ashenkin · July 28, 2016 11:04 · Jul 28, 2016
diff --git a/set_dev_contrasts.r b/set_dev_contrasts.r
@@ -0,0 +1,18 @@
+contr.sum.keepnames <- function(...) {
+    # make deviation contrasts that don't lose the names of the factors in the model results
+    # from https://stackoverflow.com/questions/10808853/why-does-changing-contrast-type-change-row-labels-in-r-lm-summary
+    conS <- contr.sum(...)
+    colnames(conS) = rownames(conS)[-length(rownames(conS))]
+    conS
+}
+
+set_dev_contrasts <- function(df, colname = "site") {
+    # Set contrasts to "deviation coding" so site effects are as compared to overall mean across all sites.  I.e., sites together should have a mean 0 effect.
+    # See http://www.ats.ucla.edu/stat/r/library/contrast_coding.htm
+    # Usage: my_df = set_dev_contrasts(my_df, colname = "col_to_set")
+    col2setup = df[,colname]
+    col2setup = as.factor(col2setup)[, drop = TRUE]
+    contrasts(col2setup) <- contr.sum.keepnames(levels(col2setup))
+    df[,colname] = col2setup
+    return(df)
+}