From dd6ee912bd0bfffaf1cc3fbc982d5b77d2c05706 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Fri, 27 Sep 2024 06:59:18 +0200
Subject: [PATCH] Syntax fixes

---
 R/greedyMix.R           | 2 +-
 R/laskeMuutokset12345.R | 8 ++++----
 R/laskeOsaDist.R        | 4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/greedyMix.R b/R/greedyMix.R
index cea602b..0ac6ff1 100644
--- a/R/greedyMix.R
+++ b/R/greedyMix.R
@@ -80,7 +80,7 @@ greedyMix <- function(
   # Generating partition summary ===============================================
   ekat <- seq(1L, ninds * c[["rowsFromInd"]], c[["rowsFromInd"]])
   c[["rows"]] <- cbind(ekat, ekat + c[["rowsFromInd"]] - 1L)
-  logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose) # FIXME: not working for FASTA, GenePop
+  logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose) # FIXME: not working for FASTA
   logml <- logml_npops_partitionSummary[["logml"]]
   npops <- logml_npops_partitionSummary[["npops"]]
   partitionSummary <- logml_npops_partitionSummary[["partitionSummary"]]
diff --git a/R/laskeMuutokset12345.R b/R/laskeMuutokset12345.R
index 78c9f5c..e940324 100644
--- a/R/laskeMuutokset12345.R
+++ b/R/laskeMuutokset12345.R
@@ -423,7 +423,7 @@ greedyMix_muutokset <- R6Class(
       globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] + diffInSumCounts
 
       if (i1 < npops) {
-        i2 <- c(1:(i1 - 1), (i1 + 1):npops)
+        i2 <- c(seq_len(i1 - 1), (i1 + 1):npops)
       } else {
         i2 <- 1:(i1 - 1)
       }
@@ -458,12 +458,12 @@ greedyMix_muutokset <- R6Class(
       muutokset <- zeros(npops2, npops)
 
       i1_logml <- globals$POP_LOGML[i1]
-      for (pop2 in 1:npops2) {
+      for (pop2 in seq_len(npops2)) {
         inds <- inds2[matlab2r::find(T2 == pop2)]
         ninds <- length(inds)
         if (ninds > 0) {
           rows <- list()
-          for (i in 1:ninds) {
+          for (i in seq_len(ninds)) {
             ind <- inds[i]
             lisa <- globalRows[ind, 1]:globalRows[ind, 2]
             rows <- c(rows, t(lisa))
@@ -480,7 +480,7 @@ greedyMix_muutokset <- R6Class(
           globals$SUMCOUNTS[i1, ] <- globals$SUMCOUNTS[i1, ] + diffInSumCounts
 
           if (i1 < npops) {
-            i2 <- c(1:(i1 - 1), (i1 + 1):npops)
+            i2 <- c(seq_len(i1 - 1), (i1 + 1):npops)
           } else {
             i2 <- 1:(i1 - 1)
           }
diff --git a/R/laskeOsaDist.R b/R/laskeOsaDist.R
index b6c8570..e915276 100644
--- a/R/laskeOsaDist.R
+++ b/R/laskeOsaDist.R
@@ -11,7 +11,7 @@ laskeOsaDist <- function(inds2, dist, ninds) {
   ninds2 <- length(inds2)
   apu <- zeros(choose(ninds2, 2), 2)
   rivi <- 1
-  for (i in 1:(ninds2 - 1)) {
+  for (i in seq_len(ninds2 - 1)) {
     for (j in (i + 1):ninds2) {
       apu[rivi, 1] <- inds2[i]
       apu[rivi, 2] <- inds2[j]
@@ -20,6 +20,6 @@ laskeOsaDist <- function(inds2, dist, ninds) {
   }
   apu <- (apu[, 1] - 1) * ninds - apu[, 1] / 2 *
     (apu[, 1] - 1) + (apu[, 2] - apu[, 1])
-  dist2 <- dist(apu)
+  dist2 <- dist[apu]
   return(dist2)
 }