various bug fixes

[ape.git] / R / SDM.R

diff --git a/R/SDM.R b/R/SDM.R
index 94a8f313590557362a9c47087192723a2ddf8140..faa263e3378009c1df57088e36f5659b7061ada8 100644 (file)
--- a/R/SDM.R
+++ b/R/SDM.R
@@ -18,7 +18,7 @@ SDM <- function(...)
         tot <- tot + length(rownames(st[[i]]))
     }
     sp <- mat.or.vec(1,k)
-    for (i in c(k+1:k))
+    for (i in c(k + 1:k))
         sp[i - k] <- st[[i]]
 
     astart <- mat.or.vec(1, tot) # start of aip, astart[p] is start of aip
@@ -65,7 +65,7 @@ SDM <- function(...)
             dijp <- -1
             if (l == p) { # calculate alpha_p
                 for (i in 1:n) {
-                    for (j in 1:n) { #check if {i,j}\subset L_l
+                    for (j in 1:n) { # check if {i,j}\subset L_l
                         d <- st[[l]]
                         if (i != j & is.element(labels[i],rownames(d)) & is.element(labels[j],colnames(d))) {
                             dij <- d[rownames(d) == labels[i], colnames(d) == labels[j]]
@@ -79,7 +79,7 @@ SDM <- function(...)
                 }
             } else {
                 for (i in 1:n) {
-                    for (j in 1:n) { #check if {i,j}\subset L_l
+                    for (j in 1:n) { # check if {i,j}\subset L_l
                         d <- st[[l]]
                         if (i != j & is.element(labels[i], rownames(d)) & is.element(labels[j], colnames(d)) & is.element(labels[i], rownames(d_p)) & is.element(labels[j], colnames(d_p))) {
                             dij <- d[rownames(d) == labels[i], colnames(d) == labels[j]]
@@ -160,11 +160,11 @@ SDM <- function(...)
         }
     }
     a <- solve(Q, col, 1e-19)
-    for(i in 1:n) {
-        for(j in 1:n) {
+    for (i in 1:n) {
+        for (j in 1:n) {
             sum <- 0
             sumv <- 0
-            for(p in 1:k) {
+            for (p in 1:k) {
                 d <- st[[p]]
                 if (is.element(labels[i], rownames(d)) & is.element(labels[j], rownames(d))) {
                     ipos <- which(rownames(d) == labels[i])