Trick or tips 0001

For the first post of the series, let’s introduce 5 R tips:

1. The %in% operator
2. The paste0() function
3. Using “\r” in cat()
4. The sprintf() function
5. The xaxs and yaxs arguments of par()

The ‘%in%’ operator

I have known this for a while, but I keep remembering how it eases my pain when I learned how to use it. Let’s consider two vector vecA and vecB, the vecA %in% vecB returns a vector of logical of the length vecA stating whether the elements of vecA are in vecB:

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vecA <- c("a", "d", "2", "4", "e", ";")
vecB <- letters # vector of lower case letters the Roman alphabet
vecA %in% vecB
#R>  [1]  TRUE  TRUE FALSE FALSE  TRUE FALSE

the i^th element of the output vector is TRUE if the i^th element of vecA is among the elements of vecB. Note that you can have a similar result calling the intersect() functions which returns elements that vecA and vecB are sharing.

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intersect(vecA, vecB)
#R>  [1] "a" "d" "e"

By the way, you should have a look to the documentation of intersect().

The paste0() function

I often concatenate strings. The natural way to do this is to use the paste() function. Let’s say I need to create a set of original file names such as: “myfile1”, “myfile2”, “myfile3”, etc. I can call paste() like so:

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paste("myfile", 1:7)
#R>  [1] "myfile 1" "myfile 2" "myfile 3" "myfile 4" "myfile 5" "myfile 6" "myfile 7"

BUT, there is a annoying space between “myfile” and the number, to remove the space, sep argument is needed:

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paste("myfile", 1:3, sep = "")
#R>  [1] "myfile1" "myfile2" "myfile3"

UNLESS you use the paste0() that is the version of paste() with the desired default parameters:

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paste0("myfile", 1:3)
#R>  [1] "myfile1" "myfile2" "myfile3"

I know… this means you’ll save 5 previous characters each time you call paste0()!

Using argument ‘\r’ in cat()

Note that for this tip, you should execute the code-chunk in your own R console

When programming we often need to monitor what we are doing, especially for time-consuming calculation. Using cat() with all its default is very helpful to report information on progress:

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for (i in 1:10) {
  cat("iteration n°", i, "\n")
}

Here "\n" is what breaks the line! Instead of breaking the line, we can erase the line, i.e. using "\r":

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for (i in 1:10) {
  Sys.sleep(.25) # I added a pause so you can see what's happening
  cat("iteration n°", i, "\r")
}

I hope this gives you some ideas :). If you are thinking “where the !&)@( is he going with this!” let me give you two extra way to monitor a for loop:

1. Use percentage:

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nmx <- 222
for (i in 1:nmx) {
  Sys.sleep(.01) # replace it by what you are doing
  cat("==>", format(100*i/nmx, digits = 4), "%", "\r")
}

2. Create you own progress bar:

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nmx <- 222
sz <- 60
for (i in 1:nmx) {
  Sys.sleep(.01) # replace it by what you are doing
  nb <- floor(sz * i / nmx)
  pgr <- paste(rep(c("="," "), c(nb, sz - nb)), collapse = "")
  cat("|", pgr, "| ", "\r")
}

I hope you like this! Otherwise, stick to use getTxtProgressBar() and setProgressBar() functions, but I swear you are missing something.

The sprintf() function

The function is a wrapper for a well-known C function sprintf(). There are so much to say about it and I won’t (so please have a careful look at the documentation) but I think it is worth a tip to present the most used features of this function.

The first argument of sprintf() is a string that includes tag to be replaced by the extra arguments. A tag starts with a %, is followed by a couple of optional characters tuning the display and ends with a letter specifying the nature of the variable(s) to be displayed (number or string). The most common letters are:

• “d” for integer value;
• “f” for double precision value;
• “s” for strings.

The most common options are:

• “n”, an integer values specifying the width of the field;
• “0” indicates whether zero-padding should be used;
• “.m” where n is an integer.

That being said, to be as clear as possible, let me exemplify!

1. Different kind of variables:

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sprintf("%d", 1)
sprintf("%f", pi)
sprintf("%s", "A")
#R>  [1] "1"
#R>  [1] "3.141593"
#R>  [1] "A"

2. Combine different variables:

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sprintf("An integer: %d, a double: %f, a string: %s", 1, pi, "A")
#R>  [1] "An integer: 1, a double: 3.141593, a string: A"

3. Tune the field width:

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sprintf("%10f", pi)
#R>  [1] "  3.141593"

4. Zero-padding:

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sprintf("%010f", pi)
#R>  [1] "003.141593"

5. Tune the precision:

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sprintf("%.50f", pi)
#R>  [1] "3.14159265358979311599796346854418516159057617187500"

Pretty cool, isn’t it? To conclude two questions. Question 1: do you remember the file naming example using to showcase paste0()? I assume your answer if yes. Let’s say you now have more than 100 files to name and you want to use zero-padding and a constant field width of 3 (e.g. “myfile001”, “myfile010”, “myfile100”). This leads me to question 2: what do you do? => Go sprintf()!

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paste0("myfile", sprintf("%03d", c(1, 10, 100)))
#R>  [1] "myfile001" "myfile010" "myfile100"

The xaxs and yaxs arguments of par()

This is also something I learned years ago and keep using for almost all my plots ever since. Default values of graphical parameters generate plot that add and extra 4% to the axes limits. This is actually useful to ensure that all graphical symbols are entirely displayed. However, I prefer using round values as axes limits and handling myself their values so that all symbols stay visible. In order to get rid of the extra 4% added on the x-axis (y-axis), you have to pass xaxs = "i" (yaxs = "i") to the par() function. I compare below a plot using the default parameters’ values and the same plot using the tip:

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par(mfrow = c(1,2), bty = "l")
plot(0:10, 0:10, pch = 20)
par(xaxs = "i", yaxs = "i")
plot(0:10, 0:10, pch = 20)

Can you tell the difference? I now add two extra lines to stress the differences out.

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par(mfrow = c(1,2), bty = "l")
plot(0:10, 0:10, pch = 20)
abline(v = c(0,10), h = c(0,10), col = 2)
par(xaxs = "i", yaxs = "i")
plot(0:10, 0:10, pch = 20)
abline(v = c(0,10), h = c(0,10), col = 2)

That’s all folks… until next time!

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sessionInfo()
#R>  R version 4.4.2 (2024-10-31)
#R>  Platform: x86_64-pc-linux-gnu
#R>  Running under: Ubuntu 22.04.5 LTS
#R>  
#R>  Matrix products: default
#R>  BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#R>  LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
#R>  
#R>  locale:
#R>   [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8    
#R>   [5] LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C             
#R>   [9] LC_ADDRESS=C           LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#R>  
#R>  time zone: UTC
#R>  tzcode source: system (glibc)
#R>  
#R>  attached base packages:
#R>  [1] stats     graphics  grDevices utils     datasets  methods   base     
#R>  
#R>  other attached packages:
#R>  [1] inSilecoRef_0.1.1
#R>  
#R>  loaded via a namespace (and not attached):
#R>   [1] sass_0.4.9        generics_0.1.3    xml2_1.3.6        blogdown_1.19     stringi_1.8.4    
#R>   [6] httpcode_0.3.0    digest_0.6.37     magrittr_2.0.3    evaluate_1.0.1    bookdown_0.41    
#R>  [11] fastmap_1.2.0     plyr_1.8.9        jsonlite_1.8.9    backports_1.5.0   crul_1.5.0       
#R>  [16] promises_1.3.2    bibtex_0.5.1      jquerylib_0.1.4   cli_3.6.3         shiny_1.10.0     
#R>  [21] rlang_1.1.4       cachem_1.1.0      yaml_2.3.10       tools_4.4.2       dplyr_1.1.4      
#R>  [26] httpuv_1.6.15     DT_0.33           rcrossref_1.2.0   curl_6.0.1        vctrs_0.6.5      
#R>  [31] R6_2.5.1          mime_0.12         lifecycle_1.0.4   stringr_1.5.1     fs_1.6.5         
#R>  [36] htmlwidgets_1.6.4 miniUI_0.1.1.1    pkgconfig_2.0.3   pillar_1.10.0     bslib_0.8.0      
#R>  [41] later_1.4.1       glue_1.8.0        Rcpp_1.0.13-1     xfun_0.49         tibble_3.2.1     
#R>  [46] tidyselect_1.2.1  knitr_1.49        xtable_1.8-4      htmltools_0.5.8.1 rmarkdown_2.29   
#R>  [51] compiler_4.4.2