From 3537f18d2ccaefa1c5ed551802fbe24d35e71f7c Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Fri, 11 Aug 2023 11:18:03 +0200
Subject: [PATCH] Incorporated handleData() on greedyMix() (#25)

---
 R/greedyMix.R    | 30 ++++++++++++++----------------
 man/greedyMix.Rd | 15 ++++++---------
 2 files changed, 20 insertions(+), 25 deletions(-)

diff --git a/R/greedyMix.R b/R/greedyMix.R
index 6715145..1826d50 100644
--- a/R/greedyMix.R
+++ b/R/greedyMix.R
@@ -27,28 +27,26 @@
 #' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
 #' greedyMix(data, "fasta")
 greedyMix <- function(
-  data, format, partitionCompare = NULL, ninds = NULL, rowsFromInd = NULL,
-  noalle = NULL, adjprior = NULL, npops = 1L, priorTerm = NULL, counts = NULL,
-  sumcounts = NULL, max_iter = 100L, alleleCodes = NULL, inp = NULL,
-  popnames = NULL, fixedK = FALSE, verbose = FALSE
+  data, format, partitionCompare = NULL, ninds = NULL, npops = 1L,
+  counts = NULL, sumcounts = NULL, max_iter = 100L, alleleCodes = NULL,
+  inp = NULL, popnames = NULL, fixedK = FALSE, verbose = FALSE
 ) {
   # Importing and handling data ================================================
   data <- importFile(data, format, verbose)
+  data <- handleData(data, tolower(format))
   c <- list(
-    # TODO: get elements from handleData()?
-    noalle = noalle,
-    rows = NA,
-    data = data,
-    adjprior = adjprior,
-    priorTerm = priorTerm,
-    rowsFromInd = rowsFromInd
+    noalle = data[["noalle"]],
+    data = data[["newData"]],
+    adjprior = data[["adjprior"]],
+    priorTerm = data[["priorTerm"]],
+    rowsFromInd = data[["rowsFromInd"]]
   )
 
   # Comparing partitions =======================================================
   if (!is.null(partitionCompare)) {
     logmls <- comparePartitions(
-      data, nrow(data), partitionCompare[["partitions"]], ninds, rowsFromInd,
-      noalle, adjprior
+      c[["data"]], nrow(c[["data"]]), partitionCompare[["partitions"]], ninds,
+      c[["rowsFromInd"]], c[["noalle"]], c[["adjprior"]]
     )
   }
 
@@ -61,9 +59,9 @@ greedyMix <- function(
 
   # Generating output object ===================================================
   out <- list(
-      "alleleCodes" = alleleCodes, "adjprior" = adjprior, "popnames" = popnames,
-      "rowsFromInd" = rowsFromInd, "data" = data, "npops" = npops,
-      "noalle" = noalle, "mixtureType" = "mix", "logml" = logml
+      "alleleCodes" = alleleCodes, "adjprior" = c[["adjprior"]], "popnames" = popnames,
+      "rowsFromInd" = c[["rowsFromInd"]], "data" = data, "npops" = npops,
+      "noalle" = c[["noalle"]], "mixtureType" = "mix", "logml" = logml
     )
   if (logml == 1) {
     return(out)
diff --git a/man/greedyMix.Rd b/man/greedyMix.Rd
index 74242b8..dc26245 100644
--- a/man/greedyMix.Rd
+++ b/man/greedyMix.Rd
@@ -9,9 +9,6 @@ greedyMix(
   format,
   partitionCompare = NULL,
   ninds = NULL,
-  rowsFromInd = NULL,
-  noalle = NULL,
-  adjprior = NULL,
   npops = 1L,
   priorTerm = NULL,
   counts = NULL,
@@ -33,12 +30,6 @@ greedyMix(
 
 \item{ninds}{number of individuals}
 
-\item{rowsFromInd}{a list of rows for each individual}
-
-\item{noalle}{number of alleles}
-
-\item{adjprior}{ajuster prior probabilities}
-
 \item{npops}{number of populations}
 
 \item{priorTerm}{prior terms}
@@ -58,6 +49,12 @@ greedyMix(
 \item{fixedK}{if \code{TRUE}, the number of populations is fixed}
 
 \item{verbose}{if \code{TRUE}, prints extra output information}
+
+\item{rowsFromInd}{a list of rows for each individual}
+
+\item{noalle}{number of alleles}
+
+\item{adjprior}{ajuster prior probabilities}
 }
 \description{
 Clustering of individuals