diff --git a/DESCRIPTION b/DESCRIPTION index 8029e6d..d712ecc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -47,7 +47,8 @@ Imports: rlang, rmarkdown, stringi, - tcltk + tcltk, + pdftools Suggests: testthat ByteCompile: yes diff --git a/NAMESPACE b/NAMESPACE index 9ea326f..a162b6a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -33,3 +33,8 @@ importFrom(graphics,plot.default) importFrom(graphics,points) importFrom(graphics,text) importFrom(rlang,.data) +importFrom(stringi,stri_enc_toutf32) +importFrom(stringi,stri_enc_fromutf32) +importFrom(stringi,stri_split_lines) +importFrom(stringi,stri_split_regex) +importFrom(pdftools,pdf_text) diff --git a/NEWS.md b/NEWS.md index 9140ae8..42e611a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,13 @@ +# statcheck 1.6.0 + +## Major changes + +## Small updates +* Changed the way pdf files are converted to text. Initially, statcheck relied on the external program Xpdf, which needed to be installed separately and added to the path. To simplify the workflow (and also have improved pdf conversions) statcheck now uses the R package pdftools. +* Updated the test files for testing text-to-file. Before, I hard coded the true values statcheck should extract, but this was error prone. Now, there is a spreadsheet with manually extracted values (the gold standard) that is used as a reference. This is easier to update if necessary; the updates then only need to happen in one place (the spreadsheet) and no longer at multiple places in the code. + +## Bug fixes + # statcheck 1.5.0 ## Major changes diff --git a/R/doc-checkdirs.R b/R/doc-checkdirs.R deleted file mode 100644 index 25c0dd3..0000000 --- a/R/doc-checkdirs.R +++ /dev/null @@ -1,20 +0,0 @@ -#' Extract statistics from folders with PDF/HTML articles and recalculate -#' p-values -#' -#' These functions search for NHST results in all PDF and/or HTML articles in a -#' certain folder and send the extracted statistics to \code{statcheck}. -#' -#' @param dir String indicating the directory to be used. If this is left empty, -#' a window will pop up from which you can choose a directory. -#' @param subdir Logical. Indicates whether you also want to check subfolders. -#' Defaults to TRUE -#' @param extension Logical. Indicates whether the HTML extension should be -#' checked. Defaults to TRUE -#' @param ... Arguments sent to \code{statcheck}. -#' -#' @name checkdirs -#' -#' @return A statcheck data frame with the extracted statistics. See -#' \code{\link{statcheck}} for details. - -NULL \ No newline at end of file diff --git a/R/doc-checkfiles.R b/R/doc-checkfiles.R deleted file mode 100644 index 405e0fb..0000000 --- a/R/doc-checkfiles.R +++ /dev/null @@ -1,14 +0,0 @@ -#' Extract statistics from PDF/HTML articles and recalculate p-values -#' -#' These functions search for NHST results in PDF and/or HTML articles and send -#' the extracted statistics to \code{statcheck}. -#' -#' @param files Vector of strings containing file paths to HTML files to check. -#' @param ... Arguments sent to \code{statcheck}. -#' -#' @name checkfiles -#' -#' @return A statcheck data frame with the extracted statistics. See -#' \code{\link{statcheck}} for details. - -NULL \ No newline at end of file diff --git a/R/file-to-txt.R b/R/file-to-txt.R index df929e0..8e43836 100644 --- a/R/file-to-txt.R +++ b/R/file-to-txt.R @@ -91,27 +91,150 @@ getHTML <- function(x){ # PDF TO TXT ------------------------------------------------------------------- getPDF <- function(x){ - txtfiles <- character(length(x)) - for (i in 1:length(x)){ - - system(paste('pdftotext -q -enc "ASCII7" "', x[i], '"', sep = "")) - if (file.exists(gsub("\\.pdf$", "\\.txt", x[i]))) { - fileName <- gsub("\\.pdf$", "\\.txt", x[i]) - strings <- readChar(fileName, file.info(fileName)$size) - - # remove carriage returns and new lines - strings <- gsub(x = strings, pattern = "[\r\n]", replacement = "") - - # save result in vector - txtfiles[i] <- strings - - } else{ - - warning(paste("Failure in file", x[i])) - txtfiles[i] <- "" - - } - } + txtfiles <- sapply(x, pdftools::pdf_text) + + # encode everything in UTF-32 + # this should ensure the same output accross multiple operating systems + txtfiles <- stringi::stri_enc_toutf32(txtfiles) + + # Replace known weird characters + + # substitute double solidous (UTF-32 Decimal 11005) with equal sign (UTF-32 + # Decimal 61) [issue in APA journals] + txtfiles <- lapply(txtfiles, gsub, pattern = "11005", + replacement = "61", fixed = TRUE) + + # substitute 1/4 (UTF-32 decimal 188) with equal sign (UTF-32 Decimal 61); + # [issue in Elsevier journal: Journal of Environmental Psychology] + txtfiles <- lapply(txtfiles, gsub, pattern = "188", + replacement = "61", fixed = TRUE) + + # substitute U+2B0D (C++ \u2b0d; UTF-32 Decimal 11021) with less than + # sign (UTF-32 Decimal 60) [issue in APA journals] + txtfiles <- lapply(txtfiles, gsub, pattern = "11021", + replacement = "60", fixed = TRUE) + + # substitute ! (UTF-32 decimal 33) with less than sign (UTF-32 Decimal 60); + # [issue in Oxford journal: Journal of Consumer Research] + txtfiles <- lapply(txtfiles, gsub, pattern = "33", + replacement = "60", fixed = TRUE) + + # substitute U+2AFA (UTF-32 Decimal 11002) with HYPHEN-MINUS sign (UTF-32 + # Decimal 45) [issue in APA journals] + txtfiles <- lapply(txtfiles, gsub, pattern = "11002", + replacement = "45", fixed = TRUE) + + # substitute U+2439 (C++ \u2439; UTF-32 Decimal 9273) with small greek chi + # (UTF-32 Decimal 967) [issue in APA journals] + txtfiles <- lapply(txtfiles, gsub, pattern = "9273", + replacement = "967", fixed = TRUE) + + # Revert to UTF-8 encoding + txtfiles <- stringi::stri_enc_fromutf32(txtfiles) + + + # Arrange text according to paper column layout + txtfiles <- pdf_columns(txtfiles) + + # Paste the differente pages together, so that each pdf is converted to + # one string of text + txtfiles <- stringr::str_c(unlist(txtfiles), collapse = "") + + + + # substitute the letter "b" in a NHST result for a "<". This is not feasible + # in utf32 encoding, because making a regex that only substitutes the b in + # a statistical result instead of ALL b's in the paper is very hard in + # utf32 encoding. [issue in Elsevier journal: JESP] + txtfiles <- lapply(txtfiles, gsub, + # don't match a b preceded by =<>, because the b itself + # should be the comparison sign. + # only match a b followed by a number, that gives further + # proof that the b is in fact the comparison sign. + pattern = RGX_B_SMALLER, + replacement = "<", perl = TRUE) + + # substitute the letter "N" in a NHST result for a ">", for the same reason + # as above. [issue in Elsevier journal: JESP] + txtfiles <- lapply(txtfiles, gsub, + # don't match a N preceded by =<>, because the N itself + # should be the comparison sign. + # only match a N followed by a number, that gives further + # proof that the N is in fact the comparison sign. + pattern = RGX_N_LARGER, + replacement = ">", perl = TRUE) + + # substitute the letter "p" that should be a "=". [issue in Oxford journal: + # journal of consumer research] + txtfiles <- lapply(txtfiles, gsub, + # don't match a p preceded by a "," or a ",\\s", because + # that is the actual p-value. + # only match a p followed by a number, that gives further + # proof that the p is in fact the comparison sign. + pattern = RGX_P_EQUAL, + replacement = "=", perl = TRUE) + + # substitute the letter "B" that should be a '"'. [issue in BRM] + txtfiles <- lapply(txtfiles, gsub, + # only match a B followed by a letter that could indicate + # a test statistic + pattern = RGX_B_QUOTE, + replacement = '"', perl = TRUE) + return(txtfiles) } + + +# helper function for getPDF() ------------------------------------------------- + +# This function helps maintaining the format of pdf files with a multiple +# columns layout. +# Credits to: +# https://github.com/fsingletonthorn/EffectSizeScraping/blob/master/R/pdf_process.R +# for original function + +true_false <- function(x, chars) { + x > chars +} + +pdf_columns <- function(x, pattern = "\\p{WHITE_SPACE}{3,}") { + # \p{L} matches a single code point in the category "letter". + # {3,} three or more + + # This function is slightly adapted from pdfsearch + # see: https://github.com/lebebr01/pdfsearch/blob/master/R/split_pdf.r + + x_lines <- stringi::stri_split_lines(x) + x_lines <- lapply(x_lines, gsub, + pattern = "^\\s{1,20}", + # ^ string that starts with + # \ creates regular expression containing following... + # \s matches any whitespace + # {1,20} between 1 and 20 of these [ in your case this will become +] + replacement = "") + + x_page <- lapply( + x_lines, + stringi::stri_split_regex, + pattern = pattern, + omit_empty = NA, + simplify = TRUE + ) + + page_lines <- unlist(lapply(x_page, nrow)) + columns <- unlist(lapply(x_page, ncol)) + + num_chars <- lapply(x_page, base::nchar) + num_chars_tf <- lapply(num_chars, true_false, chars = 3) + + for (xx in seq_along(num_chars_tf)) { + num_chars_tf[[xx]][is.na(num_chars_tf[[xx]])] <- FALSE + } + + output <- lapply(seq_along(x_page), function(xx) + x_page[[xx]][num_chars_tf[[xx]]]) + + output <- lapply(output, paste, collapse = " ") + return(output) +} \ No newline at end of file diff --git a/R/helper-load-manual-reference.R b/R/helper-load-manual-reference.R new file mode 100644 index 0000000..5c5d2c4 --- /dev/null +++ b/R/helper-load-manual-reference.R @@ -0,0 +1,41 @@ +# this script contains a helper function for the unit tests to load the +# manual reference file and select relevant rows to compare statcheck output to + + +load_manual <- function( + path_manual, # path to the reference file + apa = TRUE, # only consider apa reported stats + pdf_conversion_issues = FALSE, # exclude cases where pdf conversion led to weird characters + typesetting_issues = FALSE, # exclude cases where typesetting issues led to weird situations + file_type = c("all", "pdf", "html"), # select specific file types + file_id = NULL # select specific files based on file_id variable +){ + + # load the reference file with manually extracted statistics + manual <- read.csv2(system.file(path_manual, package = "statcheck"), header = TRUE) + + # row selection based on arguments + if(apa == TRUE){ + manual <- manual[manual$extract_apa == 1, ] + } + + if(pdf_conversion_issues == FALSE){ + manual <- manual[manual$pdf_conversion_issues == 0, ] + } + + if(typesetting_issues == FALSE){ + manual <- manual[manual$typesetting_issues == 0, ] + } + + if(file_type[1] == "pdf"){ + manual <- manual[manual$file_type == "pdf", ] + } else if(file_type[1] == "html") { + manual <- manual[manual$file_type == "pdf", ] + } + + if(!is.null(file_id)){ + manual <- manual[manual$file_id == file_id, ] + } + + return(manual) +} \ No newline at end of file diff --git a/R/regex.R b/R/regex.R index 0a7d202..50c9836 100644 --- a/R/regex.R +++ b/R/regex.R @@ -96,4 +96,24 @@ RGX_WEIRD_MINUS <- "\\s?[^\\d\\.\\s]+(?=\\d|\\.)" # F-tests and when df1 == 1, it gets typeset as the letter l or I RGX_DF1_I_L <- "I|l" +################################################################################ +###################### REGEXES FOR WEIRD PDF ENCODING ########################## +################################################################################ + +# in some JESP articles, a < is translated with a b +# this regex is used in file-to-txt.R to replace it +RGX_B_SMALLER <- "(?])b(?=\\s?-?\\s?\\.?\\d)" + +# in some JESP articles, a > is translated with a N +# this regex is used in file-to-txt.R to replace it +RGX_N_LARGER <- "(?])N(?=\\s?-?\\s?\\.?\\d)" + +# in the journal of consumer research, a = is translated with a p +# this regex is used in file-to-txt.R to replace it +RGX_P_EQUAL <- "(? .5;620;z;;;"""=""";0.17;""">""";0.5;;;;;;1;0;0; 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+mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.04, t(124.78) = -1.34, p = .182;436;t;;124.78;"""=""";-1.34;"""=""";0.182;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -1.24, t(229.88) = -1.41, p = .160;436;t;;229.88;"""=""";-1.41;"""=""";0.16;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -1.11, t(94.95) = -0.84, p = .189;436;t;;94.95;"""=""";-0.84;"""=""";0.189;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = 1.35, t(270.63) = 1.63, p =  .104;436;t;;270.63;"""=""";1.63;"""=""";0.104;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = 0.02, t(142.71) = 0.01, p = .990;436;t;;142.71;"""=""";0.01;"""=""";0.99;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -2.19, t(236.50) = -4.87, p < .001;436;t;;236.5;"""=""";-4.87;"""<""";0.001;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;"B = -0.36, t(260.52) = 2.27, p = .024 + +";437;t;;260.52;"""=""";2.27;"""=""";0.024;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.18, t(112.01) = -2.03, p = .045;437;t;;112.01;"""=""";-2.03;"""=""";0.045;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.66, t(188.83) = 2.90, p = .004;437;t;;188.83;"""=""";2.9;"""=""";0.004;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.12, t(253.82) = -1.63, p = .104;437;t;;253.82;"""=""";-1.63;"""=""";0.104;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = 0.06, t(235.65) = 1.08, p = .280;437;t;;235.65;"""=""";1.08;"""=""";0.28;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.05, t(124.76) = -1.40, p = .165;437;t;;124.76;"""=""";-1.4;"""=""";0.165;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -1.17, t(94.73) = -1.39, p = .169;437;t;;94.73;"""=""";-1.39;"""=""";0.169;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = 0.09, t(143.00) = 0.07, p = .948;437;t;;143;"""=""";0.07;"""=""";0.948;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = 1.53, t(269.88) = 1.86, p = .064;437;t;;269.88;"""=""";1.86;"""=""";0.064;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.95, t(234.28) = -1.09, p = .277;437;t;;234.28;"""=""";-1.09;"""=""";0.277;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -1.79, t(235.11) = -4.09, p < .001;437;t;;235.11;"""=""";-4.09;"""<""";0.001;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.37, t(263.15) = -2.30, p = .022;437;t;;263.15;"""=""";-2.3;"""=""";0.022;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.05, t(184.83) = -0.38, p = .703;437;t;;184.83;"""=""";-0.38;"""=""";0.703;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = 0.11, t(182.26) = 0.79, p = .432;437;t;;182.26;"""=""";0.79;"""=""";0.432;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = 0.12, t(185.73) = 1.97, p = .050;437;t;;185.73;"""=""";1.97;"""=""";0.05;;;;;;1;1;0; +mausbach_pdf;mausbach;mausbach.pdf;pdf;10.1037/a0027783;zzzY;Health Psychology;2012;ME;B = -0.57, t(186.24) = 2.41, p = .017;437;t;;186.24;"""=""";2.41;"""=""";0.017;;;;;;1;1;0; +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;t(37) = -4.93, p < .001;1206;t;;37;"""=""";-4.93;"""<""";0.001;0;0;0;0;0;1;0;0; +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;B2(1, N = 226) = 6.90, p <.01;1206;Chi2;1;;"""=""";6.9;"""<""";0.01;0;0;0;0;0;1;0;0; +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;BF(2, 70) = 4.48, MSE = 6.61, p <.02^) ;1206;F;2;70;"""=""";4.48;"""<""";0.02;0;0;0;0;0;0;0;0; +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"BF(1, 15) = 19.9 and +5.16, p <.001 and p <.05";1207;;1;15;"""=""";19.9;"""<""";0.001;0;0;0;0;0;0;0;0;two results combined in a sentence +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"BF(1, 15) = 19.9 and +5.16, p <.001 and p <.05";1207;F;1;15;"""=""";5.16;"""<""";0.05;0;0;0;0;0;0;0;0;two results combined in a sentence +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;t(28) = 2.0, p<.05;1207;t;;28;"""=""";2;"""<""";0.05;0;0;0;0;0;1;0;0; +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"F(2, 70) = 4.48, +MSE = 6.61, p <.02";1207;F;2;70;"""=""";4.48;"""<""";0.02;0;0;0;0;0;0;0;1;table not scraped in html +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"BF(2,56) = 1.203, +p < .001^";1214;F;2;56;"""=""";1.203;"""<""";0.001;1;1;0;1;1;1;0;0; +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;BF(2,56) = 12.03, p < .001^;1214;F;2;56;"""=""";12.03;"""<""";0.001;0;0;0;0;0;1;0;0; +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"F(l, 76) += 23.95, p <.001;";1220;F;1;76;"""=""";23.95;"""<""";0.001;0;0;0;0;0;0;0;0;"tables not scraped; df1 wrongly printed as letter l instead of 1; statcheck accepts this" +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;G2(1) = 6.53, p =.011;1220;Chi2;1;;"""=""";6.53;"""=""";0.011;0;0;0;0;0;1;0;1;table not scraped in html +nuijten_html;nuijten;nuijten.html;html;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;t(14) = 2.0, p <.03;1221;t;;14;"""=""";2;"""<""";0.03;1;1;1;0;0;1;0;0;footnote +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;t(37) = -4.93, p < .001;1206;t;;37;"""=""";-4.93;"""<""";0.001;0;0;0;0;0;1;0;0; +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;B2(1, N = 226) = 6.90, p <.01;1206;Chi2;1;;"""=""";6.9;"""<""";0.01;0;0;0;0;0;1;0;0; +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"BF(2, + + Behav Res (2016) 48:1205-1226 + +70) = 4.48, MSE = 6.61, p <.02^) ";1206;F;2;70;"""=""";4.48;"""<""";0.02;0;0;0;0;0;0;0;1;spanning two pages (header in between) +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"BF(1, 15) = 19.9 and +5.16, p <.001 and p <.05";1207;;1;15;"""=""";19.9;"""<""";0.001;0;0;0;0;0;0;0;0;two results combined in a sentence +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"BF(1, 15) = 19.9 and +5.16, p <.001 and p <.05";1207;F;1;15;"""=""";5.16;"""<""";0.05;0;0;0;0;0;0;0;0;two results combined in a sentence +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;t(28) = 2.0, p<.05;1207;t;;28;"""=""";2;"""<""";0.05;0;0;0;0;0;1;0;0; +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"F(2, 70) = 4.48, +MSE = 6.61, p <.02";1207;F;2;70;"""=""";4.48;"""<""";0.02;0;0;0;0;0;0;0;0; +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"BF(2,56) = 1.203, +p < .001^";1214;F;2;56;"""=""";1.203;"""<""";0.001;1;1;0;1;1;1;0;0; +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;BF(2,56) = 12.03, p < .001^;1214;F;2;56;"""=""";12.03;"""<""";0.001;0;0;0;0;0;1;0;0; +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;"F(l, 76) += 23.95, p <.001;";1220;F;1;76;"""=""";23.95;"""<""";0.001;0;0;0;0;0;1;0;0;"df1 wrongly printed as letter l instead of 1; statcheck accepts this" +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;G2(1) = 6.53, p =.011;1220;Chi2;1;;"""=""";6.53;"""=""";0.011;0;0;0;0;0;1;0;0; +nuijten_pdf;nuijten;nuijten.pdf;pdf;10.3758/s13428-015-0664-2;;Behavior Research Methods;2016;MN;t(14) = 2.0, p <.03;1221;t;;14;"""=""";2;"""<""";0.03;1;1;1;0;0;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"t +(28.30) = 1.14, p > .25";;t;;28.3;"""=""";1.14;""">""";0.25;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"F = 6.74, +p = .013)";;F;;;"""=""";6.74;"""=""";0.013;;;;;;0;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"t +(22.25) = 11.69, p < .001";;t;;22.25;"""=""";11.69;"""<""";0.001;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;F = 10.98, p = .002;;F;;;"""=""";10.98;"""=""";0.002;;;;;;0;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"F +(1, 35) = 5.63, p = .02";;F;1;35;"""=""";5.63;"""=""";0.02;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"t +(18) = 2.80, p = .006";;t;;18;"""=""";2.8;"""=""";0.006;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;t(19) = 0.0, p > .25.;;t;;19;"""=""";0;""">""";0.25;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;r(17) = .07, p > .25;;r;;17;"""=""";0.07;""">""";0.25;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"r +(18) = .02, p > .25.";;r;;18;"""=""";0.02;""">""";0.25;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"t +(24) = 0.12, p > .25.";;t;;24;"""=""";0.12;""">""";0.25;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"F(1, +36) = 4.03, p = .05";;F;1;36;"""=""";4.03;"""=""";0.05;;;;;;1;0;1;problem with rearranging columns: there is a lot of whitespace before the next column +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;t(19) = 3.66, p < .001;;t;;19;"""=""";3.66;"""<""";0.001;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;t(19) = 0.36, p > .25;;t;;19;"""=""";0.36;""">""";0.25;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;t(32) = 0.32, p > .25.;;t;;32;"""=""";0.32;""">""";0.25;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;"t +(38) = 1.73, p = .09.";;t;;38;"""=""";1.73;"""=""";0.09;;;;;;1;0;0; +sandoval_pdf;sandoval;sandoval.pdf;pdf;10.1111/cdev.12723;;Child Development;2017;MN;F(1, 35) = 14.04, p = .001,;;F;1;35;"""=""";14.04;"""=""";0.001;;;;;;1;0;0; +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;?2 (14, N= 1008)= 11.91, p= .61;40;Chi2;14;;"""=""";11.91;"""=""";0.61;;;;;;1;0;0; +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;?2 (1, N= 510)= .20, p= .65;40;Chi2;1;;"""=""";0.2;"""=""";0.65;;;;;;1;0;0; +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;F(2, 726)=7.20, pb.001;40;F;2;726;"""=""";7.2;"""<""";0.001;;;;;;1;1;0;"""<"" copied as b" +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;F(1, 726)=6.33, p=.01;40;F;1;726;"""=""";6.33;"""=""";0.01;;;;;;1;0;0; +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;F(1, 726)=12.39, pb.001;40;F;1;726;"""=""";12.39;"""<""";0.001;;;;;;1;0;0; +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;F(1, 726)=.75, p=.39;40;F;1;726;"""=""";0.75;"""=""";0.39;;;;;;1;0;0; +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;F(7, 726)=4.24, pb.001;40;F;7;726;"""=""";4.24;"""<""";0.001;;;;;;1;1;0;"""<"" copied as b" +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;F(14, 726)=1.35, p=.18;40;F;14;726;"""=""";1.35;"""=""";0.18;;;;;;1;0;0; +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;Fs(1, 248)b1.16, psN.28;40;F;1;248;"""<""";1.16;""">""";0.28;;;;;;0;1;0;plural F and p +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;F(1, 87)= 78.77, pb.001;41;F;1;87;"""=""";78.77;"""<""";0.001;;;;;;1;1;0;"""<"" copied as b" +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;t(44)= 14.73, pb.001;41;t;;44;"""=""";14.73;"""<""";0.001;;;;;;1;1;0;"""<"" copied as b" +todd_pdf;todd;Todd_JournExpSocPsych_2011_PXz;pdf;10.1016/j.jesp.2010.08.00;PXz;Journal of Experimental Social Psychology;2011;MS;?2 (39, N=1441)=46.17, p=.20;41;Chi2;39;;"""=""";46.17;"""=""";0.2;;;;;;1;0;0; 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+zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;F(1, 82) p 10.52, p ! .01;650;F;1;82;"""=""";10.52;"""<""";0.01;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;F(1, 82) p 4.14, p ! .05;650;F;1;82;"""=""";4.14;"""<""";0.05;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;F(1, 82) p 6.29, p p .01;650;F;1;82;"""=""";6.29;"""=""";0.01;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;b p .32, t(43) p 2.18, p ! .05;650;t;;43;"""=""";-2.18;"""<""";0.05;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;b p 1.27, t(43) p  3.01, p ! .01;650;t;;43;"""=""";-3.01;"""<""";0.01;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;b p .52, t(43) p 4.00, p ! .01;650;t;;43;"""=""";4;"""<""";0.01;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;p .12, t(42) p .83, NS;650;t;;42;"""=""";-0.83;ns;;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;b p .47, t(42) p 3.28, p ! .01;650;t;;42;"""=""";3.28;"""<""";0.01;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;b p .30, t(43) p 2.04, p ! .05;650;t;;43;"""=""";2.04;"""<""";0.05;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;b p .37, t(43) p 2.57, p ! .05;650;t;;43;"""=""";2.57;"""<""";0.05;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;b p .43, t(43) p 3.16, p ! .01;650;t;;43;"""=""";3.16;"""<""";0.01;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;b p .16, t(42) p 1.09, NS;650;t;;42;"""=""";1.09;ns;;;;;;;1;1;0; +zhang_pdf;zhang;Zhang_JournConsRes_2010_egKl;pdf;10.1086/655417;egKl;Journal of Consumer Research;2010;MS;p . 38, t(42) p 2.55, p ! .05;650;t;;42;"""=""";2.55;"""<""";0.05;;;;;;1;1;0; diff --git a/inst/test_materials/test_dir/Paper1.htm b/inst/test_materials/test_dir/Paper1.htm new file mode 100644 index 0000000..739f076 --- /dev/null +++ b/inst/test_materials/test_dir/Paper1.htm @@ -0,0 +1,61 @@ + + + + + + + + + + + +
+ +

Test paper to demonstrate statcheck web +app.

+ +

All tests are one-tailed.

+ +

Qb(1) = 3.78, p < .05

+ +

t(37) = -4.93, p <.001

+ +

Z = 1.54, p = .14

+ +

F(2,56) = 1.203, p < .001

+ +

 

+ +
+ + + + diff --git a/inst/test_materials/test_dir/Paper1.pdf b/inst/test_materials/test_dir/Paper1.pdf new file mode 100644 index 0000000..5cdaef1 Binary files /dev/null and b/inst/test_materials/test_dir/Paper1.pdf differ diff --git a/inst/test_materials/test_dir/Paper2.htm b/inst/test_materials/test_dir/Paper2.htm new file mode 100644 index 0000000..279b5ef --- /dev/null +++ b/inst/test_materials/test_dir/Paper2.htm @@ -0,0 +1,52 @@ + + + + + + + + + + + +
+ +

Test paper 2.

+ +

This paper does not contain statistical results.

+ +

 

+ +
+ + + + diff --git a/inst/test_materials/test_dir/Paper2.pdf b/inst/test_materials/test_dir/Paper2.pdf new file mode 100644 index 0000000..1805db8 Binary files /dev/null and b/inst/test_materials/test_dir/Paper2.pdf differ diff --git a/inst/test_materials/test_dir/Paper3.htm b/inst/test_materials/test_dir/Paper3.htm new file mode 100644 index 0000000..10408b9 --- /dev/null +++ b/inst/test_materials/test_dir/Paper3.htm @@ -0,0 +1,63 @@ + + + + + + + + + + + +
+ +

Test paper to demonstrate statcheck web +app.

+ +

All tests are one-tailed.

+ +

 

+ +

t(37) = -4.93, p <.001;

+ +

F(2, 56) = 1.203, p < .001;

+ +

Q(1) = 6.9, p < .01;

+ +

r(46) = .34, p = .03

+ +

 

+ +
+ + + + diff --git a/inst/test_materials/test_dir/Paper3.pdf b/inst/test_materials/test_dir/Paper3.pdf new file mode 100644 index 0000000..61ca2c3 Binary files /dev/null and b/inst/test_materials/test_dir/Paper3.pdf differ diff --git a/inst/test_materials/test_dir/Paper4_multiplepages.htm b/inst/test_materials/test_dir/Paper4_multiplepages.htm new file mode 100644 index 0000000..0341897 --- /dev/null +++ b/inst/test_materials/test_dir/Paper4_multiplepages.htm @@ -0,0 +1,67 @@ + + + + + + + + + + + +
+ +

Test paper to demonstrate statcheck web +app.

+ +

All tests are one-tailed.

+ +

 

+ +

t(37) = -4.93, p <.001;

+ +

Z = 1.54, p = .14;

+ +


+
+

+ +

 

+ +

F(2,56) = 1.203, p < .001

+ +

 

+ +
+ + + + diff --git a/inst/test_materials/test_dir/Paper4_multiplepages.pdf b/inst/test_materials/test_dir/Paper4_multiplepages.pdf new file mode 100644 index 0000000..58b2a2d Binary files /dev/null and b/inst/test_materials/test_dir/Paper4_multiplepages.pdf differ diff --git a/inst/test_materials/test_dir/manually_extracted_stats_testpapers.csv b/inst/test_materials/test_dir/manually_extracted_stats_testpapers.csv new file mode 100644 index 0000000..f8e7d43 --- /dev/null +++ b/inst/test_materials/test_dir/manually_extracted_stats_testpapers.csv @@ -0,0 +1,23 @@ +paper_id;file_name;file_type;doi;paper_id_SCORE_project;journal;year;coder_initials;raw_result;page;test_type;df1;df2;test_comparison;test_value;p_comparison;p;error;decision_error;one_tailed;error_1tail;decision_error_1tail;extract_apa;pdf_conversion_issues;typesetting_issues;remarks +paper1_html;Paper1.htm;html;;;;;MN;Qb(1) = 3.78, p < .05;;Qb;1;;"""=""";3.78;"""<""";0.05;1;1;1;1;1;1;0;0; +paper1_html;Paper1.htm;html;;;;;MN;"t(37) = -4.93, p <.001;";;t;;37;"""=""";-4.93;"""<""";0.001;0;0;1;0;0;1;0;0; +paper1_html;Paper1.htm;html;;;;;MN;"Z = 1.54, p = .14;";;Z;;;"""=""";1.54;"""=""";0.14;1;0;1;1;0;1;0;0; +paper1_html;Paper1.htm;html;;;;;MN;F(2,56) = 1.203, p < .001;;F;2;56;"""=""";1.203;"""<""";0.001;1;1;1;1;1;1;0;0; +paper1_pdf;Paper1.pdf;pdf;;;;;MN;Qb(1) = 3.78, p < .05;;Qb;1;;"""=""";3.78;"""<""";0.05;1;1;1;1;1;1;0;0; +paper1_pdf;Paper1.pdf;pdf;;;;;MN;"t(37) = -4.93, p <.001;";;t;;37;"""=""";-4.93;"""<""";0.001;0;0;1;0;0;1;0;0; +paper1_pdf;Paper1.pdf;pdf;;;;;MN;"Z = 1.54, p = .14;";;Z;;;"""=""";1.54;"""=""";0.14;1;0;1;1;0;1;0;0; +paper1_pdf;Paper1.pdf;pdf;;;;;MN;F(2,56) = 1.203, p < .001;;F;2;56;"""=""";1.203;"""<""";0.001;1;1;1;1;1;1;0;0; +paper3_html;Paper3.htm;html;;;;;MN;"t(37) = -4.93, p <.001;";;t;;37;"""=""";-4.93;"""<""";0.001;0;0;1;0;0;1;0;0; +paper3_html;Paper3.htm;html;;;;;MN;"F(2, 56) = 1.203, p < .001;";;F;2;56;"""=""";1.203;"""<""";0.001;1;1;1;1;1;1;0;0; +paper3_html;Paper3.htm;html;;;;;MN;"Q(1) = 6.9, p < .01;";;Q;1;;"""=""";6.9;"""<""";0.01;0;0;1;0;0;1;0;0; +paper3_html;Paper3.htm;html;;;;;MN;r(46) = .34, p = .03;;r;;46;"""=""";0.34;"""=""";0.03;1;0;1;1;0;1;0;0; +paper3_pdf;Paper3.pdf;pdf;;;;;MN;"t(37) = -4.93, p <.001;";;t;;37;"""=""";-4.93;"""<""";0.001;0;0;1;0;0;1;0;0; +paper3_pdf;Paper3.pdf;pdf;;;;;MN;"F(2, 56) = 1.203, p < .001;";;F;2;56;"""=""";1.203;"""<""";0.001;1;1;1;1;1;1;0;0; +paper3_pdf;Paper3.pdf;pdf;;;;;MN;"Q(1) = 6.9, p < .01;";;Q;1;;"""=""";6.9;"""<""";0.01;0;0;1;0;0;1;0;0; +paper3_pdf;Paper3.pdf;pdf;;;;;MN;r(46) = .34, p = .03;;r;;46;"""=""";0.34;"""=""";0.03;1;0;1;1;0;1;0;0; +paper4_html;Paper4_multiplepages.html;html;;;;;MN;"t(37) = -4.93, p <.001;";;t;;37;"""=""";-4.93;"""<""";0.001;0;0;1;0;0;1;0;0; +paper4_html;Paper4_multiplepages.html;html;;;;;MN;"Z = 1.54, p = .14;";;Z;;;"""=""";1.54;"""=""";0.14;1;0;1;1;0;1;0;0; +paper4_html;Paper4_multiplepages.html;html;;;;;MN;F(2,56) = 1.203, p < .001;;F;2;56;"""=""";1.203;"""<""";0.001;1;1;1;1;1;1;0;0; +paper4_pdf;Paper4_multiplepages.pdf;pdf;;;;;MN;"t(37) = -4.93, p <.001;";;t;;37;"""=""";-4.93;"""<""";0.001;0;0;1;0;0;1;0;0; +paper4_pdf;Paper4_multiplepages.pdf;pdf;;;;;MN;"Z = 1.54, p = .14;";;Z;;;"""=""";1.54;"""=""";0.14;1;0;1;1;0;1;0;0; +paper4_pdf;Paper4_multiplepages.pdf;pdf;;;;;MN;F(2,56) = 1.203, p < .001;;F;2;56;"""=""";1.203;"""<""";0.001;1;1;1;1;1;1;0;0; diff --git a/inst/test_materials/test_dir/manually_extracted_stats_testpapers.xlsx b/inst/test_materials/test_dir/manually_extracted_stats_testpapers.xlsx new file mode 100644 index 0000000..a6a867f Binary files /dev/null and b/inst/test_materials/test_dir/manually_extracted_stats_testpapers.xlsx differ diff --git a/tests/testthat/test-file-to-txt.R b/tests/testthat/test-file-to-txt.R index b596f56..eeb5851 100644 --- a/tests/testthat/test-file-to-txt.R +++ b/tests/testthat/test-file-to-txt.R @@ -3,110 +3,162 @@ context("Check if statistics from an article are correctly retrieved and parsed" # tests concerning parsing stats from pdf files ------------------------------ # individual pdf files -test_that("statistics from a pdf are correctly retrieved and parsed", { +# pdftools +test_that("pdftools correctly retrieves and parses statistics from a pdf", { + # load the pdf file of Nuijten et al. 2016 + # https://doi.org/10.3758/s13428-015-0664-2 pdf_file <- system.file("test_materials/nuijten.pdf", package = "statcheck") # skip test if file is not available if(pdf_file == "") skip("Test file not available.") + # load the reference file with manually extracted statistics + # load_manual is a helper function written for this package + manual <- load_manual(path_manual = "test_materials/manually_extracted_stats.csv", + file_id = "nuijten_pdf", apa = TRUE, typesetting_issues = FALSE) + result <- checkPDF(pdf_file, messages = FALSE) - result_1tailed <- checkPDF(pdf_file, messages = FALSE, OneTailedTxt = TRUE) + result_1tailed <- checkPDF(pdf_file, messages = FALSE, + OneTailedTxt = TRUE) - # extract 4 tests from paper - expect_equal(nrow(result), 8) - expect_equal(as.character(result[[VAR_TYPE]]), c("t", "Chi2", "t", "F", - "F", "F", "Chi2", "t")) - expect_equal(result[[VAR_TEST_VALUE]], c(-4.93, 6.9, 2, 1.203, - 12.03, 23.95, 6.53, 2)) + # extract 7 tests from paper + expect_equal(nrow(result), + nrow(manual)) + expect_equal(as.character(result[[VAR_TYPE]]), + manual$test_type) + expect_equal(as.character(result[[VAR_TEST_VALUE]]), + manual$test_value) # check errors - expect_equal(result[[VAR_ERROR]], c(FALSE, FALSE, FALSE, TRUE, - FALSE, FALSE, FALSE, TRUE)) - expect_equal(result[[VAR_DEC_ERROR]], c(FALSE, FALSE, FALSE, TRUE, - FALSE, FALSE, FALSE, TRUE)) + expect_equal(as.numeric(result[[VAR_ERROR]]), + manual$error) + expect_equal(as.numeric(result[[VAR_DEC_ERROR]]), + manual$decision_error) # check errors with one-tailed test detection - expect_equal(result_1tailed[[VAR_ERROR]], c(FALSE, FALSE, FALSE, TRUE, - FALSE, FALSE, FALSE, FALSE)) - expect_equal(result_1tailed[[VAR_DEC_ERROR]], c(FALSE, FALSE, FALSE, TRUE, - FALSE, FALSE, FALSE, FALSE)) + expect_equal(as.numeric(result_1tailed[[VAR_ERROR]]), + manual$error_1tail) + expect_equal(as.numeric(result_1tailed[[VAR_DEC_ERROR]]), + manual$decision_error_1tail) + }) # pdfs in folder -test_that("statistics from all pdfs in a folder are correctly retrieved and parsed", { +test_that("stats from all pdfs in a folder are correctly retrieved & parsed", { - pdf_folder <- system.file("test_materials", package = "statcheck") + # this folder contains 4 "fake" pdf papers and 3 "fake" html/htm papers + # one of the pdf papers doesn't contain any stats + pdf_dir <- system.file("test_materials/test_dir", package = "statcheck") # skip test if files are not available - if(!any(grepl(".pdf", list.files(pdf_folder)))) skip("Test files not available.") + if(!any(grepl(".pdf", list.files(pdf_dir)))) skip("Test files not available.") - result <- checkPDFdir(pdf_folder, messages = FALSE, subdir = FALSE) + # load the reference file with manually extracted statistics + manual <- + load_manual(path_manual = "test_materials/test_dir/manually_extracted_stats_testpapers.csv", + apa = TRUE, file_type = "pdf") - # extract 53 tests from 4 papers - expect_equal(nrow(result), 53) - expect_equal(length(unique(result[[VAR_SOURCE]])), 4) + result <- checkPDFdir(pdf_dir, messages = FALSE, subdir = FALSE) + + # extract 11 tests from 3 papers + expect_equal(nrow(result), + nrow(manual)) + expect_equal(length(unique(result[[VAR_SOURCE]])), + length(unique(manual$paper_id))) }) + # tests concerning parsing stats from html files ------------------------------ # individual html files test_that("statistics from a html are correctly retrieved and parsed", { html_file <- system.file("test_materials/nuijten.html", - package = "statcheck") + package = "statcheck") # skip test if file is not available if(html_file == "") skip("Test file not available.") - + + # load the reference file with manually extracted statistics + manual <- load_manual(path_manual = "test_materials/manually_extracted_stats.csv", + file_id = "nuijten_html", apa = TRUE, typesetting_issues = FALSE) + result <- checkHTML(html_file, messages = FALSE) result_1tailed <- checkHTML(html_file, messages = FALSE, OneTailedTxt = TRUE) # extract 6 tests from paper - expect_equal(nrow(result), 6) - expect_equal(as.character(result[[VAR_TYPE]]), c("t", "Chi2", "t", "F", "F", "t")) - expect_equal(result[[VAR_TEST_VALUE]], c(-4.93, 6.9, 2, 1.203, 12.03, 2)) + expect_equal(nrow(result), + nrow(manual)) + expect_equal(as.character(result[[VAR_TYPE]]), + manual$test_type) + expect_equal(as.character(result[[VAR_TEST_VALUE]]), + manual$test_value) # check errors - expect_equal(result[[VAR_ERROR]], c(FALSE, FALSE, FALSE, TRUE, FALSE, TRUE)) - expect_equal(result[[VAR_DEC_ERROR]], c(FALSE, FALSE, FALSE, TRUE, FALSE, TRUE)) + expect_equal(as.numeric(result[[VAR_ERROR]]), + manual$error) + expect_equal(as.numeric(result[[VAR_DEC_ERROR]]), + manual$decision_error) # check errors with one-tailed test detection - expect_equal(result_1tailed[[VAR_ERROR]], c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE)) - expect_equal(result_1tailed[[VAR_DEC_ERROR]], c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE)) + expect_equal(as.numeric(result_1tailed[[VAR_ERROR]]), + manual$error_1tail) + expect_equal(as.numeric(result_1tailed[[VAR_DEC_ERROR]]), + manual$decision_error_1tail) }) # htmls in folder -test_that("statistics from all htmls in a folder are correctly retrieved and parsed", { +test_that("stats from all htmls in a folder are correctly retrieved & parsed", { - html_dir <- system.file("test_materials", package = "statcheck") + # this folder contains 4 "fake" pdf papers and 3 "fake" html/htm papers + # one of the pdf papers doesn't contain any stats + html_dir <- system.file("test_materials/test_dir", package = "statcheck") # skip test if files are not available if(!any(grepl(".htm*", list.files(html_dir)))) skip("Test files not available.") + # load the reference file with manually extracted statistics + manual <- + load_manual(path_manual = "test_materials/test_dir/manually_extracted_stats_testpapers.csv", + apa = TRUE, file_type = "html") + result <- checkHTMLdir(html_dir, messages = FALSE, subdir = FALSE) - # extract 6+33 tests from papers - expect_equal(nrow(result), 39) + # extract 11 tests from 3 papers + expect_equal(nrow(result), + nrow(manual)) + expect_equal(length(unique(result[[VAR_SOURCE]])), + length(unique(manual$paper_id))) }) # tests concerning parsing stats from all files ------------------------------ # pdfs and htmls in folder -test_that("statistics from all pdfs and htmls in a folder are correctly retrieved and parsed", { - - dir <- system.file("test_materials", package = "statcheck") - - # skip test if files are not available - if(!any(grepl(".htm*|.pdf", list.files(dir)))) skip("Test files not available.") - - result <- checkdir(dir, subdir = FALSE, messages = FALSE) - - # extract 92 tests (39 from html and 53 from pdf) - expect_equal(nrow(result), 92) -}) +test_that("stats from all pdfs and htmls in a folder are correctly retrieved + & parsed", { + + dir <- system.file("test_materials/test_dir", package = "statcheck") + + # skip test if files are not available + if(!any(grepl(".htm*|.pdf", list.files(dir)))) skip("Test files not available.") + + # load the reference file with manually extracted statistics + manual <- + load_manual(path_manual = "test_materials/test_dir/manually_extracted_stats_testpapers.csv", + apa = TRUE, file_type = "all") + + result <- checkdir(dir, subdir = FALSE, messages = FALSE) + + # extract 2*11 tests from 2*3 papers + # extract 11 tests from 3 papers + expect_equal(nrow(result), + nrow(manual)) + expect_equal(length(unique(result[[VAR_SOURCE]])), + length(unique(manual$paper_id))) + })