Hi all,
I am having an issue with trying to run iterations for the same analysis
with a list of data sets. I am assuming I am missing a basic step here.
Code I am trying is below. Not certain if a NEXT call needs to be
included somewhere or not.
This is run under the Deducer GUI. I would also be content to simply
run in a basic R console if that works.
# First step, was to create a folder with the simple data files for the
analysis
# Set the WD for that directory
setwd("C://Embalonurids")
# Call all the names of the files in that folder
file.names <- dir(pattern = "*.txt")
#Make a LOOP for the analysis
for(i in 1:length(file.names)){file <-
read.table(file.names[i],header=TRUE) # read the text files one by one
# Deducer code used
file[c("TBC")] <- recode.variables(file[c("TBC")] , "0 -> NA;")
# Create new BW variable and data set then change data file name for
the analysis
BW<-within(file,BW<-Fmax-Fmin)
BW<-within(BW,FcH1<-Fc*.5)
BW<-within(BW,FcH3<-FcH1*3)
BatStats<-BW
# In the Deducer GUI this is the code that runs manually if I run these
one by one
BatStats<-Deducer::descriptive.table (vars = d
(Dur,TBC,Fmin,Fmax,BW,Fmean,Fk,FcH1,Fc,FcH3,Sc,Pmc),data=
BatStats,func.names =c("Valid N","Minimum","Maximum","Mean","St.
Deviation"),func.additional= list(p75=function(x) quantile(x, c(0.75),
na.rm=TRUE),p85=function(x) quantile(x, c(0.85),
na.rm=TRUE),p90=function(x) quantile(x,
c(0.90),na.rm=TRUE),p99=function(x) quantile(x, c(0.99),na.rm=TRUE)))
## Then the results need to be written to an outputdirectory
name <- as.character(paste(file.names[i], ".csv", sep="")) # this
creates an element that will have the name of the file that is used in
each run
# I have tried both setting a new WD or simply defined where to writ the
results
setwd("C://Embalonurids/Results")
write.csv(BatStats, name) #this should assign the names of the files
as it iterates one by one })
#also tried directing where to write the outputas I do when manually
running this
#write.csv(BatStats,name,file="C:\\Emballonurids\Results"))
I would like to run this as an iteration as I have > 200 data files to
process and would love to have it run in background while I am working
on other things.
An assistance welcomed.
Bruce
--
Bruce W. Miller, PhD.
Neotropical bat risk assessments
Conservation Fellow - Wildlife Conservation Society
If we lose the bats, we may lose much of the tropical vegetation and the lungs
of the planet
Using acoustic sampling to identify and map species distributions
and pioneering acoustic tools for ecology and conservation of bats for >25
years.
Key projects include providing free interactive identification keys and call
fact sheets for the vocal signatures of New World Bats
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