In Epiconcept-Paris/STRAP-epiuf: Epiconcept Team Utility Functions for STRAP Project

knitr::opts_chunk$set(echo = TRUE)
library(epiuf)

filesFindReplace

This function allows to find a character, string or word into a file, a series of files or a directory (with optional file filter) and to replace it by another character, string or word.

R script, text files and csv can be processed as well as xlsx files.

Some functions have been used to build that functionality

The charCount function will be used to count changes before applying them

  # A single character 
  charCount("c","cancan")
  charCount("c","ccc" )
  # A string in a sentence 
  charCount("essai"," this is an essai" )
  # A string in a vector 
  charCount("ce",c("cacec","ceci" ))
  # A string in a dataframe 
  df <- data.frame(c("cacececi","ceci" ,"non","ace"))
  charCount("ce",df)
  # A word in a dataframe  (between \b which escaped is \\b)
  charCount("\\bce\\b",df)
  df <- data.frame(c("ca cece ci","ce ci" ,"non","a ce"))
  charCount("\\bce\\b",df)
  df <- data.frame(c("ca cece ci","ce ci" ,"non","a ce"),c("ca cececi","ce ci" ,"non","ace"))
  charCount("\\bce\\b",df)
  # Verify that nothing is 0 
  charCount("","essai")
  charCount("e","")
  # A special character .
  charCount("\\.","21.15.98")

# prepare files for tests, this method avoid to store file in the package
# created files will be delete at the end of the process
file1 <- "temp_text1.R"
file2 <- "temp_text2.R"
file3 <- "temp_text3.R"
lines <- c(
"# test script for findAndReplace",
"# word to be replaced : oldword",
"#  old_word",
"#  oldword --  oldword)")

writeLines(lines, file1)
writeLines(lines, file2)
writeLines(lines, file3)

listFiles is a simplified version of list.files which accept jokers of global search * for any character and ? for one character (fullpath is automaticaly set with recursive flag)

listFiles(pattern="temp_*.R")
listFiles("R","c*")

externalFile is used for test and vignettes. In the package, you can add some data/files These are stored in a specific directory attached to the package like : "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/epiuf/extdata/testrename.xlsx" But while you are building the package, the file is into inst/extdata. Retrieving that file could be tricky from vignettes or test depending your knit directory. externalFile while always return the right path either in build mode or library mode, and whathever is your knit directory

externalFile("testrename.xlsx") "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/epiuf/extdata/testrename.xlsx"

externalFile("testrename.xlsx") "/Users/gedeonz/Dev/R Sources/STRAP-epiuf/inst/extdata/testrename.xlsx"

filesFindReplace is a generic function to make batch replacement You can call this function for one file, a list of files, a directory, a pattern to filter files or any combination of previous option. In addition you can replace a list of pattern by one single replacement The listonly parameters allow to check how many changes will be done.

  # replace in 2 files (count only)
  listchanged <- filesFindReplace(c(file1,file2),pattern="oldword",replacement = "newword",listonly=TRUE)
  # replace 2 pattern at a time (count only) 
   listchanged <- filesFindReplace(file3,pattern=c("oldword","old_word"),replacement = "newword",listonly=TRUE)
  # replace by modifying the original file
   listchanged <- filesFindReplace(file1,pattern="oldword",replacement = "newword")
  cat(readLines(file1),sep="\n")
  # replace in a directory or use a file filter
   listchanged <- filesFindReplace("temp_*.R",pattern="oldword",replacement = "newword")

   writeLines(lines, file1)
   # replace several pattern by several replacement at same time
   listchanged <- filesFindReplace(file1,pattern=c("oldword","script"),replacement = c("newword","text"))
  cat(readLines(file1),sep="\n")

filesFindReplace work on text files (R, txt, csv ...) and xlsx files.

  # we use a file stored in packages data 
  file4 <- externalFile("testrename.xlsx")
  file5 <- "temp.xlsx"
  # In ordre to not modify the original file, we copy it to a temporary file which will be deleted at the end
  file.copy(file4,file5)
  # Count the number of occurrence in file
  filesFindReplace(file5,"patient","subject",word=TRUE, ignore.case = TRUE, listonly=TRUE)
  # Replace in file
  filesFindReplace(file5,"patient","subject",word=TRUE, ignore.case = TRUE)
  # Number of occurrence should be 0 after changes 
  filesFindReplace(file5,"patient","subject",word=TRUE, ignore.case = TRUE, listonly=TRUE)
  # we can manage more than one file filter 
  filesFindReplace(c("temp_*.R","temp*.xlsx"),pattern="oldword",replacement = "newword", listonly = TRUE)

if(file.exists(file1)) r <- file.remove(file1)
if(file.exists(file2)) r <- file.remove(file2)
if(file.exists(file3)) r <- file.remove(file3)
if(file.exists(file5)) r <- file.remove(file5)

Epiconcept-Paris/STRAP-epiuf documentation built on Aug. 5, 2024, 3:41 a.m.