rename read_csv as fread_csv to avoid conflict with readr

- also change read_csv_numer to fread_csv_numer

- also internal function read_mult_csv -> fread_mult_csv

(not sure why these functions are exported; I guess because read_csv is used by qtl2cl)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qtl2
-Version: 0.32
-Date: 2023-04-21
+Version: 0.33-1
+Date: 2023-08-24
 Title: Quantitative Trait Locus Mapping in Experimental Crosses
 Description: Provides a set of tools to perform quantitative
     trait locus (QTL) analysis in experimental crosses. It is a

NAMESPACE

@@ -88,6 +88,8 @@ export(find_markerpos)
 export(find_peaks)
 export(fit1)
 export(founders)
+export(fread_csv)
+export(fread_csv_numer)
 export(genoprob_to_alleleprob)
 export(genoprob_to_snpprob)
 export(get_common_ids)
@@ -147,8 +149,6 @@ export(pull_genoprobpos)
 export(pull_markers)
 export(qtl2version)
 export(read_cross2)
-export(read_csv)
-export(read_csv_numer)
 export(read_pheno)
 export(recode_snps)
 export(reduce_map_gaps)

NEWS.md

@@ -1,3 +1,13 @@
+## qtl2 0.33-1 (2023-08-24)
+
+### Major changes
+
+- Changed `read_csv()` to `fread_csv()` to avoid conflict with
+  `readr::read_csv()`. (Issue #223)
+
+- Similarly, changed `read_csv_numer()` to `fread_csv_numer()`.
+
+
 ## qtl2 0.32 (2023-04-21)
 
 ### Major changes

R/read_csv.R → R/fread_csv.R

@@ -19,14 +19,14 @@
 #'
 #' The first column is taken to be a set of row names
 #'
-#' @seealso [read_csv_numer()]
+#' @seealso [fread_csv_numer()]
 #'
 #' @importFrom data.table fread
 #' @export
 #'
 #' @examples
-#' \dontrun{mydata <- read_csv("myfile.csv", transpose=TRUE)}
-read_csv <-
+#' \dontrun{mydata <- fread_csv("myfile.csv", transpose=TRUE)}
+fread_csv <-
     function(filename, sep=",", na.strings=c("NA", "-"), comment.char="#", transpose=FALSE,
              rownames_included=TRUE)
 {

R/read_csv_numer.R → R/fread_csv_numer.R

@@ -20,14 +20,14 @@
 #'
 #' The first column is taken to be a set of row names
 #'
-#' @seealso [read_csv()]
+#' @seealso [fread_csv()]
 #'
 #' @importFrom data.table fread
 #' @export
 #'
 #' @examples
-#' \dontrun{mydata <- read_csv_numer("myfile.csv", transpose=TRUE)}
-read_csv_numer <-
+#' \dontrun{mydata <- fread_csv_numer("myfile.csv", transpose=TRUE)}
+fread_csv_numer <-
     function(filename, sep=",", na.strings=c("NA", "-"), comment.char="#", transpose=FALSE,
              rownames_included=TRUE)
 {

R/read_cross2.R

@@ -129,9 +129,9 @@ function(file, quiet=TRUE)
                 stop_if_no_file(filename)
 
                 # read file
-                sheet <- read_csv(filename, na.strings=control$na.strings, sep=control$sep,
-                                  comment.char=control$comment.char, transpose=tr,
-                                  rownames_included=TRUE)
+                sheet <- fread_csv(filename, na.strings=control$na.strings, sep=control$sep,
+                                   comment.char=control$comment.char, transpose=tr,
+                                   rownames_included=TRUE)
             }
             else { # vector of files
                 # add dir to paths
@@ -145,15 +145,15 @@ function(file, quiet=TRUE)
                     sheet <- NULL
                     for(filename in filenames)
                         sheet <- rbind(sheet,
-                                       read_csv(filename, na.strings=control$na.strings,
-                                                sep=control$sep, comment.char=control$comment.char,
-                                                transpose=tr, rownames_included=TRUE))
+                                       fread_csv(filename, na.strings=control$na.strings,
+                                                 sep=control$sep, comment.char=control$comment.char,
+                                                 transpose=tr, rownames_included=TRUE))
                 }
                 else {
                     # read all of the files and cbind(), matching on row names
-                    sheet <- read_mult_csv(filenames, na.strings=control$na.strings,
-                                           sep=control$sep, comment.char=control$comment.char,
-                                           transpose=tr)
+                    sheet <- fread_mult_csv(filenames, na.strings=control$na.strings,
+                                            sep=control$sep, comment.char=control$comment.char,
+                                            transpose=tr)
                 }
             }
             if(length(unique(colnames(sheet))) != ncol(sheet))
@@ -487,8 +487,8 @@ function(sex_control, covar, sep, comment.char, dir, quiet=TRUE)
         if(!quiet) message(" - reading sex")
         file <- file.path(dir, sex_control$file)
         stop_if_no_file(file)
-        sex <- read_csv(file, sep=sep, na.strings=NULL, comment.char=comment.char,
-                        rownames_included=TRUE)
+        sex <- fread_csv(file, sep=sep, na.strings=NULL, comment.char=comment.char,
+                         rownames_included=TRUE)
     }
     else return(NULL)
 
@@ -556,7 +556,7 @@ function(cross_info_control, covar, sep, comment.char, dir, quiet=TRUE)
 
         file <- file.path(dir, cross_info_control$file)
         stop_if_no_file(file)
-        cross_info <- read_csv(file, sep=sep, comment.char=comment.char, rownames_included=TRUE)
+        cross_info <- fread_csv(file, sep=sep, comment.char=comment.char, rownames_included=TRUE)
 
         if(any(is.na(cross_info)))
             stop(sum(is.na(cross_info)), " missing values in cross_info (cross_info can't be missing.")
@@ -626,14 +626,14 @@ function(filename)
 
 
 # read multiple CSV files and cbind results
-read_mult_csv <-
+fread_mult_csv <-
     function(filenames, sep=",", na.strings=c("NA", "-"), comment.char="#", transpose=FALSE)
 {
     result <- NULL
     for(file in filenames) {
-        this <- read_csv(file, sep=sep, na.strings=na.strings,
-                         comment.char=comment.char, transpose=transpose,
-                         rownames_included=TRUE)
+        this <- fread_csv(file, sep=sep, na.strings=na.strings,
+                          comment.char=comment.char, transpose=transpose,
+                          rownames_included=TRUE)
 
         if(is.null(result)) result <- this
         else result <- cbind_expand(result, this)

R/read_pheno.R

@@ -94,8 +94,8 @@ read_pheno <-
     # read file
     stop_if_no_file(file)
     if(!quiet) message(" - Reading ", basename(file))
-    pheno <- read_csv_numer(file, sep=sep, na.strings=na.strings,
-                            comment.char=comment.char, transpose=transpose)
+    pheno <- fread_csv_numer(file, sep=sep, na.strings=na.strings,
+                             comment.char=comment.char, transpose=transpose)
     pheno <- as.matrix(pheno)
 
     # read phenocovarfile
@@ -150,6 +150,6 @@ read_phenocovar <-
     # read file
     stop_if_no_file(file)
     if(!quiet) message(" - Reading ", basename(file))
-    read_csv(file, sep=sep, na.strings=na.strings,
-             comment.char=comment.char, transpose=FALSE)
+    fread_csv(file, sep=sep, na.strings=na.strings,
+              comment.char=comment.char, transpose=FALSE)
 }

tests/testthat/test-read_issues.R

@@ -12,7 +12,7 @@ test_that("read_cross2 deals with missing marker info", {
 
     # drop two markers from the geno file
     geno_file <- file.path(dir, "iron_geno.csv")
-    g <- read_csv(geno_file, rownames_included=FALSE)
+    g <- fread_csv(geno_file, rownames_included=FALSE)
     dropped_index <- c(20,28)
     dropped_markers <- colnames(g)[dropped_index]
     write.table(g[,-dropped_index], file=geno_file, sep=",",
@@ -26,7 +26,7 @@ test_that("read_cross2 deals with missing marker info", {
     # drop two markers from the gmap file
     # and give another two missing positions
     gmap_file <- file.path(dir, "iron_gmap.csv")
-    gmap <- read_csv(gmap_file, rownames_included=FALSE)
+    gmap <- fread_csv(gmap_file, rownames_included=FALSE)
     dropped_index2 <- c(14, 51)
     dropped_markers2 <- gmap[dropped_index2,1]
     na_index2 <- c(5, 56)
@@ -45,7 +45,7 @@ test_that("read_cross2 deals with missing marker info", {
     # drop two markers from the pmap file
     # and give another one a missing position
     pmap_file <- file.path(dir, "iron_pmap.csv")
-    pmap <- read_csv(pmap_file, rownames_included=FALSE)
+    pmap <- fread_csv(pmap_file, rownames_included=FALSE)
     dropped_index3 <- c(4, 29)
     dropped_markers3 <- pmap[dropped_index3,1]
     na_index3 <- 33
@@ -58,7 +58,7 @@ test_that("read_cross2 deals with missing marker info", {
     expect_equal(iron_sub3, drop_markers(iron, c(dropped_markers, dropped_markers3, na_markers3)))
 
     # markers out of order in genotypes
-    g <- read_csv(geno_file)
+    g <- fread_csv(geno_file)
     g <- g[,sample(ncol(g)),drop=FALSE]
     write.table(cbind(marker=rownames(g), g), file=geno_file, sep=",",
                 row.names=FALSE, col.names=TRUE, quote=FALSE)
@@ -67,7 +67,7 @@ test_that("read_cross2 deals with missing marker info", {
     expect_equal(iron_sub3, iron_randgeno)
 
     # markers out of order in physical map
-    pmap <- read_csv(pmap_file, rownames_included=FALSE)
+    pmap <- fread_csv(pmap_file, rownames_included=FALSE)
     pmap_rand <- pmap
     pmap_rand <- pmap[sample(nrow(pmap)), , drop=FALSE]
     write.table(pmap_rand, file=pmap_file, sep=",",
@@ -77,7 +77,7 @@ test_that("read_cross2 deals with missing marker info", {
     expect_equal(iron_sub3, iron_randpmap)
 
     # markers out of order within a chromosome on genetic map
-    gmap <- read_csv(gmap_file, rownames_included=FALSE)
+    gmap <- fread_csv(gmap_file, rownames_included=FALSE)
     gmap_reordered <- gmap
     gmap_reordered[6:7,1] <- gmap[7:6,1] # swap two marker names
     write.table(gmap_reordered, file=gmap_file, sep=",",