R Under development (unstable) (2024-09-03 r87093 ucrt) -- "Unsuffered Consequences"
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> library(RCytoGPS)
> 
> sf <- system.file("PreClean", package = "RCytoGPS")
> dir(sf)
[1] "Altered.StartKaryotypes.R"   "Altered.StartKaryotypes.csv"
[3] "badStrings.txt"              "startKaryotypes.csv"        
> 
> bad <- read.delim(file.path(sf, "badStrings.txt"), header=FALSE)
> bad <- as.vector(as.matrix(bad))
> input <- read.csv(file.path(sf, "startKaryotypes.csv"))
> colnames(input)
[1] "X"                          "Pt..."                     
[3] "Status"                     "Karyotype"                 
[5] "Cytogenetics.at.start.date"
> output <- read.csv(file.path(sf, "Altered.StartKaryotypes.csv"))[, -1]
> 
> myclean <- preclean(input, 4:5, bad)
> 
> summary(output[,4] == myclean[,4])
   Mode   FALSE    TRUE    NA's 
logical     123     430       2 
> summary(output[,5] == myclean[,5])
   Mode   FALSE    TRUE    NA's 
logical     116     437       2 
> 
> if(FALSE) {
+   foo <- data.frame(IN = input[,4], OUT = output[,4], MY = myclean[,4])[output[,4] != myclean[,4],]
+   write.csv(foo, file="foo.csv")
+ }
> 
> proc.time()
   user  system elapsed 
   0.21    0.09    0.29