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Creating weighted tables with R / sum of numerics associated to some categorical variable

Creating weighted tables with R / sum of numerics associated to some categorical variable

The normal table command table() calculates the frequency of each element of a vector like this:

R> df <- data.frame(var = c("A", "A", "B", "B", "C", "C", "C"))
R> table(df)
A B C 
2 2 3 

So, it tells us, we have two times A and B and three times C, accordingly.

However, if we have now the situation like this:

df <- data.frame(var = c("A", "A", "B", "B", "C", "C", "C"), value = c(10, 20, 20, 40, 15, 25, 35))

Meaning, we have a categorical variable var and a numeric variable value and for each categorical variable we would like to get the sum over the numerical variable, we can simply use the base-R command aggregate like this

R> aggregate(value ~ var, data = df, FUN = sum)
  var wt
1   A 40
2   B 60
3   C 70

As I often use also the data.table package, here is also a simple solution using this package, assuming we do (respective have a data table from some other source, like fread)

dt <- data.table(df)

Then we can just sume over a column name with respect to another column like this (and assign the value into a new variable tot) :

setDT(dt)[, .(n = sum(value)), var] 
Couldn’t delete a failed R package installation

Couldn’t delete a failed R package installation

Today I faced a strange thing, while I tried to install an update to one of my R-packages. As usually, I installed the latest version from it like this


But the installation failed, and when I tried to reinstall it, I got this error message:

Installing package into ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
ERROR: failed to lock directory ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1’ for modifying
Try removing ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1/00LOCK-GenomicTools’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmp<...>Lv/file3c36<...>34/GenomicTools_0.2.11.tar.gz’ had non-zero exit status

So, I tried to go in said directory and delete the folder manually and there I received another error:

rm: cannot remove '00LOCK-GenomicTools/GenomicTools/libs/.nfs00000001002e2<...>d': Device or resource busy

I tried this and this, but nothing helped to delete that folder, it kept mocking my that the device is busy. Eventually, it helped just to rename the folder list this

mv 00LOCK-GenomicTools/ 00LOCK-GenomicTools-deleteThis/

It is now still hanging there in the folder, but I was able to reinstall the R-package and now I need to revisit the folder in a few days and check, if the device is still busy or if I can delete it then…

Couple of updates in R-packages

Couple of updates in R-packages

During the last weeks I updated a couple of my R-packages. The main work went into the GenomicTools package, though it required also adjustments to the two packages GenomicTools.fileHandler and hoardeR.

The changes are mainly in user-friendliness and bugfixing to catch special cases of data inputs. If someone uses the packages and finds any other bugs or has suggestions for improvements, please drop me an email, or contact me via the corresponding GitHub project page of the packages.