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Ista Zahn

2011-Mar-11 16:52 UTC

[R] Any existing functions for reading and extracting data from path names?

Hi helpeRs,

I have inherited a set of data files that use the file system as a
sort of poor man's database, i.e., the data files are nested in
directories that indicate which city they come from. For example:

dir.create("deleteme")
for(i in paste("deleteme", c("New York", "Los
Angeles"), sep="/")) {
    dir.create(i)
    for(j in paste("data", 1:2, ".csv", sep="")) {
        write.csv(data.frame(x=1:10), file=paste(i, j, sep="/"))
    }
}

list.files("deleteme", recursive=TRUE)

What I want to end up with is

  x        city wave
  1    New York    1
  1 Los Angeles    1
  1    New York    2
  1 Los Angeles    2

I've started writting a simple function to do this, but it seems like
a common situation and I'm wondering if there are any packages or
functions that might make this easier.

Thanks!
Ista
-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

Henrik Bengtsson

2011-Mar-11 18:02 UTC

head link

[R] Any existing functions for reading and extracting data from path names?

Hi,

the R.filesets package was designed for this.  It is heavily used by
the aroma framework (http://www.aroma-project.org/), so it got a fair
bit of mileage now (in a good a way).  Here is how you could setup
your data set and work with the data.


# - - - - - - - - - - - -
# Setup file data set
# - - - - - - - - - - - -
library("R.filesets");
paths <- list.files(path="deleteme", full.names=TRUE);
dsList <- lapply(paths, FUN=function(path) TabularTextFileSet$byPath(path));
ds <- Reduce(append, dsList);

# Fullname translator: Los Angeles/data1.csv => Los Angeles,data1.csv
setFullNamesTranslator(ds, function(name, file, ...) {
  path <- getPath(file);
  paste(c(basename(path), name), collapse=",");
});



# - - - - - - - - - - - -
# Examples
# - - - - - - - - - - - -
# Get the full names (a fullname consists of
# a name and comma-separated tags)> getFullNames(ds)[1] "Los Angeles,data1" "Los Angeles,data2"
[3] "New York,data1" "New York,data2"

# Get the names> getNames(ds)[1] "Los Angeles" "Los Angeles"
[3] "New York"    "New York"
> dsTabularTextFileSet:
Name: Los Angeles
Tags:
Full name: Los Angeles
Number of files: 4
Names: Los Angeles, Los Angeles, New York, New York [4]
Path (to the first file): deleteme/Los Angeles
Total file size: 0.00 MB
RAM: 0.01MB


# Get 2nd file> df <- getFile(ds, 2)
> df
TabularTextFile:
Name: Los Angeles
Tags: data2
Full name: Los Angeles,data2
Pathname: deleteme/Los Angeles/data2.csv
File size: 80 bytes
RAM: 0.01 MB
Number of data rows: 10
Columns [2]: '', 'x'
Number of text lines: 11



# Read one data file> data <- readDataFrame(df)
> data       x
1   1  1
2   2  2
3   3  3
4   4  4
5   5  5
6   6  6
7   7  7
8   8  8
9   9  9
10 10 10


# Read all data files> dataList <- lapply(ds, readDataFrame)
> dataList$`Los Angeles,data1
       x
1   1  1
2   2  2
3   3  3
4   4  4
5   5  5
6   6  6
7   7  7
8   8  8
9   9  9
10 10 10

$`Los Angeles,data2
       x
1   1  1
2   2  2
3   3  3
4   4  4
5   5  5
6   6  6
7   7  7
8   8  8
9   9  9
10 10 10

$`New York,data1`
       x
1   1  1
2   2  2
3   3  3
4   4  4
5   5  5
6   6  6
7   7  7
8   8  8
9   9  9
10 10 10

$`New York,data2`
       x
1   1  1
2   2  2
3   3  3
4   4  4
5   5  5
6   6  6
7   7  7
8   8  8
9   9  9
10 10 10

Most methods in R.filesets are currently poorly documented (no
time/resources/...), but there is more in there than documented so
feel free to ask if you have any questions.

Hope this helps

/Henrik

On Fri, Mar 11, 2011 at 8:52 AM, Ista Zahn <izahn at psych.rochester.edu>
wrote:> Hi helpeRs,
>
> I have inherited a set of data files that use the file system as a
> sort of poor man's database, i.e., the data files are nested in
> directories that indicate which city they come from. For example:
>
> dir.create("deleteme")
> for(i in paste("deleteme", c("New York", "Los
Angeles"), sep="/")) {
> ? ?dir.create(i)
> ? ?for(j in paste("data", 1:2, ".csv",
sep="")) {
> ? ? ? ?write.csv(data.frame(x=1:10), file=paste(i, j, sep="/"))
> ? ?}
> }
>
> list.files("deleteme", recursive=TRUE)
>
> What I want to end up with is
>
> ?x ? ? ? ?city wave
> ?1 ? ?New York ? ?1
> ?1 Los Angeles ? ?1
> ?1 ? ?New York ? ?2
> ?1 Los Angeles ? ?2
>
> I've started writting a simple function to do this, but it seems like
> a common situation and I'm wondering if there are any packages or
> functions that might make this easier.
>
> Thanks!
> Ista
> --
> Ista Zahn
> Graduate student
> University of Rochester
> Department of Clinical and Social Psychology
> http://yourpsyche.org
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Ista Zahn

2011-Mar-11 18:15 UTC

head link

[R] Any existing functions for reading and extracting data from path names?

Thanks Henrik, that is exactly what I was hoping for!

Best,
Ista

On Fri, Mar 11, 2011 at 1:02 PM, Henrik Bengtsson <hb at biostat.ucsf.edu>
wrote:> Hi,
>
> the R.filesets package was designed for this. ?It is heavily used by
> the aroma framework (http://www.aroma-project.org/), so it got a fair
> bit of mileage now (in a good a way). ?Here is how you could setup
> your data set and work with the data.
>
>
> # - - - - - - - - - - - -
> # Setup file data set
> # - - - - - - - - - - - -
> library("R.filesets");
> paths <- list.files(path="deleteme", full.names=TRUE);
> dsList <- lapply(paths, FUN=function(path)
TabularTextFileSet$byPath(path));
> ds <- Reduce(append, dsList);
>
> # Fullname translator: Los Angeles/data1.csv => Los Angeles,data1.csv
> setFullNamesTranslator(ds, function(name, file, ...) {
> ?path <- getPath(file);
> ?paste(c(basename(path), name), collapse=",");
> });
>
>
>
> # - - - - - - - - - - - -
> # Examples
> # - - - - - - - - - - - -
> # Get the full names (a fullname consists of
> # a name and comma-separated tags)
>> getFullNames(ds)
> [1] "Los Angeles,data1" "Los Angeles,data2"
> [3] "New York,data1" "New York,data2"
>
> # Get the names
>> getNames(ds)
> [1] "Los Angeles" "Los Angeles"
> [3] "New York" ? ?"New York"
>
>> ds
> TabularTextFileSet:
> Name: Los Angeles
> Tags:
> Full name: Los Angeles
> Number of files: 4
> Names: Los Angeles, Los Angeles, New York, New York [4]
> Path (to the first file): deleteme/Los Angeles
> Total file size: 0.00 MB
> RAM: 0.01MB
>
>
> # Get 2nd file
>> df <- getFile(ds, 2)
>> df
>
> TabularTextFile:
> Name: Los Angeles
> Tags: data2
> Full name: Los Angeles,data2
> Pathname: deleteme/Los Angeles/data2.csv
> File size: 80 bytes
> RAM: 0.01 MB
> Number of data rows: 10
> Columns [2]: '', 'x'
> Number of text lines: 11
>
>
>
> # Read one data file
>> data <- readDataFrame(df)
>> data
> ? ? ? x
> 1 ? 1 ?1
> 2 ? 2 ?2
> 3 ? 3 ?3
> 4 ? 4 ?4
> 5 ? 5 ?5
> 6 ? 6 ?6
> 7 ? 7 ?7
> 8 ? 8 ?8
> 9 ? 9 ?9
> 10 10 10
>
>
> # Read all data files
>> dataList <- lapply(ds, readDataFrame)
>> dataList
> $`Los Angeles,data1
> ? ? ? x
> 1 ? 1 ?1
> 2 ? 2 ?2
> 3 ? 3 ?3
> 4 ? 4 ?4
> 5 ? 5 ?5
> 6 ? 6 ?6
> 7 ? 7 ?7
> 8 ? 8 ?8
> 9 ? 9 ?9
> 10 10 10
>
> $`Los Angeles,data2
> ? ? ? x
> 1 ? 1 ?1
> 2 ? 2 ?2
> 3 ? 3 ?3
> 4 ? 4 ?4
> 5 ? 5 ?5
> 6 ? 6 ?6
> 7 ? 7 ?7
> 8 ? 8 ?8
> 9 ? 9 ?9
> 10 10 10
>
> $`New York,data1`
> ? ? ? x
> 1 ? 1 ?1
> 2 ? 2 ?2
> 3 ? 3 ?3
> 4 ? 4 ?4
> 5 ? 5 ?5
> 6 ? 6 ?6
> 7 ? 7 ?7
> 8 ? 8 ?8
> 9 ? 9 ?9
> 10 10 10
>
> $`New York,data2`
> ? ? ? x
> 1 ? 1 ?1
> 2 ? 2 ?2
> 3 ? 3 ?3
> 4 ? 4 ?4
> 5 ? 5 ?5
> 6 ? 6 ?6
> 7 ? 7 ?7
> 8 ? 8 ?8
> 9 ? 9 ?9
> 10 10 10
>
> Most methods in R.filesets are currently poorly documented (no
> time/resources/...), but there is more in there than documented so
> feel free to ask if you have any questions.
>
> Hope this helps
>
> /Henrik
>
> On Fri, Mar 11, 2011 at 8:52 AM, Ista Zahn <izahn at
psych.rochester.edu> wrote:
>> Hi helpeRs,
>>
>> I have inherited a set of data files that use the file system as a
>> sort of poor man's database, i.e., the data files are nested in
>> directories that indicate which city they come from. For example:
>>
>> dir.create("deleteme")
>> for(i in paste("deleteme", c("New York", "Los
Angeles"), sep="/")) {
>> ? ?dir.create(i)
>> ? ?for(j in paste("data", 1:2, ".csv",
sep="")) {
>> ? ? ? ?write.csv(data.frame(x=1:10), file=paste(i, j,
sep="/"))
>> ? ?}
>> }
>>
>> list.files("deleteme", recursive=TRUE)
>>
>> What I want to end up with is
>>
>> ?x ? ? ? ?city wave
>> ?1 ? ?New York ? ?1
>> ?1 Los Angeles ? ?1
>> ?1 ? ?New York ? ?2
>> ?1 Los Angeles ? ?2
>>
>> I've started writting a simple function to do this, but it seems
like
>> a common situation and I'm wondering if there are any packages or
>> functions that might make this easier.
>>
>> Thanks!
>> Ista
>> --
>> Ista Zahn
>> Graduate student
>> University of Rochester
>> Department of Clinical and Social Psychology
>> http://yourpsyche.org
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>


-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

Mikhail Titov

2011-Mar-12 00:39 UTC

head link

[R] Any existing functions for reading and extracting data from path names?

I'm not sure what you are trying to achieve, but I think this can be a good
starting point:

files <- list.files("deleteme", full.names=TRUE, recursive=TRUE)
names <- sapply(strsplit(files, "/", TRUE), "[", 2)
x <- lapply(files, function(f) {
    out <- read.csv(f)
    out$city <- strsplit(f, "/", TRUE)[[1]][2]
    out
    })
y <- do.call("rbind", x)

Mikhail
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Ista Zahn
> Sent: Friday, March 11, 2011 10:53 AM
> To: r-help at r-project.org
> Subject: [R] Any existing functions for reading and extracting data
> from path names?
> 
> Hi helpeRs,
> 
> I have inherited a set of data files that use the file system as a
> sort of poor man's database, i.e., the data files are nested in
> directories that indicate which city they come from. For example:
> 
> dir.create("deleteme")
> for(i in paste("deleteme", c("New York", "Los
Angeles"), sep="/")) {
>     dir.create(i)
>     for(j in paste("data", 1:2, ".csv",
sep="")) {
>         write.csv(data.frame(x=1:10), file=paste(i, j, sep="/"))
>     }
> }
> 
> list.files("deleteme", recursive=TRUE)
> 
> What I want to end up with is
> 
>   x        city wave
>   1    New York    1
>   1 Los Angeles    1
>   1    New York    2
>   1 Los Angeles    2
> 
> I've started writting a simple function to do this, but it seems like
> a common situation and I'm wondering if there are any packages or
> functions that might make this easier.
> 
> Thanks!
> Ista
> --
> Ista Zahn
> Graduate student
> University of Rochester
> Department of Clinical and Social Psychology
> http://yourpsyche.org
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.

Ista Zahn

2011-Mar-12 02:50 UTC

head link

[R] Any existing functions for reading and extracting data from path names?

Thanks Mikhail. I've been doing something very similar to your example
below, I was just wondering if anyone had packaged functions for this
task.

Thanks again,
Ista
On Sat, Mar 12, 2011 at 12:39 AM, Mikhail Titov <mlt at gmx.us>
wrote:> I'm not sure what you are trying to achieve, but I think this can be a
good
> starting point:
>
> files <- list.files("deleteme", full.names=TRUE,
recursive=TRUE)
> names <- sapply(strsplit(files, "/", TRUE), "[", 2)
> x <- lapply(files, function(f) {
> ? ?out <- read.csv(f)
> ? ?out$city <- strsplit(f, "/", TRUE)[[1]][2]
> ? ?out
> ? ?})
> y <- do.call("rbind", x)
>
> Mikhail
>
>> -----Original Message-----
>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
>> project.org] On Behalf Of Ista Zahn
>> Sent: Friday, March 11, 2011 10:53 AM
>> To: r-help at r-project.org
>> Subject: [R] Any existing functions for reading and extracting data
>> from path names?
>>
>> Hi helpeRs,
>>
>> I have inherited a set of data files that use the file system as a
>> sort of poor man's database, i.e., the data files are nested in
>> directories that indicate which city they come from. For example:
>>
>> dir.create("deleteme")
>> for(i in paste("deleteme", c("New York", "Los
Angeles"), sep="/")) {
>> ? ? dir.create(i)
>> ? ? for(j in paste("data", 1:2, ".csv",
sep="")) {
>> ? ? ? ? write.csv(data.frame(x=1:10), file=paste(i, j,
sep="/"))
>> ? ? }
>> }
>>
>> list.files("deleteme", recursive=TRUE)
>>
>> What I want to end up with is
>>
>> ? x ? ? ? ?city wave
>> ? 1 ? ?New York ? ?1
>> ? 1 Los Angeles ? ?1
>> ? 1 ? ?New York ? ?2
>> ? 1 Los Angeles ? ?2
>>
>> I've started writting a simple function to do this, but it seems
like
>> a common situation and I'm wondering if there are any packages or
>> functions that might make this easier.
>>
>> Thanks!
>> Ista
>> --
>> Ista Zahn
>> Graduate student
>> University of Rochester
>> Department of Clinical and Social Psychology
>> http://yourpsyche.org
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>


-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

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