fix colliding file

docs/_static/code/simil.R

@@ -1,38 +1,34 @@
 
 ## 
-## FUNCTION simil() similarity based on data frame coocurrences
+## FUNCTION simil() to compute similarity of entries in a given data frame
 ## (CC BY-SA 4.0) Antonio Rivero Ostoic, jaro@cas.au.dk 
 ##
-## version 0.1 (16-04-2020)
+## version 0.2 (11-03-2020)
 ##
-## Parameters
-## x  a data frame or a list object with vectors to compare
+## INPUT AND ARGUMENTS
+## x  a data frame with an ID column
 ## att (vector) column(s) in x representing attributes
 ## null (optional) include NA or NULLs?
 ## uniq (optional) remove duplicates?
 ## diag.incl (optional) include entries in diagonal?
 
+
 simil <-
 function (x, att, null, uniq, diag.incl) 
 {
-    ifelse(is.data.frame(x) == FALSE, x <- as.data.frame(do.call(rbind, 
-        x)), NA)
-    if (missing(att) == TRUE) {
-        att <- seq_len(ncol(x))
-    }
-    else {
-        ifelse(is.vector(att) == TRUE, NA, stop("\"att\" must be a vector."))
-    }
+    ifelse(missing(null) == FALSE && isTRUE(null == TRUE) == 
+        TRUE, null <- TRUE, null <- FALSE)
     ifelse(missing(uniq) == FALSE && isTRUE(uniq == FALSE) == 
-        TRUE, NA, x <- unique(x))
+        TRUE, uniq <- FALSE, uniq <- TRUE)
+    ifelse(isTRUE(uniq == TRUE) == TRUE, x <- unique(x), NA)
     ifelse(is.null(x$ID) == TRUE, mat <- matrix(0L, nrow = nrow(x), 
         ncol = nrow(x), dimnames = list(unlist(x[, 1]), unlist(x[, 
             1]))), mat <- matrix(0L, nrow = nrow(x), ncol = nrow(x), 
         dimnames = list(x$ID, x$ID)))
     for (at in att) {
         ccat <- unlist(unique(x[, at]))
-        ifelse(missing(null) == FALSE && isTRUE(null == TRUE) == 
-            TRUE, NA, ccat <- ccat[which(ccat != "NULL")])
+        ifelse(isTRUE(null == TRUE) == TRUE, NA, ccat <- ccat[which(ccat != 
+            "NULL")])
         for (i in seq_len(length(ccat))) {
             mat[which(x[, at] == ccat[i]), which(x[, at] == ccat[i])] <- mat[which(x[, 
                 at] == ccat[i]), which(x[, at] == ccat[i])] +