Merge pull request #10 from DIDSR/LOA

LOA name changes to reduce dependencies
DIDSR · Aug 9, 2024 · 698d8cf · 698d8cf
2 parents 43595a5 + c43ce3e
commit 698d8cf
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diff --git a/Rpackage/iMRMC/NAMESPACE b/Rpackage/iMRMC/NAMESPACE
@@ -1,46 +1,46 @@
-# Generated by roxygen2: do not edit by hand
-
-export(convertDFtoDesignMatrix)
-export(convertDFtoScoreMatrix)
-export(createGroups)
-export(createIMRMCdf)
-export(deleteCol)
-export(doAUCmrmc)
-export(doIMRMC)
-export(doIMRMC_java)
-export(doROCavg)
-export(doROCxy)
-export(extractPairedComparisonsBRBM)
-export(extractPairedComparisonsWRBM)
-export(getBRBM)
-export(getMRMCdataset)
-export(getMRMCscore)
-export(getWRBM)
-export(init.lecuyerRNG)
-export(laBRBM)
-export(laBRWM)
-export(laWRBM)
-export(laWRWM)
-export(renameCol)
-export(roc2binary)
-export(sim.NormalIG.Hierarchical)
-export(sim.NormalIG.Hierarchical.config)
-export(sim.gRoeMetz)
-export(sim.gRoeMetz.config)
-export(simMRMC)
-export(simRoeMetz.example)
-export(successDFtoROCdf)
-export(uStat11.conditionalD)
-export(uStat11.jointD)
-export(undoIMRMCdf)
-import(Matrix)
-import(parallel)
-import(utils)
-importFrom(methods,as)
-importFrom(stats,aov)
-importFrom(stats,model.matrix)
-importFrom(stats,qnorm)
-importFrom(stats,rbeta)
-importFrom(stats,rgamma)
-importFrom(stats,rnorm)
-importFrom(stats,var)
+# Generated by roxygen2: do not edit by hand
+
+export(convertDFtoDesignMatrix)
+export(convertDFtoScoreMatrix)
+export(createGroups)
+export(createIMRMCdf)
+export(deleteCol)
+export(doAUCmrmc)
+export(doIMRMC)
+export(doIMRMC_java)
+export(doROCavg)
+export(doROCxy)
+export(extractPairedComparisonsBRBM)
+export(extractPairedComparisonsWRBM)
+export(getBRBM)
+export(getMRMCdataset)
+export(getMRMCscore)
+export(getWRBM)
+export(init.lecuyerRNG)
+export(laBRBM)
+export(laBRWM)
+export(laWRBM)
+export(laWRWM)
+export(renameCol)
+export(roc2binary)
+export(sim.NormalIG.Hierarchical)
+export(sim.NormalIG.Hierarchical.config)
+export(sim.gRoeMetz)
+export(sim.gRoeMetz.config)
+export(simMRMC)
+export(simRoeMetz.example)
+export(successDFtoROCdf)
+export(uStat11.conditionalD)
+export(uStat11.jointD)
+export(undoIMRMCdf)
+import(Matrix)
+import(parallel)
+import(utils)
+importFrom(methods,as)
+importFrom(stats,aov)
+importFrom(stats,model.matrix)
+importFrom(stats,qnorm)
+importFrom(stats,rbeta)
+importFrom(stats,rgamma)
+importFrom(stats,rnorm)
+importFrom(stats,var)
diff --git a/Rpackage/iMRMC/R/limitsOfAgreement.R b/Rpackage/iMRMC/R/limitsOfAgreement.R
@@ -138,7 +138,7 @@ laWRBM <- function(df, modalitiesToCompare = c("testA","testB"),
   diff.df <- droplevels(subset(diff.df.all, select = c("readerID","caseID","score")))
 
   # Two-way ANOVA model
-  fit <- anova.2way(diff.df, if.aov = if.aov, type = type, reader.first = reader.first)
+  fit <- anova2(diff.df, if.aov = if.aov, type = type, reader.first = reader.first)
 
   # size of study
   N <- nrow(diff.df)
@@ -193,7 +193,7 @@ laBRWM <- function(df, modality = c("testA"),
   df <- droplevels(df[df$modalityID == modality[1], ])
 
   # Two-way ANOVA model
-  fit <- anova.2way(df, if.aov = if.aov, type = type, reader.first = reader.first)
+  fit <- anova2(df, if.aov = if.aov, type = type, reader.first = reader.first)
 
   # size of study
   nRperC <- array(table(df$caseID))
@@ -259,7 +259,7 @@ laWRWM <- function(df, replicatesToCompare = c("testA","testB"),
   diff.df <- droplevels(subset(diff.df.all, select = c("readerID","caseID","score")))
 
   # Two-way ANOVA model
-  fit <- anova.2way(diff.df, if.aov = if.aov, type = type, reader.first = reader.first)
+  fit <- anova2(diff.df, if.aov = if.aov, type = type, reader.first = reader.first)
 
   # size of study
   N <- nrow(diff.df)
@@ -316,7 +316,7 @@ laBRBM <- function(df, modalitiesToCompare = c("testA","testB"),
   df.B <- df[df$modalityID == modalitiesToCompare[2], ]
   df_2Modality <- droplevels(rbind(df.A, df.B))
 
-  fit <- anova.3way(df.A, df.B, if.aov = if.aov, type = type, reader.first = reader.first,
+  fit <- anova3(df.A, df.B, if.aov = if.aov, type = type, reader.first = reader.first,
                     is.sparseQR = is.sparseQR)
 
   # Limit of agreement result
@@ -360,7 +360,7 @@ laBRBM <- function(df, modalitiesToCompare = c("testA","testB"),
 }
 
 
-anova.2way <- function(df, if.aov = TRUE, type = 1, reader.first = TRUE
+anova2 <- function(df, if.aov = TRUE, type = 1, reader.first = TRUE
 ){
   df <- droplevels(df)
   is.incomplete <- F # whether the computation is completed
@@ -518,7 +518,7 @@ RSS_2w <- function(X, Y, Xr=NULL, Xc=NULL, Xe=diag(length(Y))){
               df=length(Y)-k))
 }
 
-anova.3way <- function(df.A, df.B, if.aov = TRUE, type = 1, reader.first = TRUE,
+anova3 <- function(df.A, df.B, if.aov = TRUE, type = 1, reader.first = TRUE,
                        is.sparseQR = T
 ){
   is.incomplete <- F # whether the computation is completed

diff --git a/Rpackage/iMRMC/inst/extra/limitsOfAgreement/CompareSimulationModels.Rmd b/Rpackage/iMRMC/inst/extra/limitsOfAgreement/CompareSimulationModels.Rmd
@@ -32,8 +32,9 @@ set.seed(1, kind = "L'Ecuyer-CMRG")
 dFrame.newH <- sim.NormalIG.Hierarchical(config)
 
 # check the first and last few lines of the simulated dataframe
-head(dFrame.newH)
-tail(dFrame.newH)
+print(dFrame.newH[1:6, ])
+print(dFrame.newH[(nrow(dFrame.newH) - 5):nrow(dFrame.newH), ])
+
 ```
 
 We simulated 5 readers and 100 cases for 2 modalities, so the total number of scores is 5x100x2=1000.
@@ -56,8 +57,9 @@ set.seed(1, kind = "L'Ecuyer-CMRG")
 dFrame.gRM <- sim.gRoeMetz(config)
 
 # check the first and last few lines of the simulated dataframe
-head(dFrame.gRM)
-tail(dFrame.gRM)
+print(dFrame.gRM[1:6, ])
+print(dFrame.gRM[(nrow(dFrame.gRM) - 5):nrow(dFrame.gRM), ])
+
 ```
 
 The simulated data starts with truth state of each case, and followed by the reading scores from each of the readers. Since we simulate 50 positive cases and 50 negative cases, there are 100 lines for the truth and 100x5x2 = 1000 lines for the scores from 5 readers for 2 modalities.
@@ -67,6 +69,7 @@ To combine the truth data and the reader scores and change the data to a datafra
 dFrame.gRM.2 <- undoIMRMCdf(dFrame.gRM)
 
 # check the first and last few lines of the simulated dataframe
-head(dFrame.gRM.2)
-tail(dFrame.gRM.2)
+print(dFrame.gRM.2[1:6, ])
+print(dFrame.gRM.2[(nrow(dFrame.gRM.2) - 5):nrow(dFrame.gRM.2), ])
+
 ```
diff --git a/Rpackage/iMRMC/inst/extra/limitsOfAgreement/CompareSimulationModels.pdf b/Rpackage/iMRMC/inst/extra/limitsOfAgreement/CompareSimulationModels.pdf
diff --git a/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.R b/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.R
@@ -19,7 +19,7 @@ str(result)
 #### TEST ####
 
 # Save the result to a file for future comparisons
-fileName <- "test_simNormalIGHierarchical.Rdata"
+fileName <- "test_simNormalIGHierarchical.rda"
 if (flagSave) {
   saveResult <- result
   save(saveResult, file = file.path("tests", "testthat", fileName))

diff --git a/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.Rdata b/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.Rdata
diff --git a/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.rda b/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.rda