From 15a8c39ef19a5588597f3bce6060947be7a54420 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Fri, 15 Jan 2021 11:47:20 +0100
Subject: [PATCH] Added/removed TODOs

---
 R/computePopulationLogml.R |  1 +
 R/indMix.R                 | 13 ++++++-------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/computePopulationLogml.R b/R/computePopulationLogml.R
index bf9782d..a6cf71c 100644
--- a/R/computePopulationLogml.R
+++ b/R/computePopulationLogml.R
@@ -6,6 +6,7 @@ computePopulationLogml <- function(pops, adjprior, priorTerm) {
 	z <- length(pops)
 
 	popLogml <- squeeze(
+		# FIXME: assumes COUNTS has 3 dims. Where does this come from?
 		sum(
 			sum(
 				reshape(
diff --git a/R/indMix.R b/R/indMix.R
index b564460..4f1d65c 100644
--- a/R/indMix.R
+++ b/R/indMix.R
@@ -26,7 +26,7 @@ indMix <- function(c, npops, dispText) {
 		dispText <- 1
 		npopstext <- matrix()
 		ready <- FALSE
-		teksti <- 'Input upper bound to the number of populations (possibly multiple values)'
+		teksti <- 'Input upper bound to the number of populations (possibly multiple values)' # TODO: add "likely ncol(Z) values"?
 		while (!ready) {
 			npopstextExtra <- inputdlg(
 				teksti,
@@ -87,11 +87,10 @@ indMix <- function(c, npops, dispText) {
 			)
 		}
 		ninds <- size(rows, 1)
-
-		initialPartition <- admixture_initialization(initData, npops, Z) # TODO: translate
-		sumcounts_counts_logml = initialCounts(
+		initialPartition <- admixture_initialization(initData, npops, Z)
+		sumcounts_counts_logml <- initialCounts(
 			initialPartition, data, npops, rows, noalle, adjprior
-		) # TODO: translate
+		)
 		sumcounts <- sumcounts_counts_logml$sumcounts
 		counts <- sumcounts_counts_logml$counts
 		logml <- sumcounts_counts_logml$logml
@@ -104,7 +103,7 @@ indMix <- function(c, npops, dispText) {
 
 		COUNTS <- counts
 		SUMCOUNTS <- sumcounts
-		POP_LOGML <- computePopulationLogml(1:npops, adjprior, priorTerm) # TODO: translate
+		POP_LOGML <- computePopulationLogml(1:npops, adjprior, priorTerm)
 		LOGDIFF <- repmat(-Inf, c(ninds, npops))
 		rm(initialPartition, counts, sumcounts)
 
@@ -564,4 +563,4 @@ indMix <- function(c, npops, dispText) {
 	return(
 		list(logml = logml, npops = npops, partitionSummary = partitionSummary)
 	)
-}
+}
\ No newline at end of file