From 228b4d808ac6647b71a603e417eaf09c9bad1147 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Mon, 9 Nov 2020 15:00:07 +0100
Subject: [PATCH] Fixed syntax

---
 R/initialPopCounts.R |  4 ++--
 R/matlab2r.R         | 13 ++++++++++---
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/R/initialPopCounts.R b/R/initialPopCounts.R
index a865243..2cb4806 100644
--- a/R/initialPopCounts.R
+++ b/R/initialPopCounts.R
@@ -6,11 +6,11 @@ initialPopCounts <- function(data, npops, rows, noalle, adjprior) {
 	for (i in 1:npops) {
 		for (j in 1:nloci) {
 			i_rivit <- rows(i, 1):rows(i, 2)
-			havainnotLokuksessa <- find(data(i_rivit, j) >= 0)
+			havainnotLokuksessa <- find(data[i_rivit, j] >= 0)
 			sumcounts(i, j) <- length(havainnotLokuksessa)
 			for (k in 1:noalle[j]) {
 				alleleCode <- k
-				N_ijk <- length(find(data(i_rivit, j) == alleleCode))
+				N_ijk <- length(find(data[i_rivit, j] == alleleCode))
 				counts(k, j, i) <- N_ijk
 			}
 		}
diff --git a/R/matlab2r.R b/R/matlab2r.R
index 12403d0..c54bde7 100644
--- a/R/matlab2r.R
+++ b/R/matlab2r.R
@@ -1,8 +1,8 @@
 #' @title Convert Matlab function to R
-#' @description Performs basic syntax conversion
+#' @description Performs basic syntax conversion from Matlab to R
 #' @param filename name of the file
 #' @param saveOutput if `TRUE`, `filename` is overwritten. Defaults to `FALSE`
-#' @return text converted to R
+#' @return text converted to R, printed to screen or replacing input file
 #' @author Waldir Leoncio
 #' @export
 matlab2r <- function(filename, saveOutput = FALSE) {
@@ -11,9 +11,16 @@ matlab2r <- function(filename, saveOutput = FALSE) {
 	# Reading file into R
 	txt <- readLines(filename)
 	# Replacing text
+	txt <- gsub(
+		pattern     = "function (.+)\\s*=\\s*(.+)\\((.+)\\)",
+		replacement = "\\2 <- function(\\3) { return(\\1)",
+		x           = txt
+	)
 	txt <- gsub(";", "", txt)
 	txt <- gsub("for (.+)=(.+)", "for (\\1 in \\2) {", txt)
 	txt <- gsub("end", "}", txt)
+	# TODO: replace forms like (:,:) with [, ]
+	# TODO: reformat if statements
 	# Returning converted code
 	if (!saveOutput) {
 		return(cat(txt, sep="\n"))
@@ -28,4 +35,4 @@ matlab2r <- function(filename, saveOutput = FALSE) {
 			)
 		)
 	}
-}
\ No newline at end of file
+}