Fixed to indMix (#25)

ocbe-uio · Aug 11, 2023 · 372891f · 372891f
1 parent 3537f18
commit 372891f
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Showing 3 changed files with 15 additions and 9 deletions.
diff --git a/R/greedyMix.R b/R/greedyMix.R
@@ -27,7 +27,7 @@
 #' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
 #' greedyMix(data, "fasta")
 greedyMix <- function(
-  data, format, partitionCompare = NULL, ninds = NULL, npops = 1L,
+  data, format, partitionCompare = NULL, ninds = 1L, npops = 1L,
   counts = NULL, sumcounts = NULL, max_iter = 100L, alleleCodes = NULL,
   inp = NULL, popnames = NULL, fixedK = FALSE, verbose = FALSE
 ) {
@@ -52,17 +52,20 @@ greedyMix <- function(
 
 
   # Generating partition summary ===============================================
+  ekat <- seq(1L, c[["rowsFromInd"]], ninds * c[["rowsFromInd"]]) # ekat = (1:rowsFromInd:ninds*rowsFromInd)';
+  c[["rows"]] <- c(ekat, ekat + c[["rowsFromInd"]] - 1L) # c.rows = [ekat ekat+rowsFromInd-1]
   logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose);
   logml <- logml_npops_partitionSummary[["logml"]]
   npops <- logml_npops_partitionSummary[["npops"]]
   partitionSummary <- logml_npops_partitionSummary[["partitionSummary"]]
 
   # Generating output object ===================================================
   out <- list(
-      "alleleCodes" = alleleCodes, "adjprior" = c[["adjprior"]], "popnames" = popnames,
-      "rowsFromInd" = c[["rowsFromInd"]], "data" = data, "npops" = npops,
-      "noalle" = c[["noalle"]], "mixtureType" = "mix", "logml" = logml
-    )
+    "alleleCodes" = alleleCodes, "adjprior" = c[["adjprior"]],
+    "popnames" = popnames, "rowsFromInd" = c[["rowsFromInd"]],
+    "data" = c[["data"]], "npops" = npops, "noalle" = c[["noalle"]],
+    "mixtureType" = "mix", "logml" = logml
+  )
   if (logml == 1) {
     return(out)
   }

diff --git a/R/indMix.R b/R/indMix.R
@@ -145,8 +145,8 @@ indMix <- function(c, npops, counts = NULL, sumcounts = NULL, max_iter = 100L, d
         if (kokeiltu[round] == 1) { # Askelta kokeiltu viime muutoksen j�lkeen
         } else if (round == 0 | round == 1) { # Yksil�n siirt�minen toiseen populaatioon.
           inds <- seq_len(ninds)
-          aputaulu <- cbind(inds, rand(ninds, 1))
-          aputaulu <- sortrows(aputaulu, 2)
+          aputaulu <- cbind(t(inds), rand(ninds, 1))
+          aputaulu <- matrix(sortrows(aputaulu, 2), nrow = nrow(aputaulu))
           inds <- t(aputaulu[, 1])
           muutosNyt <- 0
 

diff --git a/R/laskeMuutokset12345.R b/R/laskeMuutokset12345.R
@@ -349,12 +349,15 @@ greedyMix_muutokset <- R6Class(
       i1_logml <- POP_LOGML[i1]
       muutokset[i1] <- 0
 
-      rows <- globalRows[ind, 1]:globalRows[ind, 2]
+      if (is.null(dim(globalRows))) {
+        rows <- globalRows[1]:globalRows[2]
+      } else {
+        rows <- globalRows[ind, 1]:globalRows[ind, 2]
+      }
       diffInCounts <- computeDiffInCounts(
         rows, size(COUNTS, 1), size(COUNTS, 2), data
       )
       diffInSumCounts <- colSums(diffInCounts)
-
       COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
       SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - diffInSumCounts
       new_i1_logml <- computePopulationLogml(i1, adjprior, priorTerm)