diff --git a/Rpackage/iMRMC/NAMESPACE b/Rpackage/iMRMC/NAMESPACE
index bbcf0666..349cd6a8 100644
--- 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
index a2c374e4..97978e6d 100644
--- 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
index 44bedac1..5b4d86d9 100644
--- 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
index cc7f73d3..b89c1d37 100644
Binary files a/Rpackage/iMRMC/inst/extra/limitsOfAgreement/CompareSimulationModels.pdf and b/Rpackage/iMRMC/inst/extra/limitsOfAgreement/CompareSimulationModels.pdf differ
diff --git a/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.R b/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.R
index 485dad80..c30a23b3 100644
--- 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
deleted file mode 100644
index 8f9a66c7..00000000
Binary files a/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.Rdata and /dev/null differ
diff --git a/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.rda b/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.rda
new file mode 100644
index 00000000..7b43834a
Binary files /dev/null and b/Rpackage/iMRMC/tests/testthat/test_simNormalIGHierarchical.rda differ