Because scaling (reducing and centering) is meaningless for linear regression we…

Because scaling (reducing and centering) is meaningless for linear regression we removed these options

R/mprocuste.R

@@ -107,8 +107,7 @@ pm.fit = function(covmat,y,xs,
 #' @export
 pm = function (formula,data, subset, weights, na.action, method = "qr",
                singular.ok = TRUE, tol = 1e-07,
-               model = TRUE, x = TRUE, y = TRUE, A = TRUE ,
-               scale = TRUE, return.scale = TRUE) {
+               model = TRUE, x = TRUE, y = TRUE, A = TRUE) {
 
   ret.x <- x
   ret.y <- y
@@ -168,10 +167,7 @@ pm = function (formula,data, subset, weights, na.action, method = "qr",
     variances= diag(data.cov)
     std.dev = sqrt(variances)
 
-    if (scale)
-      vars.norm = mapply(function(x,s) scale(x,scale = FALSE)/s, vars,std.dev)
-    else
-      vars.norm = as.procmod.frame(mapply(function(x) scale(x,scale = FALSE), vars))
+    vars.norm = as.procmod.frame(mapply(function(x) scale(x,scale = FALSE), vars))
 
     if (is.null(w)) {
       subset.w=rep(TRUE,nvars)
@@ -192,15 +188,10 @@ pm = function (formula,data, subset, weights, na.action, method = "qr",
                singular.ok = singular.ok,
                tol = tol)
 
-    if (! scale) {
-      y.sd = std.dev[irep]
-      xs.sd= std.dev[seq_len(nvars)!=irep]
+    y.sd = std.dev[irep]
+    xs.sd= std.dev[seq_len(nvars)!=irep]
 
-      z$varpart = (z$coefficients * xs.sd / y.sd) ^ 2
-    }
-    else {
-      z$varpart = z$coefficients ^ 2
-    }
+    z$varpart = (z$coefficients * xs.sd / y.sd) ^ 2
 
 
     Y = vars.norm[[irep]]

vignettes/ProcMod.Rmd

@@ -548,24 +548,13 @@ partition = euk.anova[,"Sum Sq"]/sum(euk.anova[,"Sum Sq"])
 names(partition)=rownames(euk.anova)
 partition
 ```
-
-```{r}
-euk.pm = pm(euk ~ soil + climat +  geo + hist,data=data,scale = FALSE)
-euk.pm
-```
-
-```{r}
-plot(euk.pm)
-```
-
 ```{r}
-euk.anova = anova(euk.pm)
-euk.anova
+euk.anova.w = anova(euk.pm.w)
+euk.anova.w
 ```
-
 ```{r}
-partition = euk.anova[,"Sum Sq"]/sum(euk.anova[,"Sum Sq"])
-names(partition)=rownames(euk.anova)
+partition = euk.anova.w[,"Sum Sq"]/sum(euk.anova.w[,"Sum Sq"])
+names(partition)=rownames(euk.anova.w)
 partition
 ```