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Improved documentation

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This commit is contained in:
Waldir Leoncio 2020-06-24 12:37:38 +02:00
parent d2fb3bf90a
commit b2d1b830cd
1 changed files with 15 additions and 15 deletions
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30
R/greedyMix.R
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@ -46,12 +46,12 @@ greedyMix <- function(
} else { } else {
input_type_name <- paste0(format, "-format") input_type_name <- paste0(format, "-format")
} }
# ----------------------------------------------------------------------
# Treating BAPS-formatted files
# ----------------------------------------------------------------------
if (length(input_type_name) == 0) { if (length(input_type_name) == 0) {
stop('Invalid alternative') stop('Invalid alternative')
} else if (input_type_name == 'BAPS-format') { } else if (input_type_name == 'BAPS-format') {
# ------------------------------------------------------------------
# Treating BAPS-formatted files
# ------------------------------------------------------------------
if (!is(tietue, "character")) { if (!is(tietue, "character")) {
pathname_filename <- uigetfile( pathname_filename <- uigetfile(
"*.txt", "Load data in BAPS-format" "*.txt", "Load data in BAPS-format"
@ -65,7 +65,7 @@ greedyMix <- function(
# fprintf(1,'Data: %s\n',[pathname filename]); # fprintf(1,'Data: %s\n',[pathname filename]);
# end # end
data <- read.delim(pathname_filename) # ASK: what is the delimiter? data <- read.delim(pathname_filename) # TODO: discover delimiter
ninds <- testaaOnkoKunnollinenBapsData(data) # testing ninds <- testaaOnkoKunnollinenBapsData(data) # testing
if (ninds == 0) stop('Incorrect Data-file') if (ninds == 0) stop('Incorrect Data-file')
@ -128,10 +128,10 @@ greedyMix <- function(
save(c, file = kokonimi) save(c, file = kokonimi)
rm(c) rm(c)
} }
# ----------------------------------------------------------------------
# Treating GenePop-formatted files
# ----------------------------------------------------------------------
} else if (input_type_name == 'GenePop-format') { } else if (input_type_name == 'GenePop-format') {
# ------------------------------------------------------------------
# Treating GenePop-formatted files
# ------------------------------------------------------------------
if (!is(tietue, "character")) { if (!is(tietue, "character")) {
filename_pathname <- uigetfile( filename_pathname <- uigetfile(
filter = '*.txt', filter = '*.txt',
@ -181,10 +181,10 @@ greedyMix <- function(
save(c, file = kokonimi) save(c, file = kokonimi)
rm(c) rm(c)
} }
# ----------------------------------------------------------------------
# Handling Pre-processed data
# ----------------------------------------------------------------------
} else if (input_type_name == 'Preprocessed data') { } else if (input_type_name == 'Preprocessed data') {
# ------------------------------------------------------------------
# Handling Pre-processed data
# ------------------------------------------------------------------
file_in <- uigetfile( file_in <- uigetfile(
filter = '*.txt', filter = '*.txt',
title = 'Load pre-processed data in GenePop-format' title = 'Load pre-processed data in GenePop-format'
@ -285,9 +285,9 @@ greedyMix <- function(
# ASK remove (graphical part)? # ASK remove (graphical part)?
# if (fixedK) { # if (fixedK) {
# #logml_npops_partitionSummary <- indMix_fixK(c) # TODO translate? # #logml_npops_partitionSummary <- indMix_fixK(c) # ASK translate?
# } else { # } else {
# #logml_npops_partitionSummary <- indMix(c) # TODO translate? # #logml_npops_partitionSummary <- indMix(c) # ASK translate?
# } # }
# if (logml_npops_partitionSummary$logml == 1) return() # if (logml_npops_partitionSummary$logml == 1) return()
@ -303,7 +303,7 @@ greedyMix <- function(
# popnames, fixedK # popnames, fixedK
# ) # TODO translate # ) # TODO translate
# viewMixPartition(PARTITION, popnames) # TODO translate function # viewMixPartition(PARTITION, popnames) # ASK translate? On graph folder
talle <- questdlg( talle <- questdlg(
quest = paste( quest = paste(
@ -316,7 +316,7 @@ greedyMix <- function(
if (talle %in% c('Yes', 'y')) { if (talle %in% c('Yes', 'y')) {
filename_pathname <- uiputfile('.mat','Save results as') filename_pathname <- uiputfile('.mat','Save results as')
# ========================================================================== # ======================================================================
cond <- (sum(filename_pathname$name) == 0) | cond <- (sum(filename_pathname$name) == 0) |
(sum(filename_pathname$path) == 0) (sum(filename_pathname$path) == 0)
if (cond) { if (cond) {
@ -334,7 +334,7 @@ greedyMix <- function(
file.remove('baps4_output.baps') file.remove('baps4_output.baps')
} }
} }
# ========================================================================== # ======================================================================
c$PARTITION <- PARTITION c$PARTITION <- PARTITION
c$COUNTS <- COUNTS c$COUNTS <- COUNTS