Looping a Function Over Multiple Data Files - Mindy Morales
Timeline
SubTasks
From Gleon Fellowship
Legend: M Mandatory | States: ■ Not defined, ■ Valid, ■ Inconsistent with parent
Usefulness of skill
- DOM fluorescence spectroscopy generates many large matrix files
- Files require multiple corrections, calculations, and extraction of wavelength regions to provide useful information about DOM pool
- Usually done in MATLAB; open source code has not been developed for R
- Technique is not exclusive to EEM data and can be applied to any analysis that requires applying the same operation to multiple files.
Challenges
Working directory should only contain files of specified extension that you want to analyze
Sample code
In this example, a humification index (HIX, with corrections from Ohno 2008) is calculated from multiple .csv files
- Define function
-
HIX<-function(low,high){sum(high)/(sum(high)+sum(low))}
- Batch import csv files from wd
-
hixfiles <- list.files(pattern = "csv")
- Create NULL vector to drop data into
-
hix_o <- NULL
- Loop calculates HIX across all files in wd
-
for (i in 1:length(hixfiles)){
tmp <- read.csv(hixfiles[i])
hix_o[i] = HIX(tmp$low, tmp$high)
}
- Define vector to store results
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results = data.frame(hixfiles, hix_o) -
print(results)
- Export to wd
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write.csv(hix_o,file="hix.csv")
Properties
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