tests/testthat/test-StCompare2Iowa.R
In dpc10ster/rjafroc: Artificial Intelligence Systems and Observer Performance
# rm(list = ls())
# library(RJafroc)
# library(testthat)
library(stringr)
ExtractDataFrame <- function(lines, FindString, offSet,
nRows, rowNames, CurrentLine, nCols) {
if (FindString != "")
{while(lines[CurrentLine] != FindString) CurrentLine <- CurrentLine + 1}
CurrentLine <- CurrentLine + offSet
df <- NULL
for (i in 1:nRows) {
s <- lines[CurrentLine]
if (rowNames[i] != "") s <- str_remove(s, rowNames[i])
s <- str_remove(s, fixed("("))
s <- str_remove(s, fixed(")"))
s <- str_remove(s, fixed("1 - 2"))
numCurrentLine <- as.numeric(Numextract(s))[nCols]
dfCurrentLine <- t(data.frame(numCurrentLine,
stringsAsFactors = FALSE))
df <- rbind(df, dfCurrentLine)
CurrentLine <- CurrentLine + 1
}
return(list(
CurrentLine = CurrentLine,
df = df
))
}
Numextract <- function(string){
unlist(regmatches(string,gregexpr("[[:punct:]]?[[:digit:]]+\\.*[[:digit:]]*",string)))
}
contextStr <- "St: Compare to Iowa VanDyke dataset"
context(contextStr)
test_that(contextStr, {
fn <- paste0(test_path(), "/goodValues361/Iowa/VanDyke.txt")
lines <- readLines(fn)
DBM_RRRC <- St(dataset02, FOM = "Wilcoxon", method = "DBM", analysisOption = "RRRC")
OR_RRRC <- St(dataset02, FOM = "Wilcoxon", method = "OR", analysisOption = "RRRC")
DBM_FRRC <- St(dataset02, FOM = "Wilcoxon", method = "DBM", analysisOption = "FRRC")
OR_FRRC <- St(dataset02, FOM = "Wilcoxon", method = "OR", analysisOption = "FRRC")
DBM_RRFC <- St(dataset02, FOM = "Wilcoxon", method = "DBM", analysisOption = "RRFC")
OR_RRFC <- St(dataset02, FOM = "Wilcoxon", method = "OR", analysisOption = "RRFC")
CurrentLine <- 1
FindString <- "TREATMENT x READER AUC ESTIMATES"
offSet <- 6
nRows <- 5
rowNames <- as.character(seq(1:5))
nCols <- c(1,2)
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df1 <- ret$df
theirs <- df1;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- t(DBM_RRRC$FOMs$foms);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
FindString <- " TREATMENT AUC MEANS (averaged across readers)"
offSet <- 2
nRows <- 2
rowNames <- as.character(seq(1:2))
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df2 <- ret$df
theirs <- df2;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- as.matrix(DBM_RRRC$FOMs$trtMeans);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 2\n")
FindString <- " TREATMENT AUC MEAN DIFFERENCES"
offSet <- 2
nRows <- 1
rowNames <- "1 - 2"
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df3 <- ret$df
theirs <- df3;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- as.matrix(DBM_RRRC$FOMs$trtMeanDiffs);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 3\n")
FindString <- " TREATMENT X READER ANOVA of AUCs"
offSet <- 6
nRows <- 3
rowNames <- c("T","R","TR")
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df4 <- ret$df
theirs <- df4;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$TRanova;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 4\n")
FindString <- " READER ANOVAs of AUCs for each treatment"
offSet <- 7
nRows <- 1
rowNames <- "R"
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df5<- ret$df
theirs <- df5[2:3];colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$IndividualTrt[,2];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.vector(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 5\n")
FindString <- " ***** Variance component and error-covariance estimates *****"
offSet <- 9
nRows <- 6
nCols <- 1
rowNames <- c("Var(R)","Var(TR)","COV1","COV2","COV3","Var(Error)")
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df6<- ret$df
theirs <- as.vector(df6)#;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$VarCom;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)[,1]
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 6\n")
FindString <- " Corresponding DBM variance component and covariance estimates"
offSet <- 4
nRows <- 6
nCols <- 1
rowNames <- c("Var(R)","Var(C)","Var(T*R)","Var(T*C)","Var(R*C)","Var(T*R*C) + Var(Error)")
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df7<- ret$df
theirs <- as.vector(df7)#;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- DBM_RRRC$ANOVA$VarCom;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)[,1]
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 7\n")
FindString <- " ***** Analysis 1 (OR Analysis): Random Readers and Random Cases *****"
offSet <- 9
nRows <- 1
nCols <- 1
rowNames <- "Treatment"
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df8<- ret$df
theirs <- as.matrix(df8);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$FTests[1,];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.01, scale = abs(mine))
# cat("passed test 8\n")
FindString <- ""
offSet <- 0
nRows <- 1
nCols <- 2
rowNames <- "Error term"
nCols <- 1:2
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df9<- ret$df
theirs <- as.matrix(df9);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$FTests[2,][1:2];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 9\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df10<- ret$df
theirs <- as.matrix(df10);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 10\n")
FindString <- " c) Single-treatment 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 6
rowNames <- c("1", "2")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df11<- ret$df
theirs <- as.matrix(df11);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$ciAvgRdrEachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 11\n")
FindString <- " a) Chi-square test for H0: Treatments have the same AUC"
offSet <- 7
nRows <- 1
nCols <- 3
rowNames <- ""
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df12<- ret$df
theirs <- as.matrix(df12);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$FTests[1,2:4]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 12\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 6
rowNames <- "1 - 2"
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df13<- ret$df
theirs <- as.matrix(df13);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 13\n")
FindString <- " c) Single treatment AUC 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 4
rowNames <- c("1", "2")
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df14<- ret$df
theirs <- as.matrix(df14);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciAvgRdrEachTrt[,-3] # drop DF
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 14\n")
FindString <- " Treatment Var(Error) Cov2 "
offSet <- 2
nRows <- 2
nCols <- 2
rowNames <- c("1", "2")
nCols <- 1:2
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df15<- ret$df
theirs <- as.matrix(df15);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$IndividualTrt[,-c(1,2)] # drop DF and msREachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 15\n")
FindString <- " d) Single-reader 95% confidence intervals and tests (H0: difference = 0) for "
offSet <- 8
nRows <- 5
nCols <- 6
rowNames <- c("1", "2", "3", "4", "5", "6")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df16<- ret$df
theirs <- as.matrix(df16);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciDiffTrtEachRdr
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# insufficient decimal places in theirs
expect_equal(theirs, mine, tolerance = 0.01, scale = abs(mine))
# cat("passed test 16\n")
FindString <- " Source DF Mean Square F value Pr > F "
offSet <- 2
nRows <- 1
nCols <- 4
rowNames <- "Treatment"
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df17<- ret$df
theirs <- as.matrix(df17);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$FTests[1,]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# insufficient decimal places in theirs
expect_equal(theirs, mine, tolerance = 0.005, scale = abs(mine))
# cat("passed test 17\n")
FindString <- ""
offSet <- 0
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df18<- ret$df
theirs <- as.vector(df18[1:2]);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$FTests[2,1:2]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.numeric(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 18\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df19<- ret$df
theirs <- as.vector(df19);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.numeric(mine)
# insufficient precision printout in theirs
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 19\n")
FindString <- " c) Single treatment AUC 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 6
rowNames <- c("1" ,"2")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df20<- ret$df
theirs <- as.matrix(df20[,-2]);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$ciAvgRdrEachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 20\n")
})
contextStr <- "St: Compare to Iowa Franken dataset"
context(contextStr)
test_that(contextStr, {
fn <- paste0(test_path(), "/goodValues361/Iowa/Franken1.txt")
lines <- readLines(fn)
DBM_RRRC <- St(dataset03, FOM = "Wilcoxon", method = "DBM", analysisOption = "RRRC")
OR_RRRC <- St(dataset03, FOM = "Wilcoxon", method = "OR", analysisOption = "RRRC")
DBM_FRRC <- St(dataset03, FOM = "Wilcoxon", method = "DBM", analysisOption = "FRRC")
OR_FRRC <- St(dataset03, FOM = "Wilcoxon", method = "OR", analysisOption = "FRRC")
DBM_RRFC <- St(dataset03, FOM = "Wilcoxon", method = "DBM", analysisOption = "RRFC")
OR_RRFC <- St(dataset03, FOM = "Wilcoxon", method = "OR", analysisOption = "RRFC")
CurrentLine <- 1
FindString <- "TREATMENT x READER AUC ESTIMATES"
offSet <- 6
nRows <- 4
rowNames <- as.character(seq(1:nRows))
nCols <- c(1,2)
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df1 <- ret$df
theirs <- df1;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- t(DBM_RRRC$FOMs$foms);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
FindString <- " TREATMENT AUC MEANS (averaged across readers)"
offSet <- 2
nRows <- 2
rowNames <- as.character(seq(1:2))
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df2 <- ret$df
theirs <- df2;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- as.matrix(DBM_RRRC$FOMs$trtMeans);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 2\n")
FindString <- " TREATMENT AUC MEAN DIFFERENCES"
offSet <- 2
nRows <- 1
rowNames <- "1 - 2"
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df3 <- ret$df
theirs <- df3;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- as.matrix(DBM_RRRC$FOMs$trtMeanDiffs);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 3\n")
FindString <- " TREATMENT X READER ANOVA of AUCs"
offSet <- 6
nRows <- 3
rowNames <- c("T","R","TR")
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df4 <- ret$df
theirs <- df4;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$TRanova;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 4\n")
FindString <- " READER ANOVAs of AUCs for each treatment"
offSet <- 7
nRows <- 1
rowNames <- "R"
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df5<- ret$df
theirs <- df5[2:3];colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$IndividualTrt[,2];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.vector(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 5\n")
FindString <- " ***** Variance component and error-covariance estimates *****"
offSet <- 9
nRows <- 6
nCols <- 1
rowNames <- c("Var(R)","Var(TR)","COV1","COV2","COV3","Var(Error)")
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df6<- ret$df
theirs <- as.vector(df6)#;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$VarCom;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)[,1]
# fix from Peter
# https://github.com/dpc10ster/RJafroc/issues/79#issuecomment-1190711314
expect_error(expect_equal(theirs[1:2], mine[1:2], tolerance = 0.00001, scale = abs(mine[1:2])))
expect_equal(theirs[3:6], mine[3:6], tolerance = 0.00001, scale = abs(mine[3:6]))
FindString <- " Corresponding DBM variance component and covariance estimates"
offSet <- 4
nRows <- 6
nCols <- 1
rowNames <- c("Var(R)","Var(C)","Var(T*R)","Var(T*C)","Var(R*C)","Var(T*R*C) + Var(Error)")
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df7<- ret$df
theirs <- as.vector(df7)#;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- DBM_RRRC$ANOVA$VarCom;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)[,1]
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 7\n")
FindString <- " ***** Analysis 1 (OR Analysis): Random Readers and Random Cases *****"
offSet <- 9
nRows <- 1
nCols <- 1
rowNames <- "Treatment"
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df8<- ret$df
theirs <- as.matrix(df8);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$FTests[1,];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.01, scale = abs(mine))
# cat("passed test 8\n")
FindString <- ""
offSet <- 0
nRows <- 1
nCols <- 2
rowNames <- "Error term"
nCols <- 1:2
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df9<- ret$df
theirs <- as.matrix(df9);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$FTests[2,][1:2];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 9\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df10<- ret$df
theirs <- as.matrix(df10);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.004, scale = abs(mine))
# cat("passed test 10\n")
FindString <- " c) Single-treatment 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 6
rowNames <- c("1", "2")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df11<- ret$df
theirs <- as.matrix(df11);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$ciAvgRdrEachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 11\n")
FindString <- " a) Chi-square test for H0: Treatments have the same AUC"
offSet <- 7
nRows <- 1
nCols <- 3
rowNames <- ""
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df12<- ret$df
theirs <- as.matrix(df12);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$FTests[1,2:4]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 12\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 6
rowNames <- "1 - 2"
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df13<- ret$df
theirs <- as.matrix(df13);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.004, scale = abs(mine))
# cat("passed test 13\n")
FindString <- " c) Single treatment AUC 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 4
rowNames <- c("1", "2")
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df14<- ret$df
theirs <- as.matrix(df14);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciAvgRdrEachTrt[,-3] # drop DF
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 14\n")
FindString <- " Treatment Var(Error) Cov2 "
offSet <- 2
nRows <- 2
nCols <- 2
rowNames <- c("1", "2")
nCols <- 1:2
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df15<- ret$df
theirs <- as.matrix(df15);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$IndividualTrt[,-c(1,2)] # drop DF and msREachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 15\n")
FindString <- " d) Single-reader 95% confidence intervals and tests (H0: difference = 0) for "
offSet <- 8
nRows <- 4
nCols <- 6
rowNames <- c("1", "2", "3", "4", "5")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df16<- ret$df
theirs <- as.matrix(df16);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciDiffTrtEachRdr
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# insufficient decimal places in theirs
expect_equal(theirs, mine, tolerance = 0.01, scale = abs(mine))
# cat("passed test 16\n")
FindString <- " Source DF Mean Square F value Pr > F "
offSet <- 2
nRows <- 1
nCols <- 4
rowNames <- "Treatment"
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df17<- ret$df
theirs <- as.matrix(df17);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$FTests[1,]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# insufficient decimal places in theirs
expect_equal(theirs, mine, tolerance = 0.005, scale = abs(mine))
# cat("passed test 17\n")
FindString <- ""
offSet <- 0
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df18<- ret$df
theirs <- as.vector(df18[1:2]);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$FTests[2,1:2]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.numeric(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 18\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df19<- ret$df
theirs <- as.vector(df19);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.numeric(mine)
# insufficient precision printout in theirs
expect_equal(theirs, mine, tolerance = 0.004, scale = abs(mine))
# cat("passed test 19\n")
FindString <- " c) Single treatment AUC 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 6
rowNames <- c("1" ,"2")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df20<- ret$df
theirs <- as.matrix(df20[,-2]);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$ciAvgRdrEachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 20\n")
})
dpc10ster/rjafroc documentation built on Jan. 18, 2024, 4:37 a.m.
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# rm(list = ls())
# library(RJafroc)
# library(testthat)
library(stringr)
ExtractDataFrame <- function(lines, FindString, offSet,
nRows, rowNames, CurrentLine, nCols) {
if (FindString != "")
{while(lines[CurrentLine] != FindString) CurrentLine <- CurrentLine + 1}
CurrentLine <- CurrentLine + offSet
df <- NULL
for (i in 1:nRows) {
s <- lines[CurrentLine]
if (rowNames[i] != "") s <- str_remove(s, rowNames[i])
s <- str_remove(s, fixed("("))
s <- str_remove(s, fixed(")"))
s <- str_remove(s, fixed("1 - 2"))
numCurrentLine <- as.numeric(Numextract(s))[nCols]
dfCurrentLine <- t(data.frame(numCurrentLine,
stringsAsFactors = FALSE))
df <- rbind(df, dfCurrentLine)
CurrentLine <- CurrentLine + 1
}
return(list(
CurrentLine = CurrentLine,
df = df
))
}
Numextract <- function(string){
unlist(regmatches(string,gregexpr("[[:punct:]]?[[:digit:]]+\\.*[[:digit:]]*",string)))
}
contextStr <- "St: Compare to Iowa VanDyke dataset"
context(contextStr)
test_that(contextStr, {
fn <- paste0(test_path(), "/goodValues361/Iowa/VanDyke.txt")
lines <- readLines(fn)
DBM_RRRC <- St(dataset02, FOM = "Wilcoxon", method = "DBM", analysisOption = "RRRC")
OR_RRRC <- St(dataset02, FOM = "Wilcoxon", method = "OR", analysisOption = "RRRC")
DBM_FRRC <- St(dataset02, FOM = "Wilcoxon", method = "DBM", analysisOption = "FRRC")
OR_FRRC <- St(dataset02, FOM = "Wilcoxon", method = "OR", analysisOption = "FRRC")
DBM_RRFC <- St(dataset02, FOM = "Wilcoxon", method = "DBM", analysisOption = "RRFC")
OR_RRFC <- St(dataset02, FOM = "Wilcoxon", method = "OR", analysisOption = "RRFC")
CurrentLine <- 1
FindString <- "TREATMENT x READER AUC ESTIMATES"
offSet <- 6
nRows <- 5
rowNames <- as.character(seq(1:5))
nCols <- c(1,2)
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df1 <- ret$df
theirs <- df1;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- t(DBM_RRRC$FOMs$foms);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
FindString <- " TREATMENT AUC MEANS (averaged across readers)"
offSet <- 2
nRows <- 2
rowNames <- as.character(seq(1:2))
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df2 <- ret$df
theirs <- df2;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- as.matrix(DBM_RRRC$FOMs$trtMeans);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 2\n")
FindString <- " TREATMENT AUC MEAN DIFFERENCES"
offSet <- 2
nRows <- 1
rowNames <- "1 - 2"
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df3 <- ret$df
theirs <- df3;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- as.matrix(DBM_RRRC$FOMs$trtMeanDiffs);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 3\n")
FindString <- " TREATMENT X READER ANOVA of AUCs"
offSet <- 6
nRows <- 3
rowNames <- c("T","R","TR")
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df4 <- ret$df
theirs <- df4;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$TRanova;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 4\n")
FindString <- " READER ANOVAs of AUCs for each treatment"
offSet <- 7
nRows <- 1
rowNames <- "R"
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df5<- ret$df
theirs <- df5[2:3];colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$IndividualTrt[,2];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.vector(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 5\n")
FindString <- " ***** Variance component and error-covariance estimates *****"
offSet <- 9
nRows <- 6
nCols <- 1
rowNames <- c("Var(R)","Var(TR)","COV1","COV2","COV3","Var(Error)")
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df6<- ret$df
theirs <- as.vector(df6)#;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$VarCom;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)[,1]
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 6\n")
FindString <- " Corresponding DBM variance component and covariance estimates"
offSet <- 4
nRows <- 6
nCols <- 1
rowNames <- c("Var(R)","Var(C)","Var(T*R)","Var(T*C)","Var(R*C)","Var(T*R*C) + Var(Error)")
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df7<- ret$df
theirs <- as.vector(df7)#;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- DBM_RRRC$ANOVA$VarCom;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)[,1]
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 7\n")
FindString <- " ***** Analysis 1 (OR Analysis): Random Readers and Random Cases *****"
offSet <- 9
nRows <- 1
nCols <- 1
rowNames <- "Treatment"
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df8<- ret$df
theirs <- as.matrix(df8);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$FTests[1,];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.01, scale = abs(mine))
# cat("passed test 8\n")
FindString <- ""
offSet <- 0
nRows <- 1
nCols <- 2
rowNames <- "Error term"
nCols <- 1:2
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df9<- ret$df
theirs <- as.matrix(df9);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$FTests[2,][1:2];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 9\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df10<- ret$df
theirs <- as.matrix(df10);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 10\n")
FindString <- " c) Single-treatment 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 6
rowNames <- c("1", "2")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df11<- ret$df
theirs <- as.matrix(df11);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$ciAvgRdrEachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 11\n")
FindString <- " a) Chi-square test for H0: Treatments have the same AUC"
offSet <- 7
nRows <- 1
nCols <- 3
rowNames <- ""
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df12<- ret$df
theirs <- as.matrix(df12);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$FTests[1,2:4]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 12\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 6
rowNames <- "1 - 2"
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df13<- ret$df
theirs <- as.matrix(df13);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 13\n")
FindString <- " c) Single treatment AUC 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 4
rowNames <- c("1", "2")
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df14<- ret$df
theirs <- as.matrix(df14);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciAvgRdrEachTrt[,-3] # drop DF
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 14\n")
FindString <- " Treatment Var(Error) Cov2 "
offSet <- 2
nRows <- 2
nCols <- 2
rowNames <- c("1", "2")
nCols <- 1:2
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df15<- ret$df
theirs <- as.matrix(df15);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$IndividualTrt[,-c(1,2)] # drop DF and msREachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 15\n")
FindString <- " d) Single-reader 95% confidence intervals and tests (H0: difference = 0) for "
offSet <- 8
nRows <- 5
nCols <- 6
rowNames <- c("1", "2", "3", "4", "5", "6")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df16<- ret$df
theirs <- as.matrix(df16);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciDiffTrtEachRdr
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# insufficient decimal places in theirs
expect_equal(theirs, mine, tolerance = 0.01, scale = abs(mine))
# cat("passed test 16\n")
FindString <- " Source DF Mean Square F value Pr > F "
offSet <- 2
nRows <- 1
nCols <- 4
rowNames <- "Treatment"
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df17<- ret$df
theirs <- as.matrix(df17);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$FTests[1,]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# insufficient decimal places in theirs
expect_equal(theirs, mine, tolerance = 0.005, scale = abs(mine))
# cat("passed test 17\n")
FindString <- ""
offSet <- 0
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df18<- ret$df
theirs <- as.vector(df18[1:2]);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$FTests[2,1:2]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.numeric(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 18\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df19<- ret$df
theirs <- as.vector(df19);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.numeric(mine)
# insufficient precision printout in theirs
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 19\n")
FindString <- " c) Single treatment AUC 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 6
rowNames <- c("1" ,"2")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df20<- ret$df
theirs <- as.matrix(df20[,-2]);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$ciAvgRdrEachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 20\n")
})
contextStr <- "St: Compare to Iowa Franken dataset"
context(contextStr)
test_that(contextStr, {
fn <- paste0(test_path(), "/goodValues361/Iowa/Franken1.txt")
lines <- readLines(fn)
DBM_RRRC <- St(dataset03, FOM = "Wilcoxon", method = "DBM", analysisOption = "RRRC")
OR_RRRC <- St(dataset03, FOM = "Wilcoxon", method = "OR", analysisOption = "RRRC")
DBM_FRRC <- St(dataset03, FOM = "Wilcoxon", method = "DBM", analysisOption = "FRRC")
OR_FRRC <- St(dataset03, FOM = "Wilcoxon", method = "OR", analysisOption = "FRRC")
DBM_RRFC <- St(dataset03, FOM = "Wilcoxon", method = "DBM", analysisOption = "RRFC")
OR_RRFC <- St(dataset03, FOM = "Wilcoxon", method = "OR", analysisOption = "RRFC")
CurrentLine <- 1
FindString <- "TREATMENT x READER AUC ESTIMATES"
offSet <- 6
nRows <- 4
rowNames <- as.character(seq(1:nRows))
nCols <- c(1,2)
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df1 <- ret$df
theirs <- df1;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- t(DBM_RRRC$FOMs$foms);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
FindString <- " TREATMENT AUC MEANS (averaged across readers)"
offSet <- 2
nRows <- 2
rowNames <- as.character(seq(1:2))
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df2 <- ret$df
theirs <- df2;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- as.matrix(DBM_RRRC$FOMs$trtMeans);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 2\n")
FindString <- " TREATMENT AUC MEAN DIFFERENCES"
offSet <- 2
nRows <- 1
rowNames <- "1 - 2"
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df3 <- ret$df
theirs <- df3;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- as.matrix(DBM_RRRC$FOMs$trtMeanDiffs);colnames(mine) <- NULL;rownames(mine) <- NULL
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 3\n")
FindString <- " TREATMENT X READER ANOVA of AUCs"
offSet <- 6
nRows <- 3
rowNames <- c("T","R","TR")
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df4 <- ret$df
theirs <- df4;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$TRanova;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 4\n")
FindString <- " READER ANOVAs of AUCs for each treatment"
offSet <- 7
nRows <- 1
rowNames <- "R"
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df5<- ret$df
theirs <- df5[2:3];colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$IndividualTrt[,2];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.vector(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 5\n")
FindString <- " ***** Variance component and error-covariance estimates *****"
offSet <- 9
nRows <- 6
nCols <- 1
rowNames <- c("Var(R)","Var(TR)","COV1","COV2","COV3","Var(Error)")
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df6<- ret$df
theirs <- as.vector(df6)#;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$VarCom;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)[,1]
# fix from Peter
# https://github.com/dpc10ster/RJafroc/issues/79#issuecomment-1190711314
expect_error(expect_equal(theirs[1:2], mine[1:2], tolerance = 0.00001, scale = abs(mine[1:2])))
expect_equal(theirs[3:6], mine[3:6], tolerance = 0.00001, scale = abs(mine[3:6]))
FindString <- " Corresponding DBM variance component and covariance estimates"
offSet <- 4
nRows <- 6
nCols <- 1
rowNames <- c("Var(R)","Var(C)","Var(T*R)","Var(T*C)","Var(R*C)","Var(T*R*C) + Var(Error)")
nCols <- 1
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df7<- ret$df
theirs <- as.vector(df7)#;colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- DBM_RRRC$ANOVA$VarCom;colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)[,1]
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 7\n")
FindString <- " ***** Analysis 1 (OR Analysis): Random Readers and Random Cases *****"
offSet <- 9
nRows <- 1
nCols <- 1
rowNames <- "Treatment"
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df8<- ret$df
theirs <- as.matrix(df8);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$FTests[1,];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.01, scale = abs(mine))
# cat("passed test 8\n")
FindString <- ""
offSet <- 0
nRows <- 1
nCols <- 2
rowNames <- "Error term"
nCols <- 1:2
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df9<- ret$df
theirs <- as.matrix(df9);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$FTests[2,][1:2];colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 9\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df10<- ret$df
theirs <- as.matrix(df10);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.004, scale = abs(mine))
# cat("passed test 10\n")
FindString <- " c) Single-treatment 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 6
rowNames <- c("1", "2")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df11<- ret$df
theirs <- as.matrix(df11);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$RRRC$ciAvgRdrEachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 11\n")
FindString <- " a) Chi-square test for H0: Treatments have the same AUC"
offSet <- 7
nRows <- 1
nCols <- 3
rowNames <- ""
nCols <- 1:3
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df12<- ret$df
theirs <- as.matrix(df12);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$FTests[1,2:4]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.001, scale = abs(mine))
# cat("passed test 12\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 6
rowNames <- "1 - 2"
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df13<- ret$df
theirs <- as.matrix(df13);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# their program does not print out as many decimal places
expect_equal(theirs, mine, tolerance = 0.004, scale = abs(mine))
# cat("passed test 13\n")
FindString <- " c) Single treatment AUC 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 4
rowNames <- c("1", "2")
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df14<- ret$df
theirs <- as.matrix(df14);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciAvgRdrEachTrt[,-3] # drop DF
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.00001, scale = abs(mine))
# cat("passed test 14\n")
FindString <- " Treatment Var(Error) Cov2 "
offSet <- 2
nRows <- 2
nCols <- 2
rowNames <- c("1", "2")
nCols <- 1:2
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df15<- ret$df
theirs <- as.matrix(df15);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRRC$ANOVA$IndividualTrt[,-c(1,2)] # drop DF and msREachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 15\n")
FindString <- " d) Single-reader 95% confidence intervals and tests (H0: difference = 0) for "
offSet <- 8
nRows <- 4
nCols <- 6
rowNames <- c("1", "2", "3", "4", "5")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df16<- ret$df
theirs <- as.matrix(df16);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_FRRC$FRRC$ciDiffTrtEachRdr
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# insufficient decimal places in theirs
expect_equal(theirs, mine, tolerance = 0.01, scale = abs(mine))
# cat("passed test 16\n")
FindString <- " Source DF Mean Square F value Pr > F "
offSet <- 2
nRows <- 1
nCols <- 4
rowNames <- "Treatment"
nCols <- 1:4
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df17<- ret$df
theirs <- as.matrix(df17);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$FTests[1,]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
# insufficient decimal places in theirs
expect_equal(theirs, mine, tolerance = 0.005, scale = abs(mine))
# cat("passed test 17\n")
FindString <- ""
offSet <- 0
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df18<- ret$df
theirs <- as.vector(df18[1:2]);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$FTests[2,1:2]
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.numeric(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 18\n")
FindString <- " b) 95% confidence intervals and hypothesis tests (H0: difference = 0)"
offSet <- 6
nRows <- 1
nCols <- 7
rowNames <- "1 - 2"
nCols <- 1:7
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df19<- ret$df
theirs <- as.vector(df19);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$ciDiffTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.numeric(mine)
# insufficient precision printout in theirs
expect_equal(theirs, mine, tolerance = 0.004, scale = abs(mine))
# cat("passed test 19\n")
FindString <- " c) Single treatment AUC 95% confidence intervals"
offSet <- 6
nRows <- 2
nCols <- 6
rowNames <- c("1" ,"2")
nCols <- 1:6
ret <- ExtractDataFrame(lines, FindString, offSet, nRows, rowNames, CurrentLine, nCols)
CurrentLine <- ret$CurrentLine
df20<- ret$df
theirs <- as.matrix(df20[,-2]);colnames(theirs) <- NULL;rownames(theirs) <- NULL
mine <- OR_RRFC$RRFC$ciAvgRdrEachTrt
colnames(mine) <- NULL;rownames(mine) <- NULL
mine <- as.matrix(mine)
expect_equal(theirs, mine, tolerance = 0.000001, scale = abs(mine))
# cat("passed test 20\n")
})
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