checkPDFdir: Extract statistics and recompute p values from a directory...

In chartgerink/statcheckTEMP: Extract statistics from articles and recompute p values

Description

Extracts statistical references from a directory with PDF files. The "pdftotext" program (http://www.foolabs.com/xpdf/download.html) is used to convert PDF files to plain text files. This must be installed and PATH variables must be properly set so that this program can be used from command line.

By default a GUI window is opened that allows you to choose the directory (using tcltk).

Usage

checkPDFdir(dir, subdir = TRUE, ...)

Arguments

dir	String indicating the directory to be used.
subdir	Logical indicating whether you also want to check subfolders. Defaults to TRUE
...	Arguments sent to statcheck.

Details

See statcheck for more details. Use checkPDF to import individual PDF files. Currently only statistics in the form "stat (df1, df2) = value, p = value" are extracted. Because the Chi-square symbol can not be repressented in plain text it is often lost in the conversion. Because of this Chi-square values are extracted by finding all statistical references with one degree of freedom that do not follow the symbol "t" or "r". While this does extract most Chi-square values it is possible that other statistics, possibly due to unconventional notation, are also extracted and reported as chi-square values.

Depending on the PDF file the comparison operators can sometimes not be converted correctly, causing these to not be reported in the output. Using html versions of articles and the similar function checkHTMLdir is recommended for more stable results.

Note that the conversion to plain text and extraction of statistics can result in errors. Some statistical values can be missed, especially if the notation is unconventional. It is recommended to manually check some of the results.

Value

A data frame containing for each extracted statistic:

Source	Name of the file of which the statistic is extracted
Statistic	Character indicating the statistic that is extracted
df1	First degree of freedom
df2	Second degree of freedom (if applicable)
Value	Reported value of the statistic
Reported.Comparison	Reported comparison, when importing from pdf this will often not be converted properly
Reported.P.Value	The reported p-value, or NA if the reported value was NS
Computed	The recomputed p-value
Raw	Raw string of the statistical reference that is extracted
InExactError	Error in inexactly reported p values as compared to the recalculated p values
ExactError	Error in exactly reported p values as compared to the recalculated p values
DecisionError	The reported result is significant whereas the recomputed result is not, or vice versa.

Author(s)

Sacha Epskamp <[e-mail]> & Michele B. Nuijten <[e-mail]>

See Also

statcheck, checkPDF, checkHTMLdir, checkHTML, checkdir

Examples

  # with this command a menu will pop up from which you can select the directory with PDF articles


# checkPDFdir()





# you could also specify the directory beforehand


# for instance:


# DIR <- "C:/mydocuments/articles"


# checkPDFdir(DIR)

chartgerink/statcheckTEMP documentation built on May 13, 2019, 3:37 p.m.