/
statcheck.R
1411 lines (1161 loc) · 50.2 KB
/
statcheck.R
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statcheck <-
function(
x,
stat = c("t", "F", "cor", "chisq", "Z", "Q"),
OneTailedTests = FALSE,
alpha = .05,
pEqualAlphaSig = TRUE,
pZeroError = TRUE,
OneTailedTxt = FALSE,
AllPValues = FALSE
) {
# Create empty data frame for main result:
Res <-
data.frame(
Source = NULL,
Statistic = NULL,
df1 = NULL,
df2 = NULL,
Test.Comparison = NULL,
Value = NULL,
Reported.Comparison = NULL,
Reported.P.Value = NULL,
Computed = NULL,
Error = NULL,
DecisionError = NULL,
CopyPaste = NULL,
Location = NULL,
stringsAsFactors = FALSE,
dec = NULL,
testdec = NULL,
OneTail = NULL,
OneTailedInTxt = NULL,
APAfactor = NULL
)
class(Res) <- c("statcheck", "data.frame")
OneTailedInTxt <- NULL
# Create empty data frame for p values:
pRes <- data.frame(
Source = NULL,
Statistic = NULL,
Reported.Comparison = NULL,
Reported.P.Value = NULL,
Raw = NULL,
stringsAsFactors = FALSE
)
if (length(x) == 0)
return(Res)
if (is.null(names(x)))
names(x) <- 1:length(x)
message("Extracting statistics...")
pb <- txtProgressBar(max = length(x), style = 3)
for (i in 1:length(x)) {
txt <- x[i]
#---------------------------
# extract all p values in order to calculate the ratio (statcheck results)/(total # of p values)
# p-values
# Get location of p-values in text:
pLoc <-
gregexpr("([^a-z]ns)|(p\\s?[<>=]\\s?\\d?\\.\\d+e?-?\\d*)",
txt,
ignore.case = TRUE)[[1]]
if (pLoc[1] != -1) {
# Get raw text of p-values:
pRaw <-
substring(txt, pLoc, pLoc + attr(pLoc, "match.length") - 1)
nums <-
gregexpr("(\\d*\\.?\\d+\\s?e?-?\\d*)|ns", pRaw, ignore.case = TRUE)
# Extract p-values
suppressWarnings(pValsChar <-
substring(
pRaw,
sapply(nums, '[', 1),
sapply(nums, function(x)
x[1] + attr(x, "match.length")[1] - 1)
))
suppressWarnings(pVals <- as.numeric(pValsChar))
# Extract (in)equality
eqLoc <- gregexpr("p\\s?.?", pRaw)
pEq <- substring(
pRaw,
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
pEq[grepl("ns", pRaw, ignore.case = TRUE)] <- "ns"
pvalues <- data.frame(
Source = names(x)[i],
Statistic = "p",
Reported.Comparison = pEq,
Reported.P.Value = pVals,
Raw = pRaw,
stringsAsFactors = FALSE
)
# remove p values greater than one
pvalues <-
pvalues[pvalues$Reported.P.Value <= 1 |
is.na(pvalues$Reported.P.Value), ]
pRes <- rbind(pRes, pvalues)
rm(pvalues)
}
#---------------------------
# search for "one-sided"/"one-tailed"/"directional" in full text to detect one-sided testing
# onesided <- gregexpr("sided|tailed|directional",txt,ignore.case=TRUE)[[1]]
onesided <-
gregexpr("one.?sided|one.?tailed|directional", txt, ignore.case = TRUE)[[1]]
if (onesided[1] != -1) {
onesided <- 1
} else {
onesided <- 0
}
OneTailedInTxt <- as.logical(onesided)
#---------------------------
# t-values:
if ("t" %in% stat) {
# Get location of t-values in text:
tLoc <-
gregexpr(
"t\\s?\\(\\s?\\d*\\.?\\d+\\s?\\)\\s?[<>=]\\s?[^a-z\\d]{0,3}\\s?\\d*,?\\d*\\.?\\d+\\s?,\\s?(([^a-z]ns)|(p\\s?[<>=]\\s?\\d?\\.\\d+e?-?\\d*))",
txt,
ignore.case = TRUE
)[[1]]
if (tLoc[1] != -1) {
# Get raw text of t-values:
tRaw <-
substring(txt, tLoc, tLoc + attr(tLoc, "match.length") - 1)
# remove commas (thousands separators)
tRaw <- gsub("(?<=\\d),(?=\\d+)", "", tRaw, perl = TRUE)
# Replace weird codings of a minus sign with actual minus sign:
# First remove spaces
tRaw <-
gsub("(?<=\\=)\\s+(?=.*\\,)", "", tRaw, perl = TRUE)
# Replace any weird string with a minus sign
tRaw <-
gsub("(?<=\\=)\\s?[^\\d\\.]+(?=.*\\,)", " -", tRaw, perl = TRUE)
# Add spaces again:
tRaw <-
gsub("(?<=\\=)(?=(\\.|\\d))", " ", tRaw, perl = TRUE)
# Extract location of numbers:
nums <-
gregexpr("(\\-?\\s?\\d*\\.?\\d+\\s?e?-?\\d*)|ns",
tRaw,
ignore.case = TRUE)
# Extract df:
df <-
as.numeric(substring(
tRaw,
sapply(nums, '[', 1),
sapply(nums, function(x)
x[1] + attr(x, "match.length")[1] - 1)
))
# Extract t-values
suppressWarnings(tValsChar <-
substring(
tRaw,
sapply(nums, '[', 2),
sapply(nums, function(x)
x[2] + attr(x, "match.length")[2] - 1)
))
suppressWarnings(tVals <- as.numeric(tValsChar))
# Extract number of decimals test statistic
testdec <-
attr(regexpr("\\.\\d+", tValsChar), "match.length") - 1
testdec[testdec < 0] <- 0
# Extract (in)equality test statistic
testEqLoc <- gregexpr("\\)\\s?[<>=]", tRaw)
testEq <- substring(
tRaw,
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
# Extract p-values
suppressWarnings(pValsChar <-
substring(
tRaw,
sapply(nums, '[', 3),
sapply(nums, function(x)
x[3] + attr(x, "match.length")[3] - 1)
))
suppressWarnings(pVals <- as.numeric(pValsChar))
# Extract (in)equality
eqLoc <-
gregexpr("p\\s?[<>=]", tRaw, ignore.case = TRUE)
pEq <- substring(
tRaw,
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
pEq[grepl("ns", tRaw, ignore.case = TRUE)] <- "ns"
# determine number of decimals of p value
dec <-
attr(regexpr("\\.\\d+", pValsChar), "match.length") - 1
dec[dec < 0] <- 0
# Create data frame:
tRes <- data.frame(
Source = names(x)[i],
Statistic = "t",
df1 = NA,
df2 = df,
Test.Comparison = testEq,
Value = tVals,
Reported.Comparison = pEq,
Reported.P.Value = pVals,
Computed = pt(-1 * abs(tVals), df) * 2,
Location = tLoc,
Raw = tRaw,
stringsAsFactors = FALSE,
dec = dec,
testdec = testdec,
OneTailedInTxt = OneTailedInTxt
)
# Append, clean and close:
Res <- rbind(Res, tRes)
rm(tRes)
}
}
#---------------------------
# F-values:
if ("F" %in% stat) {
# Get location of F-values in text:
# also pick up degrees of freedom wrongly converted into letters:
# 1 --> l or I
FLoc <-
gregexpr(
"F\\s?\\(\\s?\\d*\\.?(I|l|\\d+)\\s?,\\s?\\d*\\.?\\d+\\s?\\)\\s?[<>=]\\s?\\d*,?\\d*\\.?\\d+\\s?,\\s?(([^a-z]ns)|(p\\s?[<>=]\\s?\\d?\\.\\d+e?-?\\d*))",
txt,
ignore.case = TRUE
)[[1]]
if (FLoc[1] != -1) {
# Get raw text of F-values:
FRaw <-
substring(txt, FLoc, FLoc + attr(FLoc, "match.length") - 1)
# convert wrongly printed "l" or "I" into 1
FRaw <- gsub("l|I", 1, FRaw)
# Extract location of numbers:
nums <-
gregexpr("(\\d*\\.?\\d+\\s?e?-?\\d*)|ns", FRaw, ignore.case = TRUE)
# Extract df1:
df1 <-
as.numeric(substring(
FRaw,
sapply(nums, '[', 1),
sapply(nums, function(x)
x[1] + attr(x, "match.length")[1] - 1)
))
# Extract df2:
df2 <-
as.numeric(substring(
FRaw,
sapply(nums, '[', 2),
sapply(nums, function(x)
x[2] + attr(x, "match.length")[2] - 1)
))
# remove commas (thousands separators)
Fsplit <- strsplit(FRaw, "\\)", perl = TRUE)
FValsRaw <- lapply(Fsplit, function(x)
x[2])
FandDF <- lapply(Fsplit, function(x)
x[1])
FValsRaw <-
gsub("(?<=\\d),(?=\\d+)", "", FValsRaw, perl = TRUE)
FRaw <- paste(FandDF, ")", FValsRaw, sep = "")
# Extract F-values
numsF <- gregexpr("(\\d*\\.?\\d+)|ns", FValsRaw)
suppressWarnings(FValsChar <-
substring(
FValsRaw,
sapply(numsF, '[', 1),
sapply(numsF, function(x)
x[1] + attr(x, "match.length")[1] - 1)
))
suppressWarnings(FVals <- as.numeric(FValsChar))
# Extract number of decimals test statistic
testdec <-
attr(regexpr("\\.\\d+", FValsChar), "match.length") - 1
testdec[testdec < 0] <- 0
# Extract (in)equality test statistic
testEqLoc <- gregexpr("\\)\\s?[<>=]", FRaw)
testEq <- substring(
FRaw,
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
# Extract p-values
suppressWarnings(pValsChar <-
substring(
FValsRaw,
sapply(numsF, '[', 2),
sapply(numsF, function(x)
x[2] + attr(x, "match.length")[2] - 1)
))
suppressWarnings(pVals <- as.numeric(pValsChar))
# Extract (in)equality
eqLoc <-
gregexpr("p\\s?[<>=]", FRaw, ignore.case = TRUE)
pEq <- substring(
FRaw,
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
pEq[grepl("ns", FRaw, ignore.case = TRUE)] <- "ns"
# determine number of decimals of p value
dec <-
attr(regexpr("\\.\\d+", pValsChar), "match.length") - 1
dec[dec < 0] <- NA
# Create data frame:
FRes <- data.frame(
Source = names(x)[i],
Statistic = "F",
df1 = df1,
df2 = df2,
Test.Comparison = testEq,
Value = FVals,
Reported.Comparison = pEq,
Reported.P.Value = pVals,
Computed = pf(FVals, df1, df2, lower.tail = FALSE),
Location = FLoc,
Raw = FRaw,
stringsAsFactors = FALSE,
dec = dec,
testdec = testdec,
OneTailedInTxt = OneTailedInTxt
)
# Append, clean and close:
Res <- rbind(Res, FRes)
rm(FRes)
}
}
#---------------------------
# correlations:
if (any(c("r", "cor", "correlations") %in% stat)) {
# Get location of r-values in text:
rLoc <-
gregexpr(
"r\\s?\\(\\s?\\d*\\.?\\d+\\s?\\)\\s?[<>=]\\s?[^a-z\\d]{0,3}\\s?\\d*\\.?\\d+\\s?,\\s?(([^a-z]ns)|(p\\s?[<>=]\\s?\\d?\\.\\d+e?-?\\d*))",
txt,
ignore.case = TRUE
)[[1]]
if (rLoc[1] != -1) {
# Get raw text of r-values:
rRaw <-
substring(txt, rLoc, rLoc + attr(rLoc, "match.length") - 1)
# Replace weird codings of a minus sign with actual minus sign:
# First remove spaces
rRaw <-
gsub("(?<=\\=)\\s+(?=.*\\,)", "", rRaw, perl = TRUE)
# Replace any weird string with a minus sign
rRaw <-
gsub("(?<=\\=)\\s?[^\\d\\.]+(?=.*\\,)", " -", rRaw, perl = TRUE)
# Add spaces again:
rRaw <-
gsub("(?<=\\=)(?=(\\.|\\d))", " ", rRaw, perl = TRUE)
# Extract location of numbers:
nums <-
gregexpr("(\\-?\\s?\\d*\\.?\\d+\\s?e?-?\\d*)|ns",
rRaw,
ignore.case = TRUE)
# Extract df:
df <-
as.numeric(substring(
rRaw,
sapply(nums, '[', 1),
sapply(nums, function(x)
x[1] + attr(x, "match.length")[1] - 1)
))
# Extract r-values
suppressWarnings(rValsChar <-
substring(
rRaw,
sapply(nums, '[', 2),
sapply(nums, function(x)
x[2] + attr(x, "match.length")[2] - 1)
))
suppressWarnings(rVals <- as.numeric(rValsChar))
# Extract number of decimals test statistic
testdec <-
attr(regexpr("\\.\\d+", rValsChar), "match.length") - 1
testdec[testdec < 0] <- 0
# Extract (in)equality test statistic
testEqLoc <- gregexpr("\\)\\s?[<>=]", rRaw)
testEq <- substring(
rRaw,
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
# Extract p-values
suppressWarnings(pValsChar <-
substring(
rRaw,
sapply(nums, '[', 3),
sapply(nums, function(x)
x[3] + attr(x, "match.length")[3] - 1)
))
suppressWarnings(pVals <- as.numeric(pValsChar))
# Extract (in)equality
eqLoc <-
gregexpr("p\\s?[<>=]", rRaw, ignore.case = TRUE)
pEq <- substring(
rRaw,
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
pEq[grepl("ns", rRaw, ignore.case = TRUE)] <- "ns"
# determine number of decimals of p value
dec <-
attr(regexpr("\\.\\d+", pValsChar), "match.length") - 1
dec[dec < 0] <- 0
# computed p = NA for correlations reported as >1
pComputed <-
pmin(pt(-1 * abs(r2t(rVals, df)), df) * 2, 1)
pComputed[is.nan(pComputed)] <- NA
# Create data frame:
rRes <- data.frame(
Source = names(x)[i],
Statistic = "r",
df1 = NA,
df2 = df,
Test.Comparison = testEq,
Value = rVals,
Reported.Comparison = pEq,
Reported.P.Value = pVals,
Computed = pComputed,
Location = rLoc,
Raw = rRaw,
stringsAsFactors = FALSE,
dec = dec,
testdec = testdec,
OneTailedInTxt = OneTailedInTxt
)
# Append, clean and close:
Res <- rbind(Res, rRes)
rm(rRes)
}
}
#---------------------------
# z-values:
if ("Z" %in% stat) {
# Get location of z-values in text:
zLoc <-
gregexpr(
"[^a-z]z\\s?[<>=]\\s?[^a-z\\d]{0,3}\\s?\\d*,?\\d*\\.?\\d+\\s?,\\s?(([^a-z]ns)|(p\\s?[<>=]\\s?\\d?\\.\\d+e?-?\\d*))",
txt,
ignore.case = TRUE
)[[1]]
if (zLoc[1] != -1) {
# Get raw text of z-values:
zRaw <-
substring(txt, zLoc, zLoc + attr(zLoc, "match.length") - 1)
# remove any character before test statistic
zRaw <- gsub(".?(z|Z)", "Z", zRaw, perl = TRUE)
# remove commas (thousands separators)
zRaw <-
gsub("(?<=\\d),(?=\\d+\\.)", "", zRaw, perl = TRUE)
# Replace weird codings of a minus sign with actual minus sign:
# First remove spaces
zRaw <-
gsub("(?<=\\=)\\s+(?=.*\\,)", "", zRaw, perl = TRUE)
# Replace any weird string with a minus sign
zRaw <-
gsub("(?<=\\=)\\s?[^\\d\\.]+(?=.*\\,)", " -", zRaw, perl = TRUE)
# Add spaces again:
zRaw <-
gsub("(?<=\\=)(?=(\\.|\\d))", " ", zRaw, perl = TRUE)
# Extract location of numbers:
nums <-
gregexpr("(\\-?\\s?\\d*\\.?\\d+\\s?e?-?\\d*)|ns",
zRaw,
ignore.case = TRUE)
# Extract z-values
suppressWarnings(zValsChar <-
substring(
zRaw,
sapply(nums, '[', 1),
sapply(nums, function(x)
x[1] + attr(x, "match.length")[1] - 1)
))
suppressWarnings(zVals <- as.numeric(zValsChar))
# Extract number of decimals test statistic
testdec <-
attr(regexpr("\\.\\d+", zValsChar), "match.length") - 1
testdec[testdec < 0] <- 0
# Extract (in)equality test statistic
testEqLoc <- gregexpr("(z|Z|z'|Z')\\s?[<>=]", zRaw)
testEq <- substring(
zRaw,
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
# Extract p-values
suppressWarnings(pValsChar <-
substring(
zRaw,
sapply(nums, '[', 2),
sapply(nums, function(x)
x[2] + attr(x, "match.length")[2] - 1)
))
suppressWarnings(pVals <- as.numeric(pValsChar))
# Extract (in)equality
eqLoc <-
gregexpr("p\\s?[<>=]", zRaw, ignore.case = TRUE)
pEq <- substring(
zRaw,
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
pEq[grepl("ns", zRaw, ignore.case = TRUE)] <- "ns"
# determine number of decimals of p value
dec <-
attr(regexpr("\\.\\d+", pValsChar), "match.length") - 1
dec[dec < 0] <- 0
# Create data frame:
zRes <- data.frame(
Source = names(x)[i],
Statistic = "Z",
df1 = NA,
df2 = NA,
Test.Comparison = testEq,
Value = zVals,
Reported.Comparison = pEq,
Reported.P.Value = pVals,
Computed = pnorm(abs(zVals), lower.tail = FALSE) *
2,
Location = zLoc,
Raw = zRaw,
stringsAsFactors = FALSE,
dec = dec,
testdec = testdec,
OneTailedInTxt = OneTailedInTxt
)
# Append, clean and close:
Res <- rbind(Res, zRes)
rm(zRes)
}
}
#---------------------------
# Chis2-values:
if ("chisq" %in% stat) {
# Get location of chi values or delta G in text:
chi2Loc <-
gregexpr(
"((\\[CHI\\]|\\[DELTA\\]G)\\s?|(\\s[^trFzQWBnD ]\\s?)|([^trFzQWBnD ]2\\s?))2?\\(\\s?\\d*\\.?\\d+\\s?(,\\s?N\\s?\\=\\s?\\d*\\,?\\d*\\,?\\d+\\s?)?\\)\\s?[<>=]\\s?\\s?\\d*,?\\d*\\.?\\d+\\s?,\\s?(([^a-z]ns)|(p\\s?[<>=]\\s?\\d?\\.\\d+e?-?\\d*))",
txt,
ignore.case = TRUE
)[[1]]
if (chi2Loc[1] != -1) {
# Get raw text of chi2-values:
chi2Raw <-
substring(txt, chi2Loc, chi2Loc + attr(chi2Loc, "match.length") - 1)
substr(chi2Raw, 1, 1)[grepl("\\d", substr(chi2Raw, 1, 1))] <-
" "
# remove sample size if reported for calculations
# save full result for "Raw" in final data frame
chi2Raw_inclN <- chi2Raw
chi2Raw <-
gsub("N\\s?=\\s?\\d*\\,?\\d*\\,?\\d*",
"",
chi2Raw,
ignore.case = TRUE)
# remove commas (thousands separators)
chi2Raw <-
gsub("(?<=\\d),(?=\\d+\\.)", "", chi2Raw, perl = TRUE)
# bug fix: remove extra opening brackets
# if a chi2 result is reported between brackets, and the chi is not read by statcheck
# the opening bracket is translated as the chi symbol, and extracting the numerics goes wrong
chi2Raw <-
gsub("\\((?=2\\s?\\()", "", chi2Raw, perl = TRUE)
# Extract location of numbers:
nums <-
gregexpr(
"(\\-?\\s?\\d*\\.?\\d+\\s?e?-?\\d*)|ns",
sub("^.*?\\(", "", chi2Raw),
ignore.case = TRUE
)
# Extract df:
df <-
as.numeric(substring(
sub("^.*?\\(", "", chi2Raw),
sapply(nums, '[', 1),
sapply(nums, function(x)
x[1] + attr(x, "match.length")[1] - 1)
))
# Extract chi2-values
suppressWarnings(chi2ValsChar <-
substring(
sub("^.*?\\(", "", chi2Raw),
sapply(nums, '[', 2),
sapply(nums, function(x)
x[2] + attr(x, "match.length")[2] - 1)
))
suppressWarnings(chi2Vals <- as.numeric(chi2ValsChar))
# Extract number of decimals test statistic
testdec <-
attr(regexpr("\\.\\d+", chi2ValsChar), "match.length") - 1
testdec[testdec < 0] <- 0
# Extract (in)equality test statistic
testEqLoc <- gregexpr("\\)\\s?[<>=]", chi2Raw)
testEq <- substring(
chi2Raw,
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
# Extract p-values
suppressWarnings(pValsChar <-
substring(
sub("^.*?\\(", "", chi2Raw),
sapply(nums, '[', 3),
sapply(nums, function(x)
x[3] + attr(x, "match.length")[3] - 1)
))
suppressWarnings(pVals <- as.numeric(pValsChar))
# Extract (in)equality
eqLoc <-
gregexpr("p\\s?[<>=]", chi2Raw, ignore.case = TRUE)
pEq <- substring(
chi2Raw,
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
pEq[grepl("ns", chi2Raw, ignore.case = TRUE)] <- "ns"
# determine number of decimals of p value
dec <-
attr(regexpr("\\.\\d+", pValsChar), "match.length") - 1
dec[dec < 0] <- 0
# Create data frame:
chi2Res <- data.frame(
Source = names(x)[i],
Statistic = "Chi2",
df1 = df,
df2 = NA,
Test.Comparison = testEq,
Value = chi2Vals,
Reported.Comparison = pEq,
Reported.P.Value = pVals,
Computed = pchisq(chi2Vals, df, lower.tail =
FALSE),
Location = chi2Loc,
Raw = chi2Raw_inclN,
stringsAsFactors = FALSE,
dec = dec,
testdec = testdec,
OneTailedInTxt = OneTailedInTxt
)
# Append, clean and close:
Res <- rbind(Res, chi2Res)
rm(chi2Res)
}
}
#---------------------------
# Q-values:
if ("Q" %in% stat) {
# Get location of Q-values in text:
QLoc <-
gregexpr(
"Q\\s?-?\\s?(w|within|b|between)?\\s?\\(\\s?\\d*\\.?\\d+\\s?\\)\\s?[<>=]\\s?[^a-z\\d]{0,3}\\s?\\d*,?\\d*\\.?\\d+\\s?,\\s?(([^a-z]ns)|(p\\s?[<>=]\\s?\\d?\\.\\d+e?-?\\d*))",
txt,
ignore.case = TRUE
)[[1]]
if (QLoc[1] != -1) {
# Get raw text of t-values:
QRaw <-
substring(txt, QLoc, QLoc + attr(QLoc, "match.length") - 1)
# remove commas (thousands separators)
QRaw <- gsub("(?<=\\d),(?=\\d+)", "", QRaw, perl = TRUE)
# Replace weird codings of a minus sign with actual minus sign:
# First remove spaces
QRaw <-
gsub("(?<=\\=)\\s+(?=.*\\,)", "", QRaw, perl = TRUE)
# Replace any weird string with a minus sign
QRaw <-
gsub("(?<=\\=)\\s?[^\\d\\.]+(?=.*\\,)", " -", QRaw, perl = TRUE)
# Add spaces again:
QRaw <-
gsub("(?<=\\=)(?=(\\.|\\d))", " ", QRaw, perl = TRUE)
# Extract type of Q-test (general, within, or between)
QtypeLoc <-
gregexpr("Q\\s?-?\\s?(w|within|b|between)?",
QRaw,
ignore.case = TRUE)
QtypeRaw <-
substring(QRaw,
sapply(QtypeLoc, '[', 1),
sapply(QtypeLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1))
Qtype <- rep(NA, length(QtypeRaw))
Qtype[grepl("Q\\s?-?\\s?(w|within)", QtypeRaw, ignore.case = TRUE)] <-
"Qw"
Qtype[grepl("Q\\s?-?\\s?(b|between)", QtypeRaw, ignore.case = TRUE)] <-
"Qb"
Qtype[is.na(Qtype)] <- "Q"
# Extract location of numbers:
nums <-
gregexpr("(\\-?\\s?\\d*\\.?\\d+\\s?e?-?\\d*)|ns",
QRaw,
ignore.case = TRUE)
# Extract df:
df <-
as.numeric(substring(
QRaw,
sapply(nums, '[', 1),
sapply(nums, function(x)
x[1] + attr(x, "match.length")[1] - 1)
))
# Extract Q-values
suppressWarnings(QValsChar <-
substring(
QRaw,
sapply(nums, '[', 2),
sapply(nums, function(x)
x[2] + attr(x, "match.length")[2] - 1)
))
suppressWarnings(QVals <- as.numeric(QValsChar))
# Extract number of decimals test statistic
testdec <-
attr(regexpr("\\.\\d+", QValsChar), "match.length") - 1
testdec[testdec < 0] <- 0
# Extract (in)equality test statistic
testEqLoc <- gregexpr("\\)\\s?[<>=]", QRaw)
testEq <- substring(
QRaw,
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(testEqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1)
)
# Extract p-values
suppressWarnings(pValsChar <-
substring(
QRaw,
sapply(nums, '[', 3),
sapply(nums, function(x)
x[3] + attr(x, "match.length")[3] - 1)
))
suppressWarnings(pVals <- as.numeric(pValsChar))
# Extract (in)equality
eqLoc <-
gregexpr("p\\s?[<>=]", QRaw, ignore.case = TRUE)
pEq <- substring(QRaw,
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1),
sapply(eqLoc, function(x)
x[1] + attr(x, "match.length")[1] - 1))
pEq[grepl("ns", QRaw, ignore.case = TRUE)] <- "ns"
# determine number of decimals of p value
dec <-
attr(regexpr("\\.\\d+", pValsChar), "match.length") - 1
dec[dec < 0] <- 0
# Create data frame:
QRes <- data.frame(
Source = names(x)[i],
Statistic = Qtype,
df1 = NA,
df2 = df,
Test.Comparison = testEq,
Value = QVals,
Reported.Comparison = pEq,
Reported.P.Value = pVals,
Computed = pchisq(QVals, df, lower.tail =
FALSE),
Location = QLoc,
Raw = QRaw,
stringsAsFactors = FALSE,
dec = dec,
testdec = testdec,
OneTailedInTxt = OneTailedInTxt
)
# Append, clean and close:
Res <- rbind(Res, QRes)
rm(QRes)
}
}
setTxtProgressBar(pb, i)
}
close(pb)
Source <- NULL
Res <- ddply(Res, .(Source), function(x)
x[order(x$Location), ])
if (nrow(Res) > 0) {
# remove p values greater than one
Res <- Res[Res$Reported.P.Value <= 1 |
is.na(Res$Reported.P.Value), ]
}
###---------------------------------------------------------------------
ErrorTest <- function(x, ...) {
computed <- as.vector(x$Computed)
comparison <- as.vector(x$Reported.Comparison)
reported <- as.vector(x$Reported.P.Value)
testcomp <- as.vector(x$Test.Comparison)
# replace 'ns' for > alpha
reported[comparison == "ns"] <- alpha
comparison[comparison == "ns"] <- ">"
Match <- paste(computed, comparison, reported)
#-----------------------------------------------
# select inexactly reported p values (p<../p>..)
InExTests <- grepl("<|>", Match)
# evaluate errors when test statistics are reported exactly (t()=.../F(,)=...)
if (any(InExTests)) {
InExTests[InExTests] <-
sapply(Match[InExTests], function(m)
! eval(parse(text = m)))
}
# evaluate errors when test statistics are reported inexactly (t()</>.../F(,)</>...)
smallsmall <- testcomp == "<" & comparison == "<"
smallgreat <- testcomp == "<" & comparison == ">"
greatsmall <- testcomp == ">" & comparison == "<"
greatgreat <- testcomp == ">" & comparison == ">"
if (any(smallsmall)) {
InExTests[smallsmall] <-
round(computed[smallsmall], x$dec[smallsmall]) <= round(reported[smallsmall], x$dec[smallsmall])
}
if (any(greatgreat)) {
InExTests[greatgreat] <-
round(computed[greatgreat], x$dec[greatgreat]) >= round(reported[greatgreat], x$dec[greatgreat])
}
# these combinations of < & > are logically always correct
InExTests[smallgreat] <- FALSE
InExTests[greatsmall] <- FALSE
#-----------------------------------------------
# select exactly reported p values (p=..)
ExTests <- comparison == "="
# evaluate errors when test statistics are reported exactly (t()=.../F(,)=...)
if (any(ExTests)) {