diff --git a/README.md b/README.md
index 28f178289850df2992a256b42825d0e73dfad751..f8a249ae75fc4c604347218fd428e701de67c64f 100644
--- a/README.md
+++ b/README.md
@@ -170,9 +170,14 @@ Gitlab developers
## WHAT'S NEW IN
+### v10.9.0
+
+1) no.overwrite argument of fun_report() replaced by overwrite
+
+
### v10.8.3
-1) fun.test() and fun.slide() debbuged for cute.path
+1) fun_test() and fun_slide() debbuged for cute.path
### v10.8.2
@@ -184,7 +189,7 @@ Gitlab developers
1) fun_check() and fun_info() readded for practical purposes but must not be changed. See the cute package for that
-2) cute.path parameter improved for fun.test() and fun.slide()
+2) cute.path parameter improved for fun_test() and fun_slide()
### v10.8.0
diff --git a/check/TODO.txt b/check/TODO.txt
index 8fe4f7ca6d21dd9180fd9ba4711d085b4ad5eb33..84b0d88eb82188b788aa924f425384a9a308d251 100644
--- a/check/TODO.txt
+++ b/check/TODO.txt
@@ -1,4 +1,9 @@
+See bitbucket to make the wiki pages. Example:
+https://immcantation.readthedocs.io/en/stable/docker/intro.html
+https://bitbucket.org/kleinstein/immcantation/src/c79aba1f73470e3acbefde8cdb19f27d28fc9752/docs/docker/intro.rst?mode=view
+
+
20210616
diff --git a/cute_little_R_functions.R b/cute_little_R_functions.R
index 91196fa11f9d2782ecc7d3e8bfcbb29df6c2ad5a..135aa7000fe704a837f439bde448d12e29b5a8e8 100644
--- a/cute_little_R_functions.R
+++ b/cute_little_R_functions.R
@@ -8740,7 +8740,7 @@ fun_report <- function(
data,
output = "results.txt",
path = "C:/Users/Gael/Desktop/",
- no.overwrite = TRUE,
+ overwrite = FALSE,
rownames.kept = FALSE,
vector.cat = FALSE,
noquote = TRUE,
@@ -8752,7 +8752,7 @@ fun_report <- function(
# data: object to print in the output file. If NULL, nothing is done, with no warning
# output: name of the output file
# path: location of the output file
- # no.overwrite: (logical) if output file already exists, defines if the printing is appended (default TRUE) or if the output file content is erased before printing (FALSE)
+ # overwrite: (logical) if output file already exists, defines if the printing is appended (default FALSE) or if the output file content is erased before printing (TRUE)
# rownames.kept: (logical) defines whether row names have to be removed or not in small tables (less than length.rows rows)
# vector.cat (logical). If TRUE print a vector of length > 1 using cat() instead of capture.output(). Otherwise (default FALSE) the opposite
# noquote: (logical). If TRUE no quote are present for the characters
@@ -8765,9 +8765,9 @@ fun_report <- function(
# fun_check()
# EXAMPLES
# fun_report()
- # fun_report(data = 1:3, output = "results.txt", path = "C:/Users/Gael/Desktop", no.overwrite = TRUE, rownames.kept = FALSE, vector.cat = FALSE, noquote = FALSE, sep = 2)
+ # fun_report(data = 1:3, output = "results.txt", path = "C:/Users/Gael/Desktop", overwrite = TRUE, rownames.kept = FALSE, vector.cat = FALSE, noquote = FALSE, sep = 2)
# DEBUGGING
- # data = 1:3 ; output = "results.txt" ; path = "C:/Users/Gael/Desktop" ; no.overwrite = TRUE ; rownames.kept = FALSE ; vector.cat = FALSE ; noquote = FALSE ; sep = 2 # for function debugging
+ # data = 1:3 ; output = "results.txt" ; path = "C:/Users/Gael/Desktop" ; overwrite = TRUE ; rownames.kept = FALSE ; vector.cat = FALSE ; noquote = FALSE ; sep = 2 # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
# end function name
@@ -8796,7 +8796,7 @@ fun_report <- function(
arg.check <- c(arg.check, TRUE)
}
}
- tempo <- fun_check(data = no.overwrite, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+ tempo <- fun_check(data = overwrite, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = rownames.kept, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = vector.cat, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = noquote, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
@@ -8829,24 +8829,24 @@ fun_report <- function(
rownames(data) <- rep("", nrow(data)) # identical row names allowed in matrices and tables
}
if(noquote == TRUE){
- utils::capture.output(noquote(data), file=paste0(path, "/", output), append = no.overwrite)
+ utils::capture.output(noquote(data), file=paste0(path, "/", output), append = ! overwrite)
}else{
- utils::capture.output(data, file=paste0(path, "/", output), append = no.overwrite)
+ utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
}
}else if(is.vector(data) & all(class(data) != "list") & (length(data) == 1L | vector.cat == TRUE)){
if(noquote == TRUE){
- cat(noquote(data), file= paste0(path, "/", output), append = no.overwrite)
+ cat(noquote(data), file= paste0(path, "/", output), append = ! overwrite)
}else{
- cat(data, file= paste0(path, "/", output), append = no.overwrite)
+ cat(data, file= paste0(path, "/", output), append = ! overwrite)
}
}else if(all(base::mode(data) == "character")){ # characters (array, list, factor or vector with vector.cat = FALSE)
if(noquote == TRUE){
- utils::capture.output(noquote(data), file=paste0(path, "/", output), append = no.overwrite)
+ utils::capture.output(noquote(data), file=paste0(path, "/", output), append = ! overwrite)
}else{
- utils::capture.output(data, file=paste0(path, "/", output), append = no.overwrite)
+ utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
}
}else{ # other object (S4 for instance, which do not like noquote()
- utils::capture.output(data, file=paste0(path, "/", output), append = no.overwrite)
+ utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
}
sep.final <- paste0(rep("\n", sep), collapse = "")
write(sep.final, file= paste0(path, "/", output), append = TRUE) # add a sep
@@ -11260,8 +11260,6 @@ fun_gg_boxplot <- function(
-
-
# add density
# rasterise all kind: https://cran.r-project.org/web/packages/ggrastr/vignettes/Raster_geoms.html
# log not good: do not convert as in boxplot
@@ -13633,3 +13631,4 @@ if(return == TRUE){
+
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