Nothing
R/UtilOutputReportTextFileORH.R
In RJafroc: Artificial Intelligence Systems and Observer Performance
Defines functions
OutputTextFileORH
OutputTextFileORH <- function(dataset,
method,
methodTxt,
ReportFileName,
alpha, # decided to restrict to alpha = 0.05 5/21/20 # undid 7/11/20
FOM,
analysisOption,
OR)
{
sink(ReportFileName)
Preamble(dataset, FOM, ReportFileName, OR, methodTxt)
modalityID <- dataset$descriptions$modalityID
readerID <- dataset$descriptions$readerID
I <- length(modalityID)
J <- length(readerID)
x <- c("\n",
"===========================================================================",
"***** ANOVA Tables (OR analysis of reader FOMs) *****",
"===========================================================================\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
x <- c(
"TREATMENT X READER ANOVA of FOMs",
"Used for global test of equal treatment AUCs",
"and for treatment differences confidence intervals ",
"in parts (a) and (b) of the analyses.\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$ANOVA$TRanova
print(format(df, digits = 5, justify = "left"))
msR <- as.data.frame(t(OR$ANOVA$IndividualTrt[,"msREachTrt"]))
colnames(msR) <- paste0("trt", dataset$descriptions$modalityID)
rownames(msR) <- "msR"
x <- c(
"\nREADER ANOVAs of AUCs for each treatment",
"(Used for single treatment confidence intervals in part (c) of the analyses).\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- msR
print(format(df, digits = 5, justify = "left"))
x <- c("\n",
"===========================================================================",
"***** OR Variance Components *****",
"===========================================================================\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
x <- c(
"\nObuchowski-Rockette variance component and covariance estimates",
"(for sample size estimation for future studies)",
"Note: These are ANOVA estimates which can be negative.\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$ANOVA$VarCom
print(format(df, digits = 5, justify = "left"))
x <- c("\n",
"===========================================================================",
"***** Corresponding DBM Variance Components *****",
"===========================================================================\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- UtilOR2DBMVarCom(dim(dataset$ratings$NL)[3], df)
print(format(df, digits = 5, justify = "left"))
x <- c("\n",
"===========================================================================",
"***** RRRC: Random Reader Random Case Analysis *****",
"===========================================================================\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
cat("\nRRRC (a): Test of NH of no treatment effect\n\n")
df <- OR$RRRC$FTests
print(format(df, digits = 5, justify = "left"))
if (OR$RRRC$FTests$p[1] < alpha) {
x <- c("\nCONCLUSION:",
sprintf("The treatment FOMs are different [F(%2d,%7.4f) = %6.3f, p = %7.4f, alpha = %7.4f].",
OR$RRRC$FTests$DF[1],
OR$RRRC$FTests$DF[2],
OR$RRRC$FTests$FStat[1],
OR$RRRC$FTests$p[1], alpha))
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
} else {
x <- c("\nCONCLUSION:",
sprintf("The treatment FOMs are not significantly different [F(%2d,%7.4f) = %6.3f, p = %7.4f, alpha = %7.4f].",
OR$RRRC$FTests$DF[1],
OR$RRRC$FTests$DF[2],
OR$RRRC$FTests$FStat[1],
OR$RRRC$FTests$p[1], alpha))
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
}
x <- c(
"\nCOMMENTS:",
"Df(error term) = [MS(T*R) + J*max(Cov2 - Cov3,0)]**2/{MS(T*R)**2/[(I-1)(J-1)]}",
"Note: Error term is the denominator of the F statistic and is a linear",
"combination of mean squares. The value of this linear",
"combination is given under the MS column.\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
x <- c(
"\nRRRC (b): 95% confidence intervals and hypothesis tests (H0: difference = 0)",
"for treatment FOM differences\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$RRRC$ciDiffTrt
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt{(2/J)*[MS(T*R) + J*max(Cov2 - Cov3,0)]}",
"Df same as df(error term) from (a)",
"95% CI: Difference +- t(.025;df) * StdErr\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
x <- c(
"\nRRRC (c): Single-treatment 95% confidence intervals",
"(Each analysis is based only on data for the specified treatment, i.e.,",
"on the treatment-specific reader ANOVA of AUCs and Cov2 estimates.)\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$RRRC$ciAvgRdrEachTrt
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt{1/J * [MS(R) + J*max(Cov2,0)]}",
"Df = [MS(R)+ max(J*cov2,0)]**2/[(MS(R)**2/(J-1)]",
"Note: Df is called `ddf_H_single` in Hillis (2007)",
"95% CI: FOM +- t(.025;df) * StdErr\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
x <- c("\n",
"===========================================================================",
"***** FRRC: Fixed Reader Random Case Analysis *****",
"===========================================================================\n",
"(Results apply to the population of cases but only for the readers used in",
"this study. Chi-square or Z tests are used; these are appropriate for",
"moderate or large case sample sizes)\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
cat("\nFRRC (a): Test of NH of no treatment effect\n\n")
df <- OR$FRRC$FTests
print(format(df, digits = 5, justify = "left"))
if (OR$FRRC$FTests$p[1] < alpha) {
x <- c("\nCONCLUSION:",
sprintf("The treatment AUCs are different [X2(%1d) = %6.3f, p = %7.4f, alpha = %7.4f].",
OR$FRRC$FTests$DF[1],
OR$FRRC$FTests$Chisq[1],
OR$FRRC$FTests$p[1], alpha))
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
} else {
x <- c("\nCONCLUSION:",
sprintf("The treatment AUCs are not significantly different [X2(%1d) = %6.3f, p = %7.4f, alpha = %7.4f].",
OR$FRRC$FTests$DF[1],
OR$FRRC$FTests$Chisq[1],
OR$FRRC$FTests$p[1], alpha))
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
}
x <- c("\nCOMMENTS:",
"X2 = (I-1)*MS(T)/[Var - Cov1 + (J-1)*max(Cov2 - Cov3,0)]\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
cat("\nFRRC (b): 95% confidence intervals for reader-averaged \ninter-treatment FOM differences\n\n")
df <- OR$FRRC$ciDiffTrt
print(format(df, digits = 5, justify = "left"))
x <- c("\nCOMMENTS:",
"StdErr = sqrt{2/J * [(Var(error) - Cov1 + (J-1)*max(Cov2 - Cov3,0)]}",
"95% CI: difference +- z(.025) * StdErr\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("TREATMENT X CASE ANOVAs for each reader\n")
df <- OR$ANOVA$IndividualRdr
print(format(df, digits = 5, justify = "left"))
cat("\n====================")
x <- c("\nFRRC (c): Single treatment FOM 95% confidence intervals",
"(Each analysis is based only on data for the specified treatment, i.e., on",
"the specific reader ANOVA of AUCs and error-variance and Cov2 estimates.)\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$FRRC$ciAvgRdrEachTrt
print(format(df, digits = 5, justify = "left"))
cat("\n")
df <- OR$ANOVA$IndividualTrt[,c(3,4)]
print(format(df, digits = 5, justify = "left"))
cat("\n====================")
x <- c("\nFRRC (d): Single-reader 95% confidence intervals",
"and tests (H0: difference = 0) for treatment FOM differences.",
"(Each analysis is based only on data for the specified reader,",
"i.e., on the reader-specific FOM, error-variance and Cov1 estimates.)\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$FRRC$ciDiffTrtEachRdr
print(format(df, digits = 5, justify = "left"))
cat("\n")
df <- OR$ANOVA$IndividualRdr[,c(3,4)]
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt[2*(Var - Cov1)]",
"95% CI: Difference +- z(.025) * StdErr\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
x <- c("\n",
"===========================================================================",
"***** RRFC: Random Reader Fixed Case Analysis *****",
"===========================================================================",
"(Results apply to the population of readers but only for the cases used in",
"this study)",
"These results result from using the OR model, but treating reader as a random",
"factor and treatment and case as fixed factors. Because case is treated as a fixed",
"factor, it follows that Cov1 = Cov2 = Cov3 = 0; i.e., there is no correlation",
"between reader-performance measures (e.g., FOMs) due to reading the same",
"cases. Thus the OR model reduces to a conventional treatment x reader ANOVA",
"for the reader-performance outcomes, where reader is a random factor and",
"treatment is a fixed factor. This is the same as a repeated measures ANOVA",
"where treatment is the repeated measures factor, i.e., readers provide an",
"outcome under each treatment.")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
cat("\nRRFC (a): Test for H0: Treatments have the same FOM\n\n")
df <- OR$RRFC$FTests
print(format(df, digits = 5, justify = "left"))
if(OR$RRFC$FTests["T","p"] < alpha){
x <- c("\nCONCLUSION:",
"The treatment AUCs are different,",
sprintf("[F(%1d,%2d) = %7.4f, p = %7.4f, alpha = %7.4f].",
I-1,(I-1)*(J-1),
OR$RRFC$FTests[1,3],
OR$RRFC$FTests[1,4], alpha),
"Note: If there are only 2 treatments, this is equivalent to a paired t-test applied",
"to the AUCs")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
} else {
x <- c("\nCONCLUSION:",
"The treatment AUCs are not significantly different,",
sprintf("[F(%1d,%2d) = %7.4f, p = %7.4f, alpha = %7.4f].",
I-1,(I-1)*(J-1),
OR$RRFC$FTests[1,3],
OR$RRFC$FTests[1,4], alpha),
"Note: If there are only 2 treatments, this is equivalent to a paired t-test applied",
"to the AUCs")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
}
x <- c("\nCOMMENTS:", "Error term: MS(TR) \n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
x <- c("\nRRFC (b):",
"95% confidence intervals for reader-averaged treatment differences\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$RRFC$ciDiffTrt
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt[2/J * MS(T*R)]",
"DF = df[MS(T*R)] = (I-1)(J-1)",
"95% CI: Difference +- t(.025;df) * StdErr",
"Note: If there are only 2 treatments, this is equivalent to a paired t-test applied",
"to the AUCs\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
x <- c("\nRRFC (c): Single treatment AUC 95% confidence intervals",
"(Each analysis is based only on data for the specified treatment,",
"i.e. on the treatment-specific reader ANOVA of AUCs\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$RRFC$ciAvgRdrEachTrt
df <- cbind(df, as.data.frame(OR$ANOVA$IndividualTrt[,2]))[,c(1,6,2,3,4,5)]
cnames <- colnames(df);cnames[2] <- "MS"
colnames(df) <- cnames
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt[1/J * MS(R)]",
"DF = df[MS(R)] = J-1",
"95% CI: FOM +- t(.025;df) * StdErr",
"Note: this is the conventional CI, treating the reader AUCs as a random sample.\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
sucessfulOutput <- sprintf("The report has been saved to %s.", ReportFileName)
sink()
return(sucessfulOutput)
}
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Defines functions OutputTextFileORH
OutputTextFileORH <- function(dataset,
method,
methodTxt,
ReportFileName,
alpha, # decided to restrict to alpha = 0.05 5/21/20 # undid 7/11/20
FOM,
analysisOption,
OR)
{
sink(ReportFileName)
Preamble(dataset, FOM, ReportFileName, OR, methodTxt)
modalityID <- dataset$descriptions$modalityID
readerID <- dataset$descriptions$readerID
I <- length(modalityID)
J <- length(readerID)
x <- c("\n",
"===========================================================================",
"***** ANOVA Tables (OR analysis of reader FOMs) *****",
"===========================================================================\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
x <- c(
"TREATMENT X READER ANOVA of FOMs",
"Used for global test of equal treatment AUCs",
"and for treatment differences confidence intervals ",
"in parts (a) and (b) of the analyses.\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$ANOVA$TRanova
print(format(df, digits = 5, justify = "left"))
msR <- as.data.frame(t(OR$ANOVA$IndividualTrt[,"msREachTrt"]))
colnames(msR) <- paste0("trt", dataset$descriptions$modalityID)
rownames(msR) <- "msR"
x <- c(
"\nREADER ANOVAs of AUCs for each treatment",
"(Used for single treatment confidence intervals in part (c) of the analyses).\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- msR
print(format(df, digits = 5, justify = "left"))
x <- c("\n",
"===========================================================================",
"***** OR Variance Components *****",
"===========================================================================\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
x <- c(
"\nObuchowski-Rockette variance component and covariance estimates",
"(for sample size estimation for future studies)",
"Note: These are ANOVA estimates which can be negative.\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$ANOVA$VarCom
print(format(df, digits = 5, justify = "left"))
x <- c("\n",
"===========================================================================",
"***** Corresponding DBM Variance Components *****",
"===========================================================================\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- UtilOR2DBMVarCom(dim(dataset$ratings$NL)[3], df)
print(format(df, digits = 5, justify = "left"))
x <- c("\n",
"===========================================================================",
"***** RRRC: Random Reader Random Case Analysis *****",
"===========================================================================\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
cat("\nRRRC (a): Test of NH of no treatment effect\n\n")
df <- OR$RRRC$FTests
print(format(df, digits = 5, justify = "left"))
if (OR$RRRC$FTests$p[1] < alpha) {
x <- c("\nCONCLUSION:",
sprintf("The treatment FOMs are different [F(%2d,%7.4f) = %6.3f, p = %7.4f, alpha = %7.4f].",
OR$RRRC$FTests$DF[1],
OR$RRRC$FTests$DF[2],
OR$RRRC$FTests$FStat[1],
OR$RRRC$FTests$p[1], alpha))
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
} else {
x <- c("\nCONCLUSION:",
sprintf("The treatment FOMs are not significantly different [F(%2d,%7.4f) = %6.3f, p = %7.4f, alpha = %7.4f].",
OR$RRRC$FTests$DF[1],
OR$RRRC$FTests$DF[2],
OR$RRRC$FTests$FStat[1],
OR$RRRC$FTests$p[1], alpha))
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
}
x <- c(
"\nCOMMENTS:",
"Df(error term) = [MS(T*R) + J*max(Cov2 - Cov3,0)]**2/{MS(T*R)**2/[(I-1)(J-1)]}",
"Note: Error term is the denominator of the F statistic and is a linear",
"combination of mean squares. The value of this linear",
"combination is given under the MS column.\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
x <- c(
"\nRRRC (b): 95% confidence intervals and hypothesis tests (H0: difference = 0)",
"for treatment FOM differences\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$RRRC$ciDiffTrt
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt{(2/J)*[MS(T*R) + J*max(Cov2 - Cov3,0)]}",
"Df same as df(error term) from (a)",
"95% CI: Difference +- t(.025;df) * StdErr\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
x <- c(
"\nRRRC (c): Single-treatment 95% confidence intervals",
"(Each analysis is based only on data for the specified treatment, i.e.,",
"on the treatment-specific reader ANOVA of AUCs and Cov2 estimates.)\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$RRRC$ciAvgRdrEachTrt
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt{1/J * [MS(R) + J*max(Cov2,0)]}",
"Df = [MS(R)+ max(J*cov2,0)]**2/[(MS(R)**2/(J-1)]",
"Note: Df is called `ddf_H_single` in Hillis (2007)",
"95% CI: FOM +- t(.025;df) * StdErr\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
x <- c("\n",
"===========================================================================",
"***** FRRC: Fixed Reader Random Case Analysis *****",
"===========================================================================\n",
"(Results apply to the population of cases but only for the readers used in",
"this study. Chi-square or Z tests are used; these are appropriate for",
"moderate or large case sample sizes)\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
cat("\nFRRC (a): Test of NH of no treatment effect\n\n")
df <- OR$FRRC$FTests
print(format(df, digits = 5, justify = "left"))
if (OR$FRRC$FTests$p[1] < alpha) {
x <- c("\nCONCLUSION:",
sprintf("The treatment AUCs are different [X2(%1d) = %6.3f, p = %7.4f, alpha = %7.4f].",
OR$FRRC$FTests$DF[1],
OR$FRRC$FTests$Chisq[1],
OR$FRRC$FTests$p[1], alpha))
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
} else {
x <- c("\nCONCLUSION:",
sprintf("The treatment AUCs are not significantly different [X2(%1d) = %6.3f, p = %7.4f, alpha = %7.4f].",
OR$FRRC$FTests$DF[1],
OR$FRRC$FTests$Chisq[1],
OR$FRRC$FTests$p[1], alpha))
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
}
x <- c("\nCOMMENTS:",
"X2 = (I-1)*MS(T)/[Var - Cov1 + (J-1)*max(Cov2 - Cov3,0)]\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
cat("\nFRRC (b): 95% confidence intervals for reader-averaged \ninter-treatment FOM differences\n\n")
df <- OR$FRRC$ciDiffTrt
print(format(df, digits = 5, justify = "left"))
x <- c("\nCOMMENTS:",
"StdErr = sqrt{2/J * [(Var(error) - Cov1 + (J-1)*max(Cov2 - Cov3,0)]}",
"95% CI: difference +- z(.025) * StdErr\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("TREATMENT X CASE ANOVAs for each reader\n")
df <- OR$ANOVA$IndividualRdr
print(format(df, digits = 5, justify = "left"))
cat("\n====================")
x <- c("\nFRRC (c): Single treatment FOM 95% confidence intervals",
"(Each analysis is based only on data for the specified treatment, i.e., on",
"the specific reader ANOVA of AUCs and error-variance and Cov2 estimates.)\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$FRRC$ciAvgRdrEachTrt
print(format(df, digits = 5, justify = "left"))
cat("\n")
df <- OR$ANOVA$IndividualTrt[,c(3,4)]
print(format(df, digits = 5, justify = "left"))
cat("\n====================")
x <- c("\nFRRC (d): Single-reader 95% confidence intervals",
"and tests (H0: difference = 0) for treatment FOM differences.",
"(Each analysis is based only on data for the specified reader,",
"i.e., on the reader-specific FOM, error-variance and Cov1 estimates.)\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$FRRC$ciDiffTrtEachRdr
print(format(df, digits = 5, justify = "left"))
cat("\n")
df <- OR$ANOVA$IndividualRdr[,c(3,4)]
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt[2*(Var - Cov1)]",
"95% CI: Difference +- z(.025) * StdErr\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
x <- c("\n",
"===========================================================================",
"***** RRFC: Random Reader Fixed Case Analysis *****",
"===========================================================================",
"(Results apply to the population of readers but only for the cases used in",
"this study)",
"These results result from using the OR model, but treating reader as a random",
"factor and treatment and case as fixed factors. Because case is treated as a fixed",
"factor, it follows that Cov1 = Cov2 = Cov3 = 0; i.e., there is no correlation",
"between reader-performance measures (e.g., FOMs) due to reading the same",
"cases. Thus the OR model reduces to a conventional treatment x reader ANOVA",
"for the reader-performance outcomes, where reader is a random factor and",
"treatment is a fixed factor. This is the same as a repeated measures ANOVA",
"where treatment is the repeated measures factor, i.e., readers provide an",
"outcome under each treatment.")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
cat("\nRRFC (a): Test for H0: Treatments have the same FOM\n\n")
df <- OR$RRFC$FTests
print(format(df, digits = 5, justify = "left"))
if(OR$RRFC$FTests["T","p"] < alpha){
x <- c("\nCONCLUSION:",
"The treatment AUCs are different,",
sprintf("[F(%1d,%2d) = %7.4f, p = %7.4f, alpha = %7.4f].",
I-1,(I-1)*(J-1),
OR$RRFC$FTests[1,3],
OR$RRFC$FTests[1,4], alpha),
"Note: If there are only 2 treatments, this is equivalent to a paired t-test applied",
"to the AUCs")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
} else {
x <- c("\nCONCLUSION:",
"The treatment AUCs are not significantly different,",
sprintf("[F(%1d,%2d) = %7.4f, p = %7.4f, alpha = %7.4f].",
I-1,(I-1)*(J-1),
OR$RRFC$FTests[1,3],
OR$RRFC$FTests[1,4], alpha),
"Note: If there are only 2 treatments, this is equivalent to a paired t-test applied",
"to the AUCs")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
}
x <- c("\nCOMMENTS:", "Error term: MS(TR) \n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
x <- c("\nRRFC (b):",
"95% confidence intervals for reader-averaged treatment differences\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$RRFC$ciDiffTrt
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt[2/J * MS(T*R)]",
"DF = df[MS(T*R)] = (I-1)(J-1)",
"95% CI: Difference +- t(.025;df) * StdErr",
"Note: If there are only 2 treatments, this is equivalent to a paired t-test applied",
"to the AUCs\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
cat("\n====================")
x <- c("\nRRFC (c): Single treatment AUC 95% confidence intervals",
"(Each analysis is based only on data for the specified treatment,",
"i.e. on the treatment-specific reader ANOVA of AUCs\n\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
df <- OR$RRFC$ciAvgRdrEachTrt
df <- cbind(df, as.data.frame(OR$ANOVA$IndividualTrt[,2]))[,c(1,6,2,3,4,5)]
cnames <- colnames(df);cnames[2] <- "MS"
colnames(df) <- cnames
print(format(df, digits = 5, justify = "left"))
x <- c(
"\nCOMMENTS:",
"StdErr = sqrt[1/J * MS(R)]",
"DF = df[MS(R)] = J-1",
"95% CI: FOM +- t(.025;df) * StdErr",
"Note: this is the conventional CI, treating the reader AUCs as a random sample.\n")
for (i in 1:length(x)) cat(sprintf("%-s\n", x[i]))
sucessfulOutput <- sprintf("The report has been saved to %s.", ReportFileName)
sink()
return(sucessfulOutput)
}
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