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Na.rm option #283

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merged 2 commits into from
Mar 12, 2024
Merged

Na.rm option #283

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ef3a891
Correctly fix method and add import
alanocallaghan Mar 11, 2024
51037e9
Remove C++ spec
alanocallaghan Mar 11, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -80,7 +80,7 @@ SystemRequirements: C++11
NeedsCompilation: yes
URL: https://github.com/catavallejos/BASiCS
BugReports: https://github.com/catavallejos/BASiCS/issues
RoxygenNote: 7.2.3
RoxygenNote: 7.3.1
Encoding: UTF-8
LazyData: false
Config/testthat/edition: 3
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -145,6 +145,7 @@ importFrom(stats,lag)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stats,rgamma)
importFrom(stats,rlnorm)
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6 changes: 4 additions & 2 deletions R/Methods.R
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Expand Up @@ -125,9 +125,9 @@ setMethod(
#' the high posterior density interval (probabilty equal to \code{prob})
#'
#' @param x A \code{\linkS4class{BASiCS_Chain}} object.
#' @param ... Unused, only included for consistency with the generic.
#' @param prob \code{prob} argument for \code{\link[coda]{HPDinterval}}
#' function.
#' @param ... Unused, only included for consistency with the generic.
#' @param na.rm Unused, only included for consistency with the generic.
#'
#' @return An object of class \code{\linkS4class{BASiCS_Summary}}.
Expand All @@ -139,6 +139,7 @@ setMethod(
#'
#' @author Catalina A. Vallejos \email{cnvallej@@uc.cl}
#' @author Nils Eling \email{eling@@ebi.ac.uk}
#' @importFrom stats na.omit
#' @export
setMethod("Summary",
signature = "BASiCS_Chain",
Expand All @@ -158,7 +159,8 @@ setMethod("Summary",
dimnames = list(colnames(n), c("median", "lower", "upper"))
)
HPD[, 1] <- colMedians(n, na.rm = na.rm)
HPD[, 2:3] <- apply(n, 2, function(col) {
ind_not_na <- !is.na(HPD[, 1])
HPD[ind_not_na, 2:3] <- apply(n[, ind_not_na, drop=FALSE], 2, function(col) {
if (na.rm) {
col <- na.omit(col)
# avoid coda error for no samples
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1 change: 0 additions & 1 deletion src/Makevars
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@@ -1,5 +1,4 @@
## This assume that we can call Rscript to ask Rcpp about its locations
## Use the R_HOME indirection to support installations of multiple R version
CXX_STD = CXX11
PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
1 change: 0 additions & 1 deletion src/Makevars.win
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@@ -1,5 +1,4 @@
## This assume that we can call Rscript to ask Rcpp about its locations
## Use the R_HOME indirection to support installations of multiple R version
CXX_STD = CXX11
PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
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