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Updated documentation

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This commit is contained in:
Waldir Leoncio 2020-07-31 14:05:40 +02:00
parent f89a6e9fa3
commit d57be6a8f3
10 changed files with 73 additions and 37 deletions
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62
R/greedyMix.R
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@ -156,8 +156,7 @@ greedyMix <- function(
# h0 = findobj('Tag','filename1_text');
# set(h0,'String',filename); clear h0;
browser()#TEMP
list_dranap <- handleData(data) # FIXME: debug
list_dranap <- handleData(data)
data <- list_dranap$newData
rowsFromInd <- list_dranap$rowsFromInd
alleleCodes <- list_dranap$alleleCodes
@ -253,7 +252,7 @@ greedyMix <- function(
POP_LOGML <- vector()
clearGlobalVars <- vector()
# ==========================================================================
c <- list()
c$data <- data
c$noalle <- noalle
c$adjprior <- adjprior
@ -267,34 +266,34 @@ greedyMix <- function(
c$rows <- c(ekat, ekat + rowsFromInd - 1)
# partition compare
if (!is.null(partitionCompare)) {
nsamplingunits <- size(c$rows, 1)
partitions <- partitionCompare$partitions
npartitions <- size(partitions, 2)
partitionLogml <- zeros(1, npartitions)
for (i in seq_len(npartitions)) {
# number of unique partition lables
npops <- length(unique(partitions[, i]))
# if (!is.null(partitionCompare)) {
# nsamplingunits <- size(c$rows, 1)
# partitions <- partitionCompare$partitions
# npartitions <- size(partitions, 2)
# partitionLogml <- zeros(1, npartitions)
# for (i in seq_len(npartitions)) {
# # number of unique partition lables
# npops <- length(unique(partitions[, i]))
partitionInd <- zeros(ninds * rowsFromInd, 1)
partitionSample <- partitions[, i]
for (j in seq_len(nsamplingunits)) {
partitionInd[c$rows[j, 1]:c$rows[j, 2]] <- partitionSample[j]
}
# partitionLogml[i] = initialCounts(
# partitionInd,
# data[, seq_len(end - 1)],
# npops,
# c$rows,
# noalle,
# adjprior
# ) #TODO translate
}
# return the logml result
partitionCompare$logmls <- partitionLogml
# set(h1, 'userdata', partitionCompare) # ASK remove?
return()
}
# partitionInd <- zeros(ninds * rowsFromInd, 1)
# partitionSample <- partitions[, i]
# for (j in seq_len(nsamplingunits)) {
# partitionInd[c$rows[j, 1]:c$rows[j, 2]] <- partitionSample[j]
# }
# # partitionLogml[i] = initialCounts(
# # partitionInd,
# # data[, seq_len(end - 1)],
# # npops,
# # c$rows,
# # noalle,
# # adjprior
# # ) #TODO translate
# }
# # return the logml result
# partitionCompare$logmls <- partitionLogml
# # set(h1, 'userdata', partitionCompare) # ASK remove?
# return()
# }
# ASK remove (graphical part)?
# if (fixedK) {
@ -312,10 +311,11 @@ greedyMix <- function(
# h0 = findobj('Tag','filename2_text')
# outp = get(h0,'String');
browser() # TEMP
changesInLogml <- writeMixtureInfo(
logml, rowsFromInd, data, adjprior, priorTerm, outp, inp,
popnames, fixedK
) # FIXMEL depends on get function above
) # FIXME: broken
# viewMixPartition(PARTITION, popnames) # ASK translate? On graph folder