Bunch more changes for v9210

DESCRIPTION

@@ -29,5 +29,4 @@ Remotes: ANTsX/ANTsR,
     ANTsX/ANTsRCore
 LinkingTo: Rcpp, RcppArmadillo
 NeedsCompilation: yes
-RoxygenNote: 6.1.0.9000
-
+RoxygenNote: 6.1.1.9000

NAMESPACE

@@ -5,6 +5,7 @@ export(BM)
 export(BMfast2)
 export(BMperm)
 export(checkAntsInput)
+export(checkAssumptions_ttest)
 export(checkFilenameHeaders)
 export(checkImageList)
 export(checkMask)
@@ -24,6 +25,7 @@ export(lsm_svr)
 export(lsm_ttest)
 export(minSegDistance)
 export(optimize_SCCANsparseness)
+export(printInfo)
 export(registerLesionToTemplate)
 export(regresfast)
 export(save.lesymap)
@@ -47,7 +49,9 @@ importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,residuals)
 importFrom(stats,runif)
+importFrom(stats,shapiro.test)
 importFrom(stats,t.test)
+importFrom(stats,var.test)
 importFrom(utils,capture.output)
 importFrom(utils,find)
 importFrom(utils,getSrcDirectory)

NEWS

@@ -1,11 +1,14 @@
 ==============
 LESYMAP v0.0.0.9210 (Release date: 2019-03-15)
-  - Added new method 'svr' - Support Vector Regression (experimental)
+  - Added method 'svr' - Support Vector Regression (experimental)
+  - Added assumption checks for t-test analysis
   - Fixed missing 'rawWeights.img' in SCCAN output
   - Fixed missing 'sccan.ccasummary' in save.lesymap printout
   - Switched default method from "BM" to "sccan"
-  - Some user inputs made case tolerant: i.e., 'FDR' is same as 'fdr'
-  - Documentation improvement
+  - Main arguments are now case insensitive ('FDR' same as 'fdr')
+  - Enabled correctLesSize='both' (voxel + behavior)
+  - New 'printInfo' function to route information display
+  - Documentation corrections
 
 ==============
 LESYMAP v0.0.0.9202 (Release date: 2019-01-29)

R/getLesionSize.R

@@ -24,7 +24,7 @@ getLesionSize <- function(lesions.list, showInfo=TRUE) {
   }
 
   if (inputtype == 'antsFiles' & showInfo)
-    cat('      Slow computation from filenames. Preload images with imageFileNames2ImageList() for faster processing.')
+    printInfo('      Slow computation from filenames. Preload images with imageFileNames2ImageList() for faster processing.', type='middle')
 
   lessize = rep(NA, length(lesions.list))
 

R/getUniqueLesionPatches.R

@@ -115,11 +115,11 @@ getUniqueLesionPatches <- function(lesions.list, mask=NA, returnPatchMatrix=F,
   if (returnPatchMatrix) patchmatrix = lesmat[ , patindx==1]
 
   if (showInfo) {
-    cat(paste(
+    printInfo(paste(
       numpatches, 'unique patches,',
       numvoxels, 'voxels -',
-      round(numvoxels/numpatches,1), 'times more voxels\n'
-    ))
+      round(numvoxels/numpatches,1), 'times more voxels'
+    ), type='tail')
   }
 
   output = list(

R/lesyload_mricron.R

@@ -40,29 +40,29 @@ lesyload_mricron <- function(valfile, imageFolder=NA, returnFilenames=F, checkHe
     stop(paste0('  Some of the files are not found:\n', paste(basename(valdata$ImageName[!existindx]), collapse='\n')))
   }
 
-  if (showInfo) cat('All files found.\n')
+  if (showInfo) printInfo('All files found.')
 
   # all files are there, check their headers
   if (checkHeaders) {
-    if (showInfo) cat('Checking for unusual images...')
+    if (showInfo) printInfo('Checking for unusual images...', type='head')
     checkFilenameHeaders(files = valdata$ImageName, showError = F)
-    if (showInfo) cat('all headers identical.\n')
+    if (showInfo) printInfo('all headers identical.', type='tail')
   }
 
   # prepare lesions output
   if (returnFilenames) {
-    if (showInfo) cat('Filenames will be returned.\n')
+    if (showInfo) printInfo('Filenames will be returned.')
     lesions = valdata$ImageName
   } else {
-    if (showInfo) cat('Image list will be returned, please wait...')
+    if (showInfo) printInfo('Image list will be returned, please wait...', type='head')
     lesions = imageFileNames2ImageList(valdata$ImageName)
-    if (showInfo) cat('all loaded.\n')
+    if (showInfo) printInfo('all loaded.', type='tail')
   }
 
   # prepare behavior output
   behavior = valdata[,2]
 
-  if (showInfo) cat('You can now run lesymap with these data.\n')
+  if (showInfo) printInfo('You can now run lesymap with these data.')
 
   invisible(gc())
   return(list(lesions=lesions,