtbl is the number of medians greater than 3 * bmad.} + defined by 3 times the baseline median absolute deviation (bmad); nmed_gtbl_pos and + nmed_gtbl_neg both = 0, where nmed_gtbl_pos/_neg is the number of medians greater than 3 * + bmad/less than -3 * bmad.} } } diff --git a/man/SC1_Methods.Rd b/man/SC1_Methods.Rd index 52e4df7d..15cf42c9 100644 --- a/man/SC1_Methods.Rd +++ b/man/SC1_Methods.Rd @@ -49,6 +49,8 @@ available in the package vignette, "Data_processing." \item{bval.apid.tn.med}{Calculate the baseline value (bval) as the plate-wise median, by assay plate ID (apid), of the raw values (rval) for test compound wells (wllt = t) and neutral control wells (wllt = n).} + \item{bval.nwlls.med}{Calculate the baseline value (bval) as the median of the raw values + (rval) for neutral control wells (wllt = n) by assay endpoint id (aeid).} } } diff --git a/man/assay_funcs.Rd b/man/assay_funcs.Rd index 679951f4..dbc54345 100644 --- a/man/assay_funcs.Rd +++ b/man/assay_funcs.Rd @@ -40,12 +40,7 @@ name for the given assay element. For example, \code{tcplLoadAsid} will return the assay source ID (asid) and assay source name (asnm). } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -TCPLlite <- file.path(system.file(package = "tcpl"), "example") -tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite") - +\dontrun{ ## The load assay functions can be used without any parameters to list the ## full list of registered assay elements: tcplLoadAsid() @@ -64,8 +59,6 @@ tcplListFlds("assay") a1 <- tcplLoadAeid(fld = "anm", val = "Steroidogenesis") a2 <- tcplLoadAeid(fld = "assay_name", val = "Steroidogenesis") identical(a1, a2) - -## Reset configuration -options(conf_store) +} } diff --git a/man/blineShift.Rd b/man/blineShift.Rd index 07b14f2b..029b5172 100644 --- a/man/blineShift.Rd +++ b/man/blineShift.Rd @@ -4,12 +4,12 @@ \alias{blineShift} \title{Shift the baseline to 0} \usage{ -blineShift(resp, logc, wndw) +blineShift(resp, conc, wndw) } \arguments{ \item{resp}{Numeric, the response values} -\item{logc}{Numeric, the log10 concentration values} +\item{conc}{Numeric, the concentration values} \item{wndw}{Numeric, the threshold window} } diff --git a/man/chdat.Rd b/man/chdat.Rd deleted file mode 100644 index 9c0e1df6..00000000 --- a/man/chdat.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{chdat} -\alias{chdat} -\title{Chemical library of tested chemicals in the example datasets with the corresponding sample IDs.} -\format{ -A data frame with 6 rows and 6 variables: -\describe{ - \item{spid}{sample ID} - \item{casn}{Chemical Abstract Service(CAS) number} - \item{chnm}{chemical name} - \item{dsstox_substance_id}{chemical-specific DTXSID} - \item{code}{CAS number compressed into numeric string} - \item{chid}{unique chemical ID number for tcpl} - -} -} -\source{ -ToxCast database -} -\usage{ -chdat -} -\description{ -Chemical library of tested chemicals in the example datasets with the corresponding sample IDs. -} -\keyword{datasets} diff --git a/man/config_funcs.Rd b/man/config_funcs.Rd index efbdeacc..20ba2262 100644 --- a/man/config_funcs.Rd +++ b/man/config_funcs.Rd @@ -1,12 +1,11 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/config_funcs.R, R/tcplConf.R, -% R/tcplConfDefault.R, R/tcplConfExample.R, R/tcplConfList.R, -% R/tcplConfLoad.R, R/tcplConfReset.R, R/tcplConfSave.R +% R/tcplConfDefault.R, R/tcplConfList.R, R/tcplConfLoad.R, R/tcplConfReset.R, +% R/tcplConfSave.R \name{Configure functions} \alias{Configure functions} \alias{tcplConf} \alias{tcplConfDefault} -\alias{tcplConfExample} \alias{tcplConfList} \alias{tcplConfLoad} \alias{tcplConfReset} @@ -17,8 +16,6 @@ tcplConf(drvr = NULL, user = NULL, pass = NULL, host = NULL, db = NULL, ...) tcplConfDefault() -tcplConfExample() - tcplConfList(show.pass = FALSE) tcplConfLoad(list.new = TRUE) @@ -48,8 +45,8 @@ tcplConfSave() These functions are used to configure the tcpl settings. } \details{ -Currently, the tcpl package only supports the "MySQL" and "tcplLite" database -drivers. +Currently, the tcpl package supports the "MySQL", "example", and "API" +database drivers. The settings can be stored in a configuration file to make the using the package more user-friendly. To create the configuration file, the user must @@ -82,8 +79,7 @@ tcpl settings. configuration file. \code{tcplConfDefault} changes the \code{options} to reflect the default -settings for the example tcplLite database, i.e. local directory, but does -not alter the configuration file. +settings for the API connection, but does not alter the configuration file. \code{tcplConfReset} is used to generate the initial configuration script, and can be used to reset or regenerate the configuration script by the user. diff --git a/man/mcdat.Rd b/man/mcdat.Rd index 486dc713..fb9b6bbc 100644 --- a/man/mcdat.Rd +++ b/man/mcdat.Rd @@ -27,6 +27,6 @@ mcdat } \description{ The example dataset is used to illustrate how the user can pipeline multiple-concentration -data from chemical screening using tcplLite. +data from chemical screening using tcpl. } \keyword{datasets} diff --git a/man/mthd_funcs.Rd b/man/mthd_funcs.Rd index f4c0d003..89bc4cc9 100644 --- a/man/mthd_funcs.Rd +++ b/man/mthd_funcs.Rd @@ -51,11 +51,7 @@ multiple-concentration processing. More information about method assignments and the delete cascade are available in the package vignette. } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfDefault() - +\dontrun{ ## tcplListMthd allows the user to display the available methods for ## a given level and data type head(tcplMthdList(lvl = 2, type = "mc")) @@ -66,7 +62,6 @@ head(tcplMthdList(lvl = 2, type = "mc")) ## whether an ID exists before assigning/clearing methods. tcplMthdLoad(lvl = 2, id = 55, type = "mc") -\dontrun{ ## ACID 55 does not have any methods. Assign methods from the list above. tcplMthdAssign(lvl = 2, id = 55, @@ -83,6 +78,4 @@ tcplMthdAssign(lvl = 2, ## Cleanup example method assigments tcplMthdClear(lvl = 2, id = 53:55, type = "mc") } -## Reset configuration -options(conf_store) } diff --git a/man/query_funcs.Rd b/man/query_funcs.Rd index 7b027090..328b87a6 100644 --- a/man/query_funcs.Rd +++ b/man/query_funcs.Rd @@ -41,7 +41,7 @@ These functions send a query to the given database, and are the access point for all tcpl functions that query or update the tcpl database. } \details{ -Currently, the tcpl package supports the "MySQL", "tcplLite", and "API" +Currently, the tcpl package supports the "MySQL", "example", and "API" database drivers. \code{tcplQuery} returns a data.table object with the query results. @@ -51,23 +51,13 @@ returns 'TRUE' or the error message given by the database. connected using "API" as driver. } \examples{ - -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -TCPLlite <- file.path(system.file(package = "tcpl"), "example") -tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite") - +\dontrun{ +# only with MySQL driver tcplQuery("SELECT 'Hello World';") -## When using tcplLite, name of table must be passed into tcplQuery -if (conf_store$TCPL_DRVR == 'MySQL') { - tcplQuery("SELECT * FROM assay;") -} else { - tcplQuery("SELECT * FROM assay;", tbl='assay') +# only with API driver +tcplConfDefault() +tcplQueryAPI(resource = "data", fld = "aeid", val = 2) } - -## Reset configuration -options(conf_store) } diff --git a/man/rgstr_funcs.Rd b/man/rgstr_funcs.Rd index 23ae35dd..5575e3ee 100644 --- a/man/rgstr_funcs.Rd +++ b/man/rgstr_funcs.Rd @@ -49,13 +49,7 @@ rather than the full "assay_component_endpoint_name." More information about the registration process and all of the fields is available in the vignette. } \examples{ - \dontrun{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfDefault() - ## Load current ASID information tcplLoadAsid() @@ -76,17 +70,6 @@ tcplLoadAsid(add.fld = "assay_source_desc") ## Remove the created ASID. Note: Manually deleting primary keys can cause ## serious database problems and should not generally be done. - -## If using the tcplLite DRVR, must specify table name -if (conf_store$TCPL_DRVR == 'MySQL') { - tcplSendQuery(paste0("DELETE FROM assay_source WHERE asid = ", i1, ";")) -} else { - qy <- paste0("SELECT * FROM assay_source WHERE NOT asid = ", i1, ";") - tcplSendQuery(qy, tbl='assay_source', delete=TRUE) -} - -## Reset configuration -options(conf_store) } } diff --git a/man/scdat.Rd b/man/scdat.Rd index df9e6d39..c6eb0a36 100644 --- a/man/scdat.Rd +++ b/man/scdat.Rd @@ -28,6 +28,6 @@ scdat } \description{ The example dataset is used to illustrate how the user can pipeline single-concentration -data from chemical screening using tcplLite. +data from chemical screening using tcpl. } \keyword{datasets} diff --git a/man/tcplCytoPt.Rd b/man/tcplCytoPt.Rd index b22af93d..08fd2f6f 100644 --- a/man/tcplCytoPt.Rd +++ b/man/tcplCytoPt.Rd @@ -88,11 +88,7 @@ The resulting data.table has the following fields: } } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfDefault() - +\dontrun{ ## Can only calculate the cytotox burst if using the MySQL database and ## TCPL_DRVR == 'MySQL' @@ -115,8 +111,6 @@ tcplCytoPt(aeid = 1:2) ## Changing 'default.pt' will change cyto_pt in the resulting data.table tcplCytoPt(aeid = 1:2, default.pt = 6) } - -## Reset configuration -options(conf_store) +} } diff --git a/man/tcplGetAeid.Rd b/man/tcplGetAeid.Rd index ea990ee8..ef175b59 100644 --- a/man/tcplGetAeid.Rd +++ b/man/tcplGetAeid.Rd @@ -15,16 +15,10 @@ aeids associated with those names.The function performs a regular expression lik assay component endpoint name column in the assay component endpoint table. } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ ## Search for aenm (assay name) case insensitive tcplGetAeid("TOX21") tcplGetAeid("tox21") - -## Reset configuration -options(conf_store) +} } diff --git a/man/tcplListFlds.Rd b/man/tcplListFlds.Rd index 4643d69f..e28f57d6 100644 --- a/man/tcplListFlds.Rd +++ b/man/tcplListFlds.Rd @@ -22,7 +22,9 @@ This function can be particularly useful in defining the 'fld' param in the tcplLoad- functions. } \examples{ +\dontrun{ ## Gives the fields in the mc1 table tcplListFlds("mc1") +} } diff --git a/man/tcplLoadChem.Rd b/man/tcplLoadChem.Rd index 88163b76..cc4184ce 100644 --- a/man/tcplLoadChem.Rd +++ b/man/tcplLoadChem.Rd @@ -34,11 +34,7 @@ setting 'val' to "phenol" when 'field' is "chnm" and 'exact' is the string in 'val' to an RLIKE statement within the MySQL query. } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ ## Passing no parameters gives all of the registered chemicals with their ## sample IDs tcplLoadChem() @@ -52,8 +48,6 @@ tcplLoadChem(field = 'chem.only') ## Other examples: tcplLoadChem(field = "chnm", val = "Bisphenol A") tcplLoadChem(field = "chid", val = 20182) - -## Reset configuration -options(conf_store) +} } diff --git a/man/tcplLoadChemList.Rd b/man/tcplLoadChemList.Rd index f06be224..5cc9c4d8 100644 --- a/man/tcplLoadChemList.Rd +++ b/man/tcplLoadChemList.Rd @@ -31,11 +31,7 @@ When chemicals belong to more than one list, the chemical is listed multiple times (one for each distinct list). } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ ## Passing no parameters gives all of the chemical IDs that have a chemical ## list registered clist <- tcplLoadChemList() @@ -55,8 +51,6 @@ clist[ , unique(list_acronym)] tcplLoadChemList(field = "list_acronym", val = "CPDBAS") tcplLoadChemList(field = "chid", val = 20182) tcplLoadChemList(field = "dsstox_substance_id", val = "DTXSID7020182") - -## Reset configuration -options(conf_store) +} } diff --git a/man/tcplLoadData.Rd b/man/tcplLoadData.Rd index 1cbf873c..d2821623 100644 --- a/man/tcplLoadData.Rd +++ b/man/tcplLoadData.Rd @@ -66,11 +66,7 @@ mc \tab 7 \tab mc4, mc7 } } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ ## Load all of level 0 for multiple-concentration data, note 'mc' is the ## default value for type tcplLoadData(lvl = 0) @@ -85,9 +81,7 @@ tcplListFlds(tbl = "mc1") ## Load level 0 data where the well type is "t" and the concentration ## index is 3 or 4 tcplLoadData(lvl = 1, fld = c("wllt", "cndx"), val = list("t", c(3:4))) - -## Reset configuration -options(conf_store) +} } \seealso{ \code{\link{tcplQuery}}, \code{\link{data.table}} diff --git a/man/tcplLvlCount.Rd b/man/tcplLvlCount.Rd index 7c7c24ba..d9031572 100644 --- a/man/tcplLvlCount.Rd +++ b/man/tcplLvlCount.Rd @@ -26,16 +26,10 @@ for single concentration data. Leaving \code{lvls} NULL will return all data. } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -TCPLlite <- file.path(system.file(package = "tcpl"), "example") -tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite") - +\dontrun{ ## Get all counts for level 1 for multiple-concentration tcplLvlCount(lvls = 1) -\dontrun{ ## Get all counts for levels 4 through 7 for multiple-concentration tcplLvlCount(lvls = 4:7) @@ -44,9 +38,6 @@ tcplLvlCount(lvls = 4:7) tcplLvlCount() } -## Reset configuration -options(conf_store) - } \seealso{ \code{\link{tcplQuery}}, \code{\link{data.table}} diff --git a/man/tcplPlot.Rd b/man/tcplPlot.Rd index 792e0f31..7d4cbc09 100644 --- a/man/tcplPlot.Rd +++ b/man/tcplPlot.Rd @@ -85,13 +85,7 @@ the 'sc' tables. Leaving \code{fld} NULL will return all data. } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ tcplPlot(fld = "m4id", val = c(18609966)) ## Create a level 4 plot - -## Reset configuration -options(conf_store) +} } diff --git a/man/tcplPlotFits.Rd b/man/tcplPlotFits.Rd index 5bc77085..f605ff0f 100644 --- a/man/tcplPlotFits.Rd +++ b/man/tcplPlotFits.Rd @@ -52,12 +52,7 @@ ID. Inputs with multiple assay endpoints will first be ordered by assay endpoint ID. } \examples{ - -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfDefault() - +\dontrun{ ## tcplPlotFits needs data.tables supplying the concentration/response ## data stored in mc4_agg, as well as the fit information from mc4 or mc5. ## Additionally, tcplPlotFits can take level 6 data from mc6 and add the @@ -68,11 +63,9 @@ tcplConfDefault() l5 <- tcplLoadData(lvl = 5, fld = "m4id", val = 18609966) l4_agg <- tcplLoadData(lvl = "agg", fld = "m4id", val = 18609966) -\dontrun{ pdf(file = "tcplPlotFits.pdf", height = 6, width = 10, pointsize = 10) tcplPlotFits(dat = l5, agg = l4_agg) graphics.off() -} ## While it is most likely the user will want to just save all of the plots ## to view in a PDF, the 'browse' parameter can be used to quickly view @@ -82,13 +75,9 @@ graphics.off() ## a subset of the data. This browse function is admittedly clunky. bpa <- tcplLoadChem(field = "chnm", val = "Bisphenol A")[ , spid] l5_sub <- l5[spid \%in\% bpa] -\dontrun{ tcplPlotFits(dat = l5_sub, agg = l4_agg[m4id \%in\% l5_sub$m4id], browse = TRUE) } - -## Reset configuration -options(conf_store) } diff --git a/man/tcplPlotLoadData.Rd b/man/tcplPlotLoadData.Rd index b15bada6..00f6dd80 100644 --- a/man/tcplPlotLoadData.Rd +++ b/man/tcplPlotLoadData.Rd @@ -37,11 +37,7 @@ The data \code{type} can be either 'mc' for multiple concentration data, or 'sc' for single concentration data. } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ ## load mc plot data for an entire endpoint dat <- tcplPlotLoadData(fld = "aeid", val = 703) @@ -65,9 +61,8 @@ tcplPlot(dat = dat, output = "pdf", flags = TRUE, fileprefix="example") +} -## Reset configuration -options(conf_store) } \seealso{ \code{\link{tcplPlot}} diff --git a/man/tcplPlotM4ID.Rd b/man/tcplPlotM4ID.Rd index 9a049669..d7a41c6c 100644 --- a/man/tcplPlotM4ID.Rd +++ b/man/tcplPlotM4ID.Rd @@ -31,17 +31,11 @@ Level 7 plots in addition to all of the level 4, 5, and 6 information, include the AC50 confidence interval and hit percentage information from bootstrapping. } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ tcplPlotM4ID(m4id = 18609966, lvl = 4) ## Create a level 4 plot tcplPlotM4ID(m4id = 18609966, lvl = 5) ## Create a level 5 plot tcplPlotM4ID(m4id = 18609966, lvl = 6) ## Create a level 6 plot - -#' ## Reset configuration -options(conf_store) +} } \seealso{ diff --git a/man/tcplPlotPlate.Rd b/man/tcplPlotPlate.Rd index 2dbab05f..d4ed1a96 100644 --- a/man/tcplPlotPlate.Rd +++ b/man/tcplPlotPlate.Rd @@ -41,17 +41,8 @@ For the optimal output size, use width = 10, height = 10*(2/3), pointsize = 10, units = "in" } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfDefault() - -d1 <- tcplLoadData(lvl = 1, fld = "acid", val = 1) \dontrun{ +d1 <- tcplLoadData(lvl = 1, fld = "acid", val = 1) tcplPlotPlate(dat = d1, apid = "09Apr2014.Plate.17") } - -## Reset configuration -options(conf_store) - } diff --git a/man/tcplPrepOtpt.Rd b/man/tcplPrepOtpt.Rd index e01cbed0..47aec601 100644 --- a/man/tcplPrepOtpt.Rd +++ b/man/tcplPrepOtpt.Rd @@ -28,12 +28,7 @@ and assay endpoint ID (aeid) values. However, if 'ids' is not null, the function will only attempt to map the ID fields given by 'ids.' } \examples{ - -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ ## Load some example data d1 <- tcplLoadData(1) @@ -49,9 +44,6 @@ d2 <- tcplPrepOtpt(d1) ## d3 <- tcplPrepOtpt(d1, ids = "spid") "chnm" \%in\% names(d3) ## TRUE "acnm" \%in\% names(d3) ## FALSE - -## Reset configuration -options(conf_store) - +} } diff --git a/man/tcplSubsetChid.Rd b/man/tcplSubsetChid.Rd index 9e9ab2e5..9952511d 100644 --- a/man/tcplSubsetChid.Rd +++ b/man/tcplSubsetChid.Rd @@ -33,7 +33,7 @@ chemical and assay information mapped with \code{\link{tcplPrepOtpt}}. To select a single sample, first a "consensus hit-call" is made by majority rule, with ties defaulting to active. After the chemical-wise hit call is made, the samples corresponding to to chemical-wise hit call are logically -ordered using the fit category, the number of the flags, and the modl_ga, +ordered using the fit category, the number of the flags, and AC50 (or modl_ga), then the first sample for every chemical is selected. The \code{flag} param can be used to specify a subset of flags to be used in @@ -42,11 +42,7 @@ Setting \code{flag} to \code{FALSE} will do the subsetting without considering any flags. } \examples{ -## Store the current config settings, so they can be reloaded at the end -## of the examples -conf_store <- tcplConfList() -tcplConfExample() - +\dontrun{ ## Load the example level 5 data d1 <- tcplLoadData(lvl = 5, fld = "aeid", val = 797) d1 <- tcplPrepOtpt(d1) @@ -59,9 +55,7 @@ d2[, list(m4id, hitc, fitc, modl_ga)] ## all equal. Therefore, if the flags are ignored, the selected sample will ## be the sample with the lowest modl_ga. tcplSubsetChid(dat = d2, flag = FALSE)[, list(m4id, modl_ga)] - -## Reset configuration -options(conf_store) +} } \seealso{ diff --git a/man/tcpldbStats.Rd b/man/tcpldbStats.Rd index b7f3e567..3f2373e8 100644 --- a/man/tcpldbStats.Rd +++ b/man/tcpldbStats.Rd @@ -12,7 +12,7 @@ tcpldbStats(type = "all", val = NULL) \item{val}{integer if type = "aeid" , string if type = "spid"} } \description{ -\code{tcpldbStats} takes a string(type) and an optional parameter(val) to return the summary statistics on the entire tcplLite database +\code{tcpldbStats} takes a string(type) and an optional parameter(val) to return the summary statistics on the entire tcpl database When type = "all" the val is ignored. the function returns the number of distinct spid and aeids in the database at each level When type = "aeid", the val parameter has to be a valid aeid in the database. The function returns a table consisting of the number of distinct spids at each level of processing for the aeid given in 'val' diff --git a/tests/testthat/test-tcplConf.R b/tests/testthat/test-tcplConf.R index 18e8eefa..5b0eaedf 100644 --- a/tests/testthat/test-tcplConf.R +++ b/tests/testthat/test-tcplConf.R @@ -9,7 +9,7 @@ test_that("unsupported driver error message", { drvr <- "test" expect_error( tcplConf(drvr), - paste0(drvr," is not a supported database driver. Must be 'MySQL', 'tcplLite', 'API' or 'example'.") + paste0(drvr," is not a supported database driver. Must be 'MySQL', 'API', or 'example'.") ) }) diff --git a/vignettes/Introduction_Appendices.Rmd b/vignettes/Introduction_Appendices.Rmd index eaecc470..beb476f7 100644 --- a/vignettes/Introduction_Appendices.Rmd +++ b/vignettes/Introduction_Appendices.Rmd @@ -783,15 +783,22 @@ Thus, users should be advised that while assay naming is used to infer informati With the minimal assay information registered, the next step is to register the necessary chemical and sample information with **tcplRegister**. The **tcplLoadChem** function returns all chemical information or can be filtered for user specified parameters, e.g. the chemical name (chnm) and chemical id (chid). -The "chdat" dataset included in the package contains the sample and chemical information for the data that will be loaded. The following shows an example of how to load chemical information. Similar to the order in registering assay information, the user must first register chemicals, then register the samples that map to the corresponding chemical. +The "chdat" example below contains the sample and chemical information for the data that will be loaded. The following shows an example of how to load chemical information. Similar to the order in registering assay information, the user must first register chemicals, then register the samples that map to the corresponding chemical. -```{r eval = FALSE, echo=FALSE} -## Obtain the Data ## -# Load the 'chdat' data from the package. -data(chdat, package = "tcpl") -# Convert 'chdat' object to a data.table. -setDT(chdat) +```{r echo=FALSE} +# example set of chemical/sample information +chdat <- data.table( + spid = c("Tox21_400088","Tox21_303655","Tox21_110011","Tox21_400081","DMSO","Tox21_400037"), + casn = c("80-05-7","521-18-6","150-30-1","22224-92-6","67-68-5","95-83-0"), + chnm = c("Bisphenol A","5alpha-Dihydrotestosterone","Phenylalanine","Fenamiphos","Dimethyl sulfoxide","4-Chloro-1,2-diaminobenzene"), + dsstox_substance_id = c("DTXSID7020182","DTXSID9022364","DTXSID9023463","DTXSID3024102","DTXSID2021735","DTXSID5020283"), + code = c("C80057","C521186","C150301","C22224926","C67685","C95830"), + chid = c("20182","22364","23463","24102","21735","20283") +) +chdat +``` +```{r eval = FALSE} ## Register the Chemicals ## # Obtain chemicals already registered in the database. cmap <- tcplLoadChem() @@ -802,6 +809,7 @@ tcplRegister(what = "chid", flds = chdat.register[,unique(.SD), .SDcols = c("cas ``` The "chdat" dataset contains a map of sample to chemical information, but chemical and sample information have to be registered separately because a chemical could potentially have multiple samples. Registering chemicals only takes a chemical CAS registry number ($\mathit{casn}$) and name ($\mathit{chnm}$). In the above example, only the unique chemicals were loaded. The casn and chnm fields have unique constraints; trying to register multiple chemicals with the same name or CAS registry number is not possible and will result in an error. With the chemicals registered and loaded, the samples can be registered by mapping the sample ID ($\mathit{spid}$) to the chemical ID. Note, the user needs to load the chemical information to get the chemical IDs then merge the new chemical IDs with the sample IDs from the original file by chemical name or CASRN. + ```{r eval = FALSE, message = FALSE} tcplRegister(what = "spid", flds = merge(chdat[ , list(spid, casn)],