Changed norm.mode to rescale.mode as suggested in issue #134

Author: helenhe96

pkg/R/processtree.R

@@ -55,7 +55,7 @@ parse.newick <- function(tree) {
     stop(".preprocess.tree() requires phylo or character (Newick) object for tree")
   }
   tree <- ladderize(tree)
-  tree <- .rescale.tree(tree, config$norm.mode)
+  tree <- .rescale.tree(tree, config$rescale.mode)
 
   return(tree)
 }

pkg/R/smcABC.R

@@ -49,7 +49,7 @@ simulate.trees <- function(workspace, theta, model, seed=NA, ...) {
 
 
 # formally 'distance'
-kernel.dist <- function(t1, t2, decay.factor, rbf.variance, sst.control, norm.mode, labelPattern, labelReplacement, gamma) {
+kernel.dist <- function(t1, t2, decay.factor, rbf.variance, sst.control, rescale.mode, labelPattern, labelReplacement, gamma) {
   if (is.null(t1$kernel)) {
     stop("t1 missing self kernel in distance()")
   }

pkg/R/smcConfig.R

@@ -43,7 +43,7 @@ load.config <- function(file) {
     decay.factor=0.2,
     rbf.variance=100.0,
     sst.control=1.0,
-    norm.mode='NONE',
+    rescale.mode='NONE',
     labelPattern="",
     labelReplacement="",
     gamma=0
@@ -121,7 +121,7 @@ load.config <- function(file) {
       config$decay.factor <- kernel.settings$decay.factor
       config$rbf.variance <- kernel.settings$rbf.variance
       config$sst.control <- kernel.settings$sst.control
-      config$norm.mode <- kernel.settings$norm.mode
+      config$rescale.mode <- kernel.settings$rescale.mode
       config$labelPattern <- kernel.settings$labelPattern
       config$labelReplacement <- kernel.settings$labelReplacement
       config$gamma <- kernel.settings$gamma
@@ -148,7 +148,7 @@ load.config <- function(file) {
         config$decay.factor <- as.numeric(values["decay.factor"])
         config$rbf.variance <- as.numeric(values["rbf.variance"])
         config$sst.control <- as.numeric(values["sst.control"])
-        config$norm.mode <- values["norm.mode"]
+        config$rescale.mode <- values["rescale.mode"]
         config$labelPattern <- values["labelPattern"]
         config$labelReplacement <- values["labelReplacement"]
         config$gamma <- as.numeric(values["gamma"])

tests/fixtures/test-bisse.yaml

@@ -76,7 +76,7 @@ distances:
     decay.factor: 0.2
     rbf.variance: 100.0
     sst.control: 1.0
-    norm.mode: 'NONE'
+    rescale.mode: 'NONE'
     labelPattern: "'^.+_([01])$'"
     labelReplacement: "'\\1'"
     gamma: 1