Merge branch 'develop'

.Rbuildignore

@@ -9,4 +9,7 @@
 ^docs$
 ^README\.md$
 ^_pkgdown.yml$
-
+^.lintr$
+^check_package.R$
+^codemeta\.json$
+^revdep$

.gitignore

@@ -51,3 +51,4 @@ rsconnect/
 *.txt
 *~
 *.cdl
+^revdep$

.lintr

@@ -0,0 +1,9 @@
+linters:linters_with_defaults(
+    indentation_linter=NULL,
+    line_length_linter(150),
+    object_name_linter=NULL,
+    infix_spaces_linter=NULL,
+    brace_linter=NULL,
+    commented_code_linter=NULL,
+    object_length_linter(length=40L),
+    cyclocomp_linter(complexity_limit=400L))

DESCRIPTION

@@ -1,19 +1,22 @@
 Package: ocencdf
-Title: Provide Netcdf Interface for Oce
-Version: 0.0.3
+Title: NetCDF Interface for Oce Objects
+Version: 0.0.4
 Authors@R: c(
-    person(given="Dan", family="Kelley", email="[email protected]", role=c("aut", "cre"), comment=c(ORCID="https://orcid.org/0000-0001-7808-5911")))
-Description: This provides a way to export `oce` objects to `netcdf` format, perhaps for data archiving, or perhaps for secondary analysis outside R.
+    person(given="Dan", family="Kelley", email="[email protected]", role=c("aut", "cre"), comment=c(ORCID="https://orcid.org/0000-0001-7808-5911")),
+    person(given="Clark", family="Richards", email="[email protected]", role=c("ctb"), comment=c(ORCID="https://orcid.org/0000-0002-7833-206X")))
+Description: This provides a way to export `oce` objects to `NetCDF` format, perhaps for data archiving, or perhaps for secondary analysis outside R.
 Depends: R (>= 4.00), oce (>= 1.8.0)
 Imports: jsonlite, ncdf4, methods, yaml
 License: GPL (>= 2)
 Encoding: UTF-8
+URL: https://dankelley.github.io/ocencdf/
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests:
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)
+BugReports: https://github.com/dankelley/ocencdf/issues
 Config/testthat/edition: 3
 BuildVignettes: true
 VignetteBuilder: knitr

NEWS.md

@@ -1,3 +1,8 @@
+# ocencdf 0.0.4
+
+* Specify `force_v4` in all conversions to NetCDF, which permits the handling
+  of large files.
+
 # ocencdf 0.0.3
 
 * Handle ADV data with `adv2ncdf()` and `ncdf2adv()`.

R/adp.R

@@ -1,7 +1,7 @@
-#' Save an adp object to a netcdf file
+#' Save an ADP object to a NetCDF file
 #'
 #' Given an `adp` object created by the `oce` package, this function
-#' creates a netcdf file that can later by read by [ncdf2adp()] to approximately
+#' creates a NetCDF file that can later by read by [ncdf2adp()] to approximately
 #' reproduce the original contents.
 #'
 #' Note that [adp2ncdf()] defaults `varTable` to `"adp"`.
@@ -21,97 +21,103 @@
 #' and
 #' `"oceCoordinate"`.
 #'
-#' @param x an oce object of class `adp`, as created by e.g. [oce::read.adp()].
+#' @param x an `oce` object of class `adp`, as created by e.g. [oce::read.adp()].
 #'
 #' @inheritParams oce2ncdf
 #'
 #' @examples
 #' library(ocencdf)
 #'
-#' # Example with an adp file from oce package
-#' data(adp, package="oce")
+#' # Example with an ADP file from `oce` package
+#' data(adp, package = "oce")
 #' summary(adp)
 #' plot(adp)
-#' # Transfer to netcdf and back to see if results make sense
-#' oce2ncdf(adp, ncfile="adp.nc")
-#' ADP <- ncdf2adp("adp.nc")
+#' # Transfer to NetCDF and back to see if results make sense.
+#' # Use a temporary nc file to let package pass CRAN checks.
+#' ncfile <- tempfile(pattern = "adp", fileext = ".nc")
+#' oce2ncdf(adp, ncfile = ncfile)
+#' ADP <- ncdf2adp(ncfile)
 #' summary(ADP)
 #' plot(ADP)
-#'
-#' # Remove temporary file
-#' file.remove("adp.nc")
+#' file.remove(ncfile)
 #'
 #' @family things related to adp data
 #'
 #' @author Dan Kelley and Clark Richards
 #'
 #' @export
-adp2ncdf <- function(x, varTable=NULL, ncfile=NULL, force_v4=TRUE, debug=0)
-{
+adp2ncdf <- function(x, varTable = NULL, ncfile = NULL, force_v4 = TRUE, debug = 0) {
     dmsg(debug, "adp2ncdf(..., ncfile=\"", ncfile, "\") {\n")
-    if (!inherits(x, "adp"))
+    if (!inherits(x, "adp")) {
         stop("'x' must be a adp object")
+    }
     if (is.null(varTable)) {
         varTable <- "adp"
-        #message("Defaulting varTable to \"", varTable, "\".")
+        # message("Defaulting varTable to \"", varTable, "\".")
     }
     if (is.null(ncfile)) {
         ncfile <- "adp.nc"
-        #message("Will save adp object to \"", ncfile, "\".")
+        # message("Will save adp object to \"", ncfile, "\".")
     }
     varTableOrig <- varTable
     varTable <- read.varTable(varTable)
     vdim <- dim(x@data$v)
     extant <- list()
-    for (item in c("v", "a", "g", "q"))
+    for (item in c("v", "a", "g", "q")) {
         extant[[item]] <- item %in% names(x@data)
-    if (!extant$v)
+    }
+    if (!extant$v) {
         stop("there is no data item named 'v', which is mandatory for an oce adp object")
-    #time <- ncdim_def(name="TIME", units="s", vals=as.numeric(x@data$time))
-    time <- ncdim_def(name="TIME", units="", vals=seq_len(vdim[1]), create_dimvar=FALSE,
-        longname="seconds since 1970-01-01 UTC")
-    #cell <- ncdim_def(name="DISTANCE", units="m", vals=x@data$distance, longname="Distance to cell")
-    distance <- ncdim_def(name="DISTANCE", units="", vals=seq_len(vdim[2]), create_dimvar=FALSE,
-        longname="Distance to cell")
-    beam <- ncdim_def(name="BEAM", units="", vals=seq_len(vdim[3]))
+    }
+    # time <- ncdim_def(name="TIME", units="s", vals=as.numeric(x@data$time))
+    time <- ncdim_def(
+        name = "TIME", units = "", vals = seq_len(vdim[1]), create_dimvar = FALSE,
+        longname = "seconds since 1970-01-01 UTC"
+    )
+    # cell <- ncdim_def(name="DISTANCE", units="m", vals=x@data$distance, longname="Distance to cell")
+    distance <- ncdim_def(
+        name = "DISTANCE", units = "", vals = seq_len(vdim[2]), create_dimvar = FALSE,
+        longname = "Distance to cell"
+    )
+    beam <- ncdim_def(name = "BEAM", units = "", vals = seq_len(vdim[3]))
     vars <- list()
-    FillValue <- getVarInfo("-", varTable=varTable)$FillValue
+    FillValue <- getVarInfo("-", varTable = varTable)$FillValue
     # time and distance (do they show up as n$var now?)
     dmsg(debug, "    time (length ", vdim[1], ")\n")
-    vars[["time"]] <- ncvar_def(name="time", units="seconds since 1970-01-01 UTC", dim=time, prec="double")
+    vars[["time"]] <- ncvar_def(name = "time", units = "seconds since 1970-01-01 UTC", dim = time, prec = "double")
     dmsg(debug, "    distance (length ", vdim[2], ")\n")
-    vars[["distance"]] <- ncvar_def(name="distance", units="m", dim=distance)
-    dmsg(debug, "  Setting up variable dimensions for ", paste(vdim, collapse="x"), " arrays:\n")
+    vars[["distance"]] <- ncvar_def(name = "distance", units = "m", dim = distance)
+    dmsg(debug, "  Setting up variable dimensions for ", paste(vdim, collapse = "x"), " arrays:\n")
     # array data
     dmsg(debug, "    v\n")
-    vars[["v"]] <- ncvar_def(name="v", units="m/s", dim=list(time, distance, beam))
+    vars[["v"]] <- ncvar_def(name = "v", units = "m/s", dim = list(time, distance, beam))
     if (extant$a) {
         dmsg(debug, "    a\n")
-        vars[["a"]] <- ncvar_def("a", units="", dim=list(time, distance, beam))
+        vars[["a"]] <- ncvar_def("a", units = "", dim = list(time, distance, beam))
     }
     if (extant$g) {
         dmsg(debug, "    g\n")
-        vars[["g"]] <- ncvar_def("g", units="", dim=list(time, distance, beam))
+        vars[["g"]] <- ncvar_def("g", units = "", dim = list(time, distance, beam))
     }
     if (extant$q) {
         dmsg(debug, "    q\n")
-        vars[["q"]] <- ncvar_def("q", units="", dim=list(time, distance, beam))
+        vars[["q"]] <- ncvar_def("q", units = "", dim = list(time, distance, beam))
     }
     # time-series data
     dmsg(debug, "  Setting up dimensions for time-series vectors of length ", vdim[1], ":\n")
-    #cat("NEXT: names in @data:\n");print(sort(names(x@data)))
+    # cat("NEXT: names in @data:\n");print(sort(names(x@data)))
     for (item in names(x@data)) {
         if (item != "time" && item != "distance" && is.vector(x@data[[item]])) {
             dmsg(debug, "    ", item, "\n")
-            vars[[item]] <- ncvar_def(item, units="", dim=time)
+            vars[[item]] <- ncvar_def(item, units = "", dim = time)
         }
     }
-    nc <- nc_create(ncfile, vars, force_v4=force_v4)
+    nc <- nc_create(ncfile, vars, force_v4 = force_v4)
     dmsg(debug, "  Storing time and distance\n")
     dmsg(debug, "    time\n")
     ncvar_put(nc, "time", as.numeric(x@data$time))
-    #message("first 3 times: ", paste(x@data$time[1:3], collapse=" "))
-    #message("first 3 times: ", paste(as.numeric(x@data$time)[1:3], collapse=" "))
+    # message("first 3 times: ", paste(x@data$time[1:3], collapse=" "))
+    # message("first 3 times: ", paste(as.numeric(x@data$time)[1:3], collapse=" "))
     dmsg(debug, "    distance\n")
     ncvar_put(nc, "distance", as.numeric(x@data[["distance"]]))
     dmsg(debug, "  Storing arrays:\n")
@@ -132,33 +138,37 @@ adp2ncdf <- function(x, varTable=NULL, ncfile=NULL, force_v4=TRUE, debug=0)
     dmsg(debug, "    metadata_explanation\n")
     explanation <- paste("This file was created with adp2ncdf from the ocencdf R package,\n",
         "available at www.github.com/dankelley/ocencdf.\n",
-        readLines(system.file("extdata", "ncdf_explanation.md", package="ocencdf")), collapse="\n")
+        readLines(system.file("extdata", "ncdf_explanation.md", package = "ocencdf")),
+        collapse = "\n"
+    )
     ncatt_put(nc, 0, "metadata_explanation", explanation)
     dmsg(debug, "    metadata\n")
     ncatt_put(nc, 0, "metadata", metadata2json(x@metadata))
     # Store some individual metadata items, for simple access
-    for (item in c("beamAngle", "frequency",
-            "instrumentType", "instrumentSubtype",
-            "numberOfBeams", "numberOfBeams",
-            "oceCoordinate")) {
+    for (item in c(
+        "beamAngle", "frequency",
+        "instrumentType", "instrumentSubtype",
+        "numberOfBeams", "numberOfBeams",
+        "oceCoordinate"
+    )) {
         dmsg(debug, "    ", item, "\n")
-        storeNetcdfAttribute(x, item, nc, item)
+        storeNetCDFAttribute(x, item, nc, item)
     }
     dmsg(debug, "    varTable\n")
-    ncatt_put(nc=nc, varid=0, attname="varTable", attval=varTableOrig)
+    ncatt_put(nc = nc, varid = 0, attname = "varTable", attval = varTableOrig)
     dmsg(debug, "    class\n")
-    ncatt_put(nc=nc, varid=0, attname="class", attval=as.character(class(x)))
+    ncatt_put(nc = nc, varid = 0, attname = "class", attval = as.character(class(x)))
     dmsg(debug, "    creator\n")
-    ncatt_put(nc=nc, varid=0, attname="creator", attval=paste0("ocencdf version ", packageVersion("ocencdf")))
+    ncatt_put(nc = nc, varid = 0, attname = "creator", attval = paste0("ocencdf version ", packageVersion("ocencdf")))
     nc_close(nc)
     dmsg(debug, paste0("} # adp2ncdf created file \"", ncfile, "\"\n"))
 }
 
-#' Read a netcdf file and create an adp object
+#' Read a NetCDF file and create an ADP object
 #'
 #' This works by calling [ncdf2oce()] and then using [class()] on
 #' the result to make it be of subclass `"adp"`.  This is intended
-#' to work with Netcdf files created with [adp2ncdf()], which embeds
+#' to work with NetCDF files created with [adp2ncdf()], which embeds
 #' sufficient information in the file to permit [ncdf2adp()] to
 #' reconstruct the original adp object. See the documentation
 #' for [adp2ncdf()] to learn more about what it stores, and therefore
@@ -173,25 +183,26 @@ adp2ncdf <- function(x, varTable=NULL, ncfile=NULL, force_v4=TRUE, debug=0)
 #' @examples
 #' library(ocencdf)
 #'
-#' # Example with an adp file from oce package
-#' data(adp, package="oce")
+#' # Example with an ADP file from `oce` package
+#' data(adp, package = "oce")
 #' summary(adp)
 #' plot(adp)
-#' # Transfer to netcdf and back to see if results make sense
-#' oce2ncdf(adp, ncfile="adp.nc")
-#' ADP <- ncdf2adp("adp.nc")
+#' # Transfer to NetCDF and back to see if results make sense
+#' # Use a temporary nc file to let package pass CRAN checks.
+#' ncfile <- tempfile(pattern = "adp", fileext = ".nc")
+#' oce2ncdf(adp, ncfile = ncfile)
+#' ADP <- ncdf2adp(ncfile)
 #' summary(ADP)
 #' plot(ADP)
+#' file.remove(ncfile)
 #'
-#' # Remove temporary file
-#' file.remove("adp.nc")
+#' @family things related to adp data
 #'
 #' @author Dan Kelley
 #'
 #' @export
-ncdf2adp <- function(ncfile=NULL, varTable=NULL, debug=0)
-{
-    adp <- ncdf2oce(ncfile=ncfile, varTable=varTable, debug=debug)
+ncdf2adp <- function(ncfile = NULL, varTable = NULL, debug = 0) {
+    adp <- ncdf2oce(ncfile = ncfile, varTable = varTable, debug = debug)
     class(adp) <- "adp"
     adp
 }