Package inpdfr

April 18, 2016

Type Package
Title Analyse Text Documents Using Ecological Tools
Version 0.1.3
Date 2016-04-17
Author Rebaudo Francois (IRD, UMR EGCE, Univ.ParisSud-CNRS-IRDUniv.ParisSaclay)
Maintainer Rebaudo Francois <[email protected]>
Description A set of functions and a graphical user interface
to analyse and compare texts, using classical text mining
functions, as well as those from theoretical ecology.
License GPL-2
LazyData TRUE
Imports wordcloud (>= 2.5), RColorBrewer (>= 1.1-2), tm (>= 0.6-2),
SnowballC (>= 0.5.1), ca (>= 0.58), cluster (>= 2.0.1),
entropart (>= 1.4.1), metacom (>= 1.4.4), RGtk2 (>= 2.20.31),
parallel (>= 3.1.3), stringi (>= 1.0-1), R.devices (>= 2.14.0)
SystemRequirements XPDF (http://www.foolabs.com/xpdf/download.html)
Suggests knitr, rmarkdown, testthat
VignetteBuilder knitr
RoxygenNote 5.0.1
NeedsCompilation no
Repository CRAN
Date/Publication 2016-04-18 08:45:42

R topics documented:
askQuit . .
checkEntry
doCA . . .
doCluster .

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2
3
3
4

askQuit
doKmeansClust . . . . . . .
doMetacomEntropart . . . .
doMetacomMetacom . . . .
excludeStopWords . . . . .
exclusionList_FR . . . . . .
exclusionList_SP . . . . . .
exclusionList_UK . . . . . .
getAllAnalysis . . . . . . .
getListFiles . . . . . . . . .
getMostFreqWord . . . . . .
getMostFreqWordCor . . . .
getPDF . . . . . . . . . . .
getStopWords . . . . . . . .
getSummaryStatsBARPLOT
getSummaryStatsHISTO . .
getSummaryStatsOCCUR .
getTXT . . . . . . . . . . .
getwordOccuDF . . . . . . .
getXFreqWord . . . . . . .
inpdfr . . . . . . . . . . . .
loadGUI . . . . . . . . . . .
loremIpsum . . . . . . . . .
makeMainWindowsContent
makeMenuMainWindow . .
makeWordcloud . . . . . . .
mergeWordFreq . . . . . . .
open_cb . . . . . . . . . . .
open_cbFile . . . . . . . . .
postProcTxt . . . . . . . . .
preProcTxt . . . . . . . . .
quitSpaceFromChars . . . .
switchOffDialogWait . . . .
switchOnDialogWait . . . .
truncNumWords . . . . . . .

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Index

askQuit

5
6
7
8
9
9
10
10
11
12
13
14
15
15
16
17
18
18
19
20
20
21
21
22
22
23
24
24
25
26
26
27
27
28
29

RGtk2 GUI function: ask confirmation to quit if topright button is used

to quit.

Description
This function is provided so that you can easily see its content. It is not intended to be used, prefer
loadGUI() to load the RGtk2 GUI.

checkEntry

Usage
askQuit(myobject)
Arguments
myobject

checkEntry

The parent window to be closed.

RGtk2 GUI function: check data validity in entries.

Description
This function is provided so that you can easily see its content. It is not intended to be used, prefer
loadGUI() to load the RGtk2 GUI.
Usage
checkEntry(validatedEntry, myRegEx)
Arguments
validatedEntry Entry to be checked.
myRegEx
Regular expression to test the validatedEntry.

doCA

Performs a correspondance analysis on the basis of the wordoccurrence data.frame.

Description
Performs a correspondance analysis on the basis of the word-occurrence data.frame using ca function.
Usage
doCA(wordF, getPlot = TRUE, mwidth = 800, mheight = 800,
formatType = "png", ...)
Arguments
wordF
getPlot
mwidth
mheight
formatType
...

The data.frame containing word occurrences.

If TRUE, save the ca plot in the RESULTS directory.
The width of the plot in pixels.
The height of the plot in pixels.
The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").
Additional arguments from the ca function.

doCluster

Value
The results of the ca function.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"), excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
doCA(wordF = wordOccuDF)

doCluster

Performs a cluster analysis on the basis of the word-occurrence

data.frame.

Description
Performs a cluster analysis on the basis of the word-occurrence data.frame using hclust function.
Usage
doCluster(wordF, myMethod = "ward.D2", gp = FALSE, nbGp = 5,
getPlot = TRUE, mwidth = 800, mheight = 800, formatType = "png", ...)
Arguments
wordF

The data.frame containing word occurrences.

myMethod

The method to compute distances, see dist function.

gp

A logical to specify if groups should be made.

nbGp

An intger to specify the number of groups. Ignored if gp=FALSE.

getPlot

If TRUE, save the cluster plot in the RESULTS directory.

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

...

Additional arguments from the hclust function.

doKmeansClust

Value
An object of class hclust.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"), excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
doCluster(wordF = wordOccuDF, myMethod = "ward.D2")

doKmeansClust

Performs a k-means cluster analysis on the basis of the wordoccurrence data.frame.

Description
Performs a k-means cluster analysis on the basis of the word-occurrence data.frame using kmeans
function.
Usage
doKmeansClust(wordF, nbClust = 4, nbIter = 10, algo = "Hartigan-Wong",
getPlot = TRUE, mwidth = 800, mheight = 800, formatType = "png", ...)
Arguments
wordF
nbClust
nbIter
algo
getPlot
mwidth
mheight
formatType
...

The data.frame containing word occurrences.

The number of clusters.
The number of iterations allowed.
The algoritm used (see kmeans).
If TRUE, save the k-means cluster plot in the RESULTS directory.
The width of the plot in pixels.
The height of the plot in pixels.
The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").
Additional arguments from the kmeans function.

doMetacomEntropart

Value
An object of class kmeans (see kmeans).
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"), excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
doKmeansClust(wordF = wordOccuDF, nbClust = 2)

doMetacomEntropart

Performs an analysis of ecological diversity and structure.

Description
Uses the entropart-package to analyse the word-occurrence data.frame, considering words as
species and documents as communities.
Usage
doMetacomEntropart(wordF, getPlot = c(TRUE, TRUE, TRUE, TRUE),
getTextSink = c(TRUE, TRUE, TRUE, TRUE), mwidth = 800, mheight = 800,
formatType = "png")
Arguments
wordF
getPlot

getTextSink

The data.frame containing word occurrences.

A vector with four logical values. If getPlot[1]==TRUE, the MetaCommunity
object is plotted and saved in the RESULTS directory. If getPlot[2]==TRUE,
the DivPart analisis is plotted and saved in the RESULTS directory. If getPlot[3]==TRUE,
the DivEst analisis is plotted and saved in the RESULTS directory. If getPlot[4]==TRUE,
the DivProfile analisis is plotted and saved in the RESULTS directory.
A vector with four logical values. If getTextSink[1]==TRUE, the MetaCommunity
object is saved in the RESULTS directory. If getTextSink[2]==TRUE, the
DivPart analisis is saved in the RESULTS directory. If getTextSink[3]==TRUE,
the DivEst analisis is saved in the RESULTS directory. If getTextSink[4]==TRUE,
the DivProfile analisis is saved in the RESULTS directory.

doMetacomMetacom

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

Value
A MetaCommunity object (see entropart-package).
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
doMetacomEntropart(wordF = wordOccuDF)

doMetacomMetacom

Performs a metacomunity analysis.

Description
Use the package Metacommunity to analyse the word-occurrence data.frame, considering words as
species and documents as communities.
Usage
doMetacomMetacom(wordF, numSim = 10, limit = "Inf", getPlot = TRUE,
getTextSink = TRUE, mwidth = 800, mheight = 800, formatType = "png")
Arguments
wordF

The data.frame containing word occurrences.

numSim

Number of simulated null matrices, see Metacommunity.

limit

An integer to limit the number of words to use in the analysis.

getPlot

If TRUE, save the plot in the RESULTS directory.

excludeStopWords
getTextSink

If TRUE, save the console output in the RESULTS directory.

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

Value
An object of class Metacommunity.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
doMetacomMetacom(wordF = wordOccuDF)

excludeStopWords

Exclude StopWords form the word-occurrence data.frame.

Description
Exclude StopWords form the word occurrences data.frame. excludeStopWords uses parallel to
perform parallel computation.
Usage
excludeStopWords(wordF, lang = "English")
Arguments
wordF

The data.frame containing word occurrences.

lang

The language used ("French", "English", "Spanish").

Value
The word-occurrence data.frame.

exclusionList_FR

Examples
## Not run:
excludeStopWords(wordF = myDF, lang = "French")
## End(Not run)

exclusionList_FR

Stop words in French.

Description
A vector containing stop words in French.
Usage
exclusionList_FR
Format

A vector with 173 elements (character), with UTF-8 characters escaped using stringi::stri_escape_unicode(exclusion
Source
Adapted from http://www.ranks.nl/stopwords/french.

exclusionList_SP

Stop words in Spanish.

Description
A vector containing stop words in Spanish
Usage
exclusionList_SP
Format

A vector with 190 elements (character), with UTF-8 characters escaped using stringi::stri_escape_unicode(exclusion
Source
Adapted from http://www.ranks.nl/stopwords/spanish.

10

getAllAnalysis

Stop words in English.

exclusionList_UK

Description
A vector containing stop words in English.
Usage
exclusionList_UK
Format
A vector with 542 elements (character).
Source
Adapted from http://www.ranks.nl/stopwords.

getAllAnalysis

A quick way to compute a set of analysis from the word-occurrence

data.frame.

Description
A quick way to compute a set of analysis from the word-occurrence data.frame.
Usage
getAllAnalysis(dataset, wcloud = TRUE, sumStats = TRUE, freqW = TRUE,
corA = TRUE, clust = TRUE, metacom = TRUE)
Arguments
dataset

A single word-occurrrence data.frame.

wcloud

A logical to for word cloud analysis.

sumStats

A logical to for summary statistics analysis.

freqW

A logical to for word frequency analysis.

corA

A logical to for correspondence analysis.

clust

A logical to for cluster analysis.

metacom

A logical to for metacommunity analysis.

Value
A set of analyses available from the inpdfr package.

getListFiles

11

Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
getAllAnalysis(dataset = wordOccuDF, wcloud = FALSE, sumStats = FALSE)

List files in a specified directory sorted by extension.

getListFiles

Description
List files in a specified directory sorted by extension. The function takes into account .txt and .pdf
files based on strsplit function.
Usage
getListFiles(mywd)
Arguments
mywd

A string containing the working directory.

Value
A list of length 2 with file names sorted by extension (pdf and txt).
Examples
getListFiles(mywd = getwd())

12

getMostFreqWord

getMostFreqWord

Returns most frequent words.

Description
Returns most frequent words and plots their frequencies per document.
Usage
getMostFreqWord(wordF, numWords, getPlot = TRUE, mwidth = 1024,
mheight = 800, formatType = "png")
Arguments
wordF

The data.frame containing word occurrences.

numWords

The number of words to be returned.

getPlot

If TRUE, save a scatter plot in the RESULTS directory.

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

Value
The numWords most frequent words.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
getMostFreqWord(wordF = wordOccuDF, numWords = 5)

getMostFreqWordCor

13

getMostFreqWordCor

Test for correlation between the most frequent words.

Description
Test for correlation between the most frequent words.
Usage
getMostFreqWordCor(wordF, numWords, getPlot = c(TRUE, TRUE),
getTextSink = TRUE, mwidth = 1024, mheight = 1024, formatType = "png")
Arguments
wordF

The data.frame containing word occurrences.

numWords

The number of words to be returned.

getPlot

A vector with two logical values. If plots[1]==TRUE, an image of the correlation matrix is saved in the RESULTS directory. If plots[2]==TRUE, the image
of the p-value matrix associated with the correlation is saved in the RESULTS
directory.

getTextSink

If TRUE, save the correlation matrix and the associated p-values in a text file in
the RESULTS directory.

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

Value
A list with the correlation matrix and the p-value matrix.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)

14

getPDF
file.remove(list.files(pattern = "loremIpsum"))
getMostFreqWordCor(wordF = wordOccuDF, numWords = 5)

getPDF

Extract text from PDF files and return a word-occurrence data.frame.

Description

getPDF returns a word-occurrence data.frame from PDF files. It needs XPDF in order to run (http://www.foolabs.com/xpdf/dow
and uses parallel to perform parallel computation.
Usage
getPDF(myPDFs, minword = 1, maxword = 20, minFreqWord = 1,
pathToPdftotext = "")
Arguments
myPDFs

A character vector containing PDF file names.

minword

An integer specifying the minimum number of letters per word into the returned
data.frame.

maxword

An integer to specifying the maximum number of letters per word into the returned data.frame.

minFreqWord
An integer specifying the minimum word frequency into the returned data.frame.
pathToPdftotext
A character containing an alternative path to XPDF pdftotext function, see
Details section.
Details
getPDF uses XPDF pdftotext function to extract the content of PDF files into a TXT file. If
pdftotext is not in the PATH, an alternative is to provide the full path of the program into the
pathToPdftotext parameter.
Value
A list of list with word-occurrence data.frame and file name.
Examples
## Not run:
getPDF(myPDFs = "mypdf.pdf")
## End(Not run)

getStopWords

15

Load a list of stopwords.

getStopWords

Description
getStopWords returns a list of stopwords.
Usage
getStopWords()
Value
A list of vectors with stopwords for French, English, and Spanish languages.
Examples
getStopWords()

getSummaryStatsBARPLOT
Perform a barplot with the number of unique words per document

Description
Perform a barplot with the number of unique words per document using barplot function.
Usage
getSummaryStatsBARPLOT(wordF, getPlot = TRUE, mwidth = 480, mheight = 480,
formatType = "png", ...)
Arguments
wordF

The data.frame containing word occurrences.

getPlot

If TRUE, save the bar plot in the RESULTS directory.

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

...

Additional arguments from barplot function.

Value
The number of unique words per document.

16

getSummaryStatsHISTO

Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
getSummaryStatsBARPLOT(wordF = wordOccuDF)

getSummaryStatsHISTO

Plot an histogram with the number of words excluding stop words

Description
Plot a histogram with the number of words excluding stop words using hist function.
Usage
getSummaryStatsHISTO(wordF, mwidth = 800, mheight = 800,
formatType = "png", ...)
Arguments
wordF

The data.frame containing word occurrences.

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

...

Additional arguments from hist function.

Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"

getSummaryStatsOCCUR

17

dir.create(file.path(getwd(), subDir), showWarnings = FALSE)

write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
getSummaryStatsHISTO(wordF = wordOccuDF)

getSummaryStatsOCCUR

Plot a scatter plot with the proportion of documents using similar

words.

Description
Plot a scatter plot with the proportion of documents using similar words.
Usage
getSummaryStatsOCCUR(wordF, getPlot = TRUE, mwidth = 800, mheight = 800,
formatType = "png")
Arguments
wordF

The data.frame containing word occurrences.

getPlot

If TRUE, save the scatter plot in the RESULTS directory.

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

Value
A data.frame containing the proportion of documents and the number of similar words.
Examples
## Not run:
getSummaryStatsOCCUR(wordF = myDF)
## End(Not run)

18

getwordOccuDF

getTXT

Extract text from TXT files and return a word-occurrence data.frame.

Description
Extract text from TXT files and return a word-occurrence data.frame.
Usage
getTXT(myTXTs)
Arguments
myTXTs

A character vector containing TXT file names (or complete path to these files).

Value
A list of list with word-occurrence data.frame and file name.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuFreq <- getTXT(myTXTs = list.files(path = paste0(getwd(),
"/RESULTS/"), pattern = "loremIpsum", full.names = TRUE))
file.remove(list.files(pattern = "loremIpsum"))

getwordOccuDF

A quick way to obtain the word-occurrence data.frame from a set of

documents.

Description
A quick way to obtain the word-occurrence data.frame from a set of documents.

getXFreqWord

19

Usage
getwordOccuDF(mywd, language = "English", excludeSW = TRUE)
Arguments
mywd

A character variable containing the working directory.

language

The language used ("French", "English", "Spanish").

excludeSW

A logical to exclude stop words.

Value
A single word-occurrrence data.frame.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))

getXFreqWord

Returns most frequent words

Description
Returns most frequent words
Usage
getXFreqWord(wordF, occuWords)
Arguments
wordF

The data.frame containing word occurrences.

occuWords

The minimum number of occurrences for words to be returned.

20

loadGUI

Value
A vector with most frequent words.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuDF <- getwordOccuDF(mywd = paste0(getwd(), "/RESULTS"),
excludeSW = FALSE)
file.remove(list.files(pattern = "loremIpsum"))
getXFreqWord(wordF = wordOccuDF, occuWords = 5)

inpdfr

inpdfr: A package to analyse PDF Files Using Ecological Tools.

Description
The inpdfr package allows analysing and comparing PDF/TXT documents using both classical
text mining tools and those from theoretical ecolgy. In the later, words are considered as species
and documents as communities, therefore allowing analysis at the community and metacommunity
levels. The inpdfr package provides three cathegories of functions: functions to extract and process
text into a word-occurrence data.frame, functions to analyse the word-occurrence data.frame with
standard and ecological tools, and functions to use inpdfr through a Gtk2 Graphical User Interface.

loadGUI

RGtk2 GUI function: Load the Graphical user Interface

Description
Load the Graphical user Interface in order to use inpdfr package through a user-friendly interface.
Usage
loadGUI()

loremIpsum

21

Details
inpdfr package uses RGtk2 package for its GUI. Non-linux users may need to download additional
files such as the "gtk-file" icon, or the "hicolor" theme, which can be found by downloading GTK+
from http://www.gtk.org/. They are not needed for the GUI to work as intended, but you may get
a "GTK-WARNING" when using loadGUI(). Feel free to ignore this warning. The RGtk2 GUI is
not needed to access all funcionalities of inpdfr package. Some options are only available through
the command line interface.
Examples
## Not run:
loadGUI()
## End(Not run)

loremIpsum

Lorem Ipsum text.

Description
A vector containing a Lorem Ipsum text for testing purposes.
Usage
loremIpsum
Format
A vector with 556 elements, each element corresponds to a line in the original text (character).
Source
http://lipsum.com/.

makeMainWindowsContent
RGtk2 GUI function: dynamic content of main window.

Description
This function is provided so that you can easily see its content. It is not intended to be used, prefer
loadGUI() to load the RGtk2 GUI.
Usage
makeMainWindowsContent(main_window)

22

makeWordcloud

Arguments
main_window

Main window where the content is created.

makeMenuMainWindow

RGtk2 GUI function: main window.

Description
This function is provided so that you can easily see its content. It is not intended to be used, prefer
loadGUI() to load the RGtk2 GUI.
Usage
makeMenuMainWindow(main_window)
Arguments
main_window

makeWordcloud

Main window where the menu is created.

Word cloud based on the word-occurrence data.frame.

Description
Plot a word cloud from the word-occurrence data.frame using wordcloud function.
Usage
makeWordcloud(wordF, wcFormat = "png", wcminFreq = 3, wcmaxWords = Inf,
wcRandOrder = FALSE, wcCol = RColorBrewer::brewer.pal(8, "Dark2"),
getPlot = c(TRUE, TRUE), mwidth = 1000, mheight = 1000,
formatType = "png")
Arguments
wordF

The data.frame containing word occurrences.

wcFormat

Output format for the word cloud (deprecated, only "png").

wcminFreq

Minimum word frequency for words to be ploted (see wordcloud).

wcmaxWords

Maximum number of words to be ploted (see wordcloud).

wcRandOrder

Plot words in random order (see wordcloud).

wcCol

Color words (see wordcloud).

getPlot

A vector with two logical values. If plots[1]==TRUE, a word cloud is made for
each document. If plots[2]==TRUE, a word cloud is made for the combinaison
of all documents.

mergeWordFreq

23

mwidth

The width of the plot in pixels.

mheight

The height of the plot in pixels.

formatType

The format for the output file ("eps", "pdf", "png", "svg", "tiff", "jpeg", "bmp").

Examples
## Not run:
makeWordcloud(wordF = myDF)
## End(Not run)

Merge word-occurrence data.frames into a single data.frame.

mergeWordFreq

Description
Merge word-occurrence data.frames into a single data.frame.
Usage
mergeWordFreq(wordF)
Arguments
wordF

The data.frame containing word occurrences.

Value
A single word-occurrrence data.frame with each column corresponding to a text file.
Examples
data("loremIpsum")
loremIpsum01 <- loremIpsum[1:100]
loremIpsum02 <- loremIpsum[101:200]
loremIpsum03 <- loremIpsum[201:300]
loremIpsum04 <- loremIpsum[301:400]
loremIpsum05 <- loremIpsum[401:500]
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum01, file = "RESULTS/loremIpsum01.txt")
write(x = loremIpsum02, file = "RESULTS/loremIpsum02.txt")
write(x = loremIpsum03, file = "RESULTS/loremIpsum03.txt")
write(x = loremIpsum04, file = "RESULTS/loremIpsum04.txt")
write(x = loremIpsum05, file = "RESULTS/loremIpsum05.txt")
wordOccuFreq <- getTXT(myTXTs = list.files(path = paste0(getwd(),
"/RESULTS/"), pattern = "loremIpsum", full.names = TRUE))
wordOccuDF <- mergeWordFreq(wordF = wordOccuFreq)
file.remove(list.files(pattern = "loremIpsum"))

24

open_cbFile

open_cb

RGtk2 GUI function: open a window in order to choose the working

directory.

Description
This function is provided so that you can easily see its content. It is not intended to be used, prefer
loadGUI() to load the RGtk2 GUI.
Usage
open_cb(widget, window)
Arguments
widget

Widget to open.

window

A window to contain the widget.

Value
The path to the user-defeined working directory.

open_cbFile

RGtk2 GUI function: open a window in order to choose an R data file

(rda, RDA, RData).

Description
This function is provided so that you can easily see its content. It is not intended to be used, prefer
loadGUI() to load the RGtk2 GUI.
Usage
open_cbFile(widget, window)
Arguments
widget

Widget to open.

window

A window to contain the widget.

Value
The path to the user-defeined file.

postProcTxt

postProcTxt

25

Prossess vectors containing words into a data.frame of word occurrences.

Description
Prossess vectors containing words into a data.frame of word occurrences.

Usage
postProcTxt(txt, minword = 1, maxword = 20, minFreqWord = 1)

Arguments
txt

A vector containing text.

minword

An integer specifying the minimum number of letters per word into the returned
data.frame.

maxword

An integer to specifying the maximum number of letters per word into the returned data.frame.

minFreqWord

An integer specifying the minimum word frequency into the returned data.frame.

Value
A data.frame (freq = occurrences, stem = stem words, word = words), sorted by word occurrences.

Examples
## Not run:
postProcTxt(txt = preProcTxt(filetxt = "loremIpsum.txt"))
## End(Not run)
data("loremIpsum")
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum, file = "RESULTS/loremIpsum.txt")
preProcTxt(filetxt = paste0(getwd(), "/RESULTS/loremIpsum.txt"))
postProcTxt(txt = preProcTxt(filetxt = paste0(getwd(), "/RESULTS/loremIpsum.txt")))
file.remove(list.files(pattern = "loremIpsum"))

26

quitSpaceFromChars

Extract text from txt files and pre-process content.

preProcTxt

Description
Extract text from txt files and pre-process content.
Usage
preProcTxt(filetxt, encodingIn = "UTF-8", encodingOut = "UTF-8")
Arguments
filetxt

A character containing the name of a txt file.

encodingIn

Encoding of the text file (default = "UTF-8").

encodingOut

Encoding of the text extracted (default = "UTF-8").

Value
A character vector with the content of the pre-process txt file (one element per line).
Examples
data("loremIpsum")
subDir <- "RESULTS"
dir.create(file.path(getwd(), subDir), showWarnings = FALSE)
write(x = loremIpsum, file = "RESULTS/loremIpsum.txt")
preProcTxt(filetxt = paste0(getwd(), "/RESULTS/loremIpsum.txt"))
file.remove(list.files(pattern = "loremIpsum"))

quitSpaceFromChars

Delete spaces in file names.

Description
Delete spaces in file names located in the current working directory.
Usage
quitSpaceFromChars(vectxt)
Arguments
vectxt

A vector containing character entries corresponding to the names of files in the

current working directory.

switchOffDialogWait

27

Value
The function returns a logical for each file, with TRUE if the file has been found, and FALSE
otherwise.
Examples
quitSpaceFromChars(c("my pdf.pdf","my other pdf.pdf"))

switchOffDialogWait

RGtk2 GUI function: switch off the "Processing..." message.

Description
This function is provided so that you can easily see its content. It is not intended to be used, prefer
loadGUI() to load the RGtk2 GUI.
Usage
switchOffDialogWait(dialogX)
Arguments
dialogX

The dialog window to be closed.

switchOnDialogWait

RGtk2 GUI function: switch on the "Processing..." message.

Description
This function is provided so that you can easily see its content. It is not intended to be used, prefer
loadGUI() to load the RGtk2 GUI.
Usage
switchOnDialogWait()

28

truncNumWords

truncNumWords

Truncate the word-occurrence data.frame.

Description
Truncate the word-occurrence data.frame.
Usage
truncNumWords(wordF, maxWords)
Arguments
wordF

The data.frame containing word occurrences.

maxWords

The maximum number of words in the data.frame.

Value
The data.frame containing word occurrences.
Examples
## Not run:
truncNumWords(wordF = myWordOccurrenceDF, maxWords = 50)
## End(Not run)

Index
Topic datasets
exclusionList_FR, 9
exclusionList_SP, 9
exclusionList_UK, 10
loremIpsum, 21

inpdfr, 20
inpdfr-package (inpdfr), 20
kmeans, 5, 6
loadGUI, 20
loremIpsum, 21

askQuit, 2

makeMainWindowsContent, 21
makeMenuMainWindow, 22
makeWordcloud, 22
mergeWordFreq, 23
Metacommunity, 7, 8

barplot, 15
ca, 3, 4
checkEntry, 3
dist, 4
doCA, 3
doCluster, 4
doKmeansClust, 5
doMetacomEntropart, 6
doMetacomMetacom, 7

open_cb, 24
open_cbFile, 24
postProcTxt, 25
preProcTxt, 26
quitSpaceFromChars, 26

excludeStopWords, 8
exclusionList_FR, 9
exclusionList_SP, 9
exclusionList_UK, 10

switchOffDialogWait, 27
switchOnDialogWait, 27
truncNumWords, 28

getAllAnalysis, 10
getListFiles, 11
getMostFreqWord, 12
getMostFreqWordCor, 13
getPDF, 14
getStopWords, 15
getSummaryStatsBARPLOT, 15
getSummaryStatsHISTO, 16
getSummaryStatsOCCUR, 17
getTXT, 18
getwordOccuDF, 18
getXFreqWord, 19

wordcloud, 22

hclust, 4, 5
hist, 16
29