[R] iterators : checkFunc with ireadLines

[William Michels]

Dear Laurent,

I'm going through your code quickly, and the first question I have is
whether you loaded the "gmp" library?

> library(gmp)

Attaching package: ‘gmp’

The following objects are masked from ‘package:base’:

    %*%, apply, crossprod, matrix, tcrossprod

> library(iterators)
> iter(1:100, checkFunc = function(n) isprime(n))
$state
<environment: 0x7fbead8837f0>

$length
[1] 100

$checkFunc
function (n)
isprime(n)

$recycle
[1] FALSE

attr(,"class")
[1] "containeriter" "iter"
>

HTH, Bill.

W. Michels, Ph.D.



On Sun, May 17, 2020 at 5:43 PM Laurent Rhelp <LaurentRHelp using free.fr> wrote:
>
> Dear R-Help List,
>
>     I would like to use an iterator to read a file filtering some
> selected lines according to the line name in order to use after a
> foreach loop. I wanted to use the checkFunc argument as the following
> example found on internet to select only prime numbers :
>
> |                                iprime <- ||iter||(1:100, checkFunc =
> ||function||(n) ||isprime||(n))|
>
> |(https://datawookie.netlify.app/blog/2013/11/iterators-in-r/)
> <https://datawookie.netlify.app/blog/2013/11/iterators-in-r/>|
>
> but the checkFunc argument seems not to be available with the function
> ireadLines (package iterators). So, I did the code below to solve my
> problem but I am sure that I miss something to use iterators with files.
> Since I found nothing on the web about ireadLines and the checkFunc
> argument, could somebody help me to understand how we have to use
> iterator (and foreach loop) on files keeping only selected lines ?
>
> Thank you very much
> Laurent
>
> Presently here is my code:
>
> ##        mock file to read: test.txt
> ##
> # Time    0    0.000999    0.001999    0.002998    0.003998 0.004997
> 0.005997    0.006996    0.007996
> # N023    -0.031323    -0.035026    -0.029759    -0.024886 -0.024464
> -0.026816    -0.03369    -0.041067    -0.038747
> # N053    -0.014083    -0.004741    0.001443    -0.010152 -0.012996
> -0.005337    -0.008738    -0.015094    -0.012104
> # N123    -0.019008    -0.013494    -0.01318    -0.029208 -0.032748
> -0.020243    -0.015089    -0.014439    -0.011681
> # N163    -0.054023    -0.049345    -0.037158    -0.04112 -0.044612
> -0.036953    -0.036061    -0.044516    -0.046436
> # N193    -0.022171    -0.022384    -0.022338    -0.023304 -0.022569
> -0.021827    -0.021996    -0.021755    -0.021846
>
>
> # sensors to keep
>
> sensors <-  c("N053", "N163")
>
>
> library(iterators)
>
> library(rlist)
>
>
> file_name <- "test.txt"
>
> con_obj <- file( file_name , "r")
> ifile <- ireadLines( con_obj , n = 1 )
>
>
> ## I do not do a loop for the example
>
> res <- list()
>
> r <- get_Lines_iter( ifile , sensors)
> res <- list.append( res , r )
> res
> r <- get_Lines_iter( ifile , sensors)
> res <- list.append( res , r )
> res
> r <- get_Lines_iter( ifile , sensors)
> do.call("cbind",res)
>
> ## the function get_Lines_iter to select and process the line
>
> get_Lines_iter  <-  function( iter , sensors, sep = '\t', quiet = FALSE){
>    ## read the next record in the iterator
>    r = try( nextElem(iter) )
>   while(  TRUE ){
>      if( class(r) == "try-error") {
>            return( stop("The iterator is empty") )
>     } else {
>     ## split the read line according to the separator
>      r_txt <- textConnection(r)
>      fields <- scan(file = r_txt, what = "character", sep = sep, quiet =
> quiet)
>       ## test if we have to keep the line
>       if( fields[1] %in% sensors){
>         ## data processing for the selected line (for the example
> transformation in dataframe)
>         n <- length(fields)
>         x <- data.frame( as.numeric(fields[2:n]) )
>         names(x) <- fields[1]
>         ## We return the values
>         print(paste0("sensor ",fields[1]," ok"))
>         return( x )
>       }else{
>        print(paste0("Sensor ", fields[1] ," not selected"))
>        r = try(nextElem(iter) )}
>     }
> }# end while loop
> }
>
>
>
>
>
>
>
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