Merge pull request #3 from LAPKB/v1.9.3

V1.9.3
LAPKB · Apr 15, 2020 · 3daf3b4 · 3daf3b4
2 parents cf000c7 + 40df60a
commit 3daf3b4
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Showing 4 changed files with 34 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -17,7 +17,7 @@ Description: Parametric and non-parametric
     which used to be available on CRAN.
 Authors@R: person("Michael", "Neely",
     email = "mneely@usc.edu", role = c("aut", "cre"))
-Version: 1.9.2
+Version: 1.9.3
 URL: http://www.lapk.org
 Date: 2020-02-29
 Depends: 

diff --git a/R/PMreport.R b/R/PMreport.R
@@ -193,8 +193,7 @@ PMreport <- function(wd, rdata, icen = "median", type = "NPAG", parallel = F) {
     writeHTML("<label for=\"tab4\">Parameter Values</label>")
     writeHTML("<div id=\"tab-content4\" class=\"tab-content\">")
     if (!all(is.null(final))) {
-      report.table <- data.frame(mean = final$popMean, sd = final$popSD, CV = final$popCV, var = final$popVar,
-                                 median = final$popMedian, shrink = 100 * final$shrinkage$shrinkage)
+      report.table <- data.frame(mean = t(final$popMean), sd = t(final$popSD), CV = t(final$popCV), var = t(final$popVar), median = t(final$popMedian), shrink = t(100 * final$shrinkage))
       names(report.table) <- c("Mean", "SD", "CV%", "Var", "Median", "Shrink%")
       if (reportType == 1) {
         #only for NPAG

diff --git a/R/makeFinal.R b/R/makeFinal.R
@@ -69,10 +69,14 @@ makeFinal <- function(data){
     }
     #summarize weighted corden
     wParVol <- prod(data$ab[,2]-data$ab[,1]) / gridpts
-    if (nrow(data$corden)>1) {popMean <- colSums(data$corden[,1:data$nvar] * data$corden[,data$nvar+1] )  * wParVol} else {
+    if (nrow(data$corden)>1) {
+      popMean <- colSums(data$corden[,1:data$nvar] * data$corden[,data$nvar+1] )  * wParVol
+    } else {
       popMean <- data$corden[1:data$nvar] * data$corden[data$nvar+1]  * wParVol
     }
 
+    names(popMean) <- data$par
+
     if(nrow(data$corden)>1){
       popCov <- matrix(NA,ncol=data$nvar,nrow=data$nvar)
       for (i in 1:data$nvar){
@@ -86,15 +90,17 @@ makeFinal <- function(data){
       popCor <- matrix(rep(NA,data$nvar**2),nrow=data$nvar)
       diag(popCor) <- rep(1,data$nvar)
     }
+    popMean <- data.frame(t(popMean))
+
+
 
     popPoints <- data.frame(data$corden)
     names(popPoints) <- c(data$par,"prob")
     popPoints$prob <- popPoints$prob*wParVol
     class(popPoints) <- c("popPoints","data.frame")
 
-    names(popMean) <- data$par
-    dimnames(popCov) <- list(data$par,data$par)
-    if (all(!is.na(popCor))) dimnames(popCor) <- list(data$par,data$par)
+
+
 
     if(length(data$postden)>0){
       # temp1 <- melt(data$postden)
@@ -121,7 +127,7 @@ makeFinal <- function(data){
     popMedian <- pointSum[pointSum$parameter=="WtMed" & pointSum$percentile==0.5,1:length(data$par)]
     names(popMedian) <- data$par
 
-    popVar <- diag(popCov)
+    popVar <- data.frame(t(diag(popCov)))
     names(popVar) <- data$par
 
     popSD <- sqrt(popVar)
@@ -156,13 +162,18 @@ makeFinal <- function(data){
     #shrinkage
     varEBD <- apply(postVar[,-1],2,mean)
     sh <- varEBD/popVar
-    sh.DF <- data.frame(par=data$par,shrinkage=sh)
+    sh.DF <- data.frame(sh)
 
     if(is.null(data$nranfix)) data$nranfix <- 0
     if(data$nranfix>0){
       popRanFix <- data$valranfix
       names(popRanFix) <- data$parranfix
     } else {popRanFix <- NULL}
+
+    popCov <- data.frame(popCov, row.names = data$par)
+    popCor <- data.frame(popCor, row.names = data$par)
+    names(popCov) <- data$par
+    if (all(!is.na(popCor))) names(popCor) <- data$par
 
 
     outlist <- list(popPoints=popPoints,popMean=popMean,popSD=popSD,popCV=popCV,popVar=popVar,
@@ -205,7 +216,12 @@ makeFinal <- function(data){
     #shrinkage
     varEBD <- apply(postVar[,-1],2,mean)
     sh <- varEBD/popVar
-    sh.DF <- data.frame(par=data$par,shrinkage=sh)
+    sh.DF <- data.frame(sh)
+
+    popCov <- data.frame(popCov, row.names = data$par)
+    popCor <- data.frame(popCor, row.names = data$par)
+    names(popCov) <- data$par
+    if (all(!is.na(popCor))) names(popCor) <- data$par
 
 
     outlist <- list(popMean=popMean,popSD=popSD,popCV=popCV,popVar=popVar,

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -1,6 +1,15 @@
 \name{NEWS}
 \title{NEWS file for the Pmetrics package}
 
+\section{Changes in version 1.9.3}{
+
+\subsection{BUG FIXES}{
+\itemize{
+\item A bug that made some tables in the report have wrong headers was fixed.
+}
+}
+}
+
 \section{Changes in version 1.9.2}{
 
 \subsection{NEW FEATURES}{