[R] list indexing problem reading in files from a directory

[stephen sefick]

here is an intermediate solution that works just fine.  Thank you all
for your help.

Stephen Sefick

#level logger read in
read.ll <- function(path){
library(chron)
library(zoo)
list.of.files <- list.files(path)
length.files <- length(list.of.files)
	df <- vector(mode = "list", length = length.files)
	for(i in 1:length.files){
	df[[i]] <- read.table(paste(sep="/", path, list.of.files[i]),
skip=45, as.is=TRUE)
	length.1 <- length(df[[i]][,1])
	length.2 <- length(df[[i]][,1])-1
	df[[i]] <- df[[i]][-c(length.1, length.2),]
	df[[i]] <- data.frame(chron(as.character(df[[i]][,1]),
as.character(df[[i]][,2]), format=c(dates="Y/m/d", times="H:M:S")),
as.numeric(df[[i]][,3]), as.numeric(df[[i]][,4]),
as.factor(list.of.files[[i]]))
	names(df[[i]]) <- c("datetime", "level", "temp", "site")
	}
	return(df)
}

a <- read.ll("C:/Documents and Settings/Feminella
Lab/Desktop/WB_LL_Data/Wolf Bay Data/Raw solinist data/Compensated by
Brad")


On Tue, Aug 11, 2009 at 1:14 PM, Gavin Simpson<gavin.simpson at ucl.ac.uk> wrote:
> On Tue, 2009-08-11 at 12:45 -0500, stephen sefick wrote:
>> I am running into a problem with allocating these files to a list as
>> they are read in through a for loop.  I know I am probably doing
>> something wrong, but I can't figure out what.  I know this is not
>> reproducible.  I am ending up with a data frame of the very last file
>> to be read in.  I know it is in the indexing, but I can't wrap my head
>> around it.
>> thanks for all of the help,
>>
>> Stephen Sefick
>
> A missing return() or explicit statement about what should be return
> from your function.
>
> Your function is not right either. You keep killing df at the start of
> each iteration of the for loop so df is a list with a single component
> each time.
>
>>
>>
>> #level logger read in
>> read.ll <- function(path){
>> library(chron)
>> library(zoo)
>> list.of.files <- list.files(path)
>> length.files <- length(list.of.files)
>>       for(i in 1:length.files){
>>       df <- list()
>
> Move the line above outside of the loop, above. Better would be to
> allocate storage so you know everything is correct, rather than an empty
> list. It doesn't improve speed at all IIRC, but is a bit tidier, so try
>
> df <- vector(mode = "list", length = length.files)
>
> immediately after length.files <- ....
>
>>       df[[i]] <- read.table(paste(sep="/", path, list.of.files[i]), skip=45)
>>       length.1 <- length(df[[i]][,1])
>>       length.2 <- length(df[[i]][,1])-1
>>       df[[i]] <- df[[i]][-c(length.1, length.2),]
>>       df[[i]] <- data.frame(chron(as.character(df[[i]][,1]),
>> as.character(df[[i]][,2]), format=c(dates="Y/m/d", times="H:M:S")),
>> as.numeric(df[[i]][,3]), as.numeric(df[[i]][,4]),
>> as.factor(list.of.files[[i]]))
>>
>>       }
>
> Here you probably want
>
> return(df)
>
> or just
>
> df
>
> But I prefer return(....) as it is pretty explicit about your intentions
> that, in this case, 'df' is what you want the function to return.
>
> You function is probably return the last value of the for loop, but as I
> say, your loop can't possibly work as you keep killing the list so it
> will only ever contain a single processed data.frame.
>
> You could check this yourself by debugging, by:
>
> debug(read.ll)
>
> Then call your function and step through, and at each stage in the loop,
> see what df contains. If you do this on the function as you posted,
> you'll quickly see what the problem is.
>
> HTH
>
> G
>
>> }
>>
>> a <- read.ll("C:/Documents and Settings/Feminella
>> Lab/Desktop/WB_LL_Data/Wolf Bay Data/Raw solinist data/Compensated by
>> Brad")
>>
> --
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>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
>  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
>  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
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>
>



-- 
Stephen Sefick

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

								-K. Mullis