Internalized all functions except greedyMix() and load_fasta() (#25)

NAMESPACE

@@ -1,45 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-export(addAlleles)
-export(admix1)
-export(calculatePopLogml)
-export(computeAllFreqs2)
-export(computeIndLogml)
-export(computePersonalAllFreqs)
-export(computeRows)
-export(etsiParas)
-export(fgetl)
-export(fopen)
 export(greedyMix)
-export(greedyPopMix)
-export(handleData)
-export(handlePopData)
-export(initPopNames)
-export(learn_partition_modified)
-export(learn_simple_partition)
-export(linkage)
 export(load_fasta)
-export(logml2String)
-export(lueGenePopData)
-export(lueGenePopDataPop)
-export(lueNimi)
-export(noIndex)
-export(ownNum2Str)
-export(poistaLiianPienet)
-export(proportion2str)
-export(randdir)
-export(rivinSisaltamienMjonojenLkm)
-export(selvitaDigitFormat)
-export(simulateAllFreqs)
-export(simulateIndividuals)
-export(simuloiAlleeli)
-export(suoritaMuutos)
-export(takeLine)
-export(testaaKoordinaatit)
-export(testaaOnkoKunnollinenBapsData)
-export(testaaPop)
-export(writeMixtureInfo)
-export(writeMixtureInfoPop)
 importFrom(R6,R6Class)
 importFrom(Rsamtools,scanBam)
 importFrom(adegenet,.readExt)

R/addAlleles.R

@@ -4,7 +4,6 @@
 #' @param line line
 #' @param divider divider
 #' @return data (after alleles were added)
-#' @export
 addAlleles <- function(data, ind, line, divider) {
   # Lisaa BAPS-formaatissa olevaan datataulukkoon
   # yksil<69><6C> ind vastaavat rivit. Yksil<69>n alleelit

R/admix1.R

@@ -6,7 +6,6 @@
 #' alleleCodes, adjprior, popnames, rowsFromInd, data, npops, noalle
 #' @param tietue tietue
 #' @importFrom methods is
-#' @export
 admix1 <- function(tietue) {
   if (!is.list(tietue)) {
     message("Load mixture result file. These are the files in this directory:")

R/calculatePopLogml.R

@@ -4,7 +4,6 @@
 #' for the mean parameter.
 #' @param points points
 #' @param fii fii
-#' @export
 calculatePopLogml <- function(points, fii) {
   n <- length(points)
   fuzzy_ones <- sum(points)

R/computeAllFreqs2.R

@@ -2,7 +2,6 @@
 #' @description Lisää a priori jokaista alleelia joka populaation joka lokukseen
 #' j 1/noalle(j) verran.
 #' @param noalle noalle
-#' @export
 computeAllFreqs2 <- function(noalle) {
   COUNTS <- ifelse(isGlobalEmpty(COUNTS), vector(), COUNTS)
   SUMCOUNTS <- ifelse(isGlobalEmpty(SUMCOUNTS), vector(), COUNTS)

R/computeIndLogml.R

@@ -3,7 +3,6 @@
 #' määritellyiksi kuten osuusTaulu:ssa.
 #' @param omaFreqs own Freqs?
 #' @param osuusTaulu Percentage table?
-#' @export
 computeIndLogml <- function(omaFreqs, osuusTaulu) {
   omaFreqs <- as.matrix(omaFreqs)
   osuusTaulu <- as.matrix(osuusTaulu)

R/computePersonalAllFreqs.R

@@ -7,8 +7,6 @@
 #' @param data data
 #' @param allFreqs allFreqs
 #' @param rowsFromInd rowsFromInd
-#' @export
-
 computePersonalAllFreqs <- function(ind, data, allFreqs, rowsFromInd) {
   if (isGlobalEmpty(COUNTS)) {
     nloci <- npops <- 1

R/computeRows.R

@@ -4,7 +4,6 @@
 #' @param rowsFromInd rowsFromInd
 #' @param inds matrix
 #' @param ninds ninds
-#' @export
 computeRows <- function(rowsFromInd, inds, ninds) {
   if (!is(inds, "matrix")) inds <- as.matrix(inds)
   if (identical(dim(inds), c(nrow(inds), 1L))) {

R/etsiParas.R

@@ -1,4 +1,3 @@
-#' @export
 #' @title Etsi Paras
 #' @description Search for the best?
 #' @param osuus Percentages?

R/fgetl-fopen.R

@@ -6,7 +6,6 @@
 #' fgetl returns tline as a numeric value -1.
 #' @author Waldir Leoncio
 #' @seealso fopen
-#' @export
 fgetl <- function(file) {
   # ==========================================================================
   # Validation
@@ -27,5 +26,4 @@ fgetl <- function(file) {
 #' @return The same as `readLines(filename)`
 #' @author Waldir Leoncio
 #' @seealso fgetl
-#' @export
 fopen <- function(filename) readLines(filename)

R/greedyPopMix.R

@@ -11,7 +11,6 @@
 #' @importFrom matlab2r uiputfile
 #' @references Samtools: a suite of programs for interacting
 #' with high-throughput sequencing data. <http://www.htslib.org/>
-#' @export
 greedyPopMix <- function(data, format, partitionCompare = NULL, verbose = TRUE
 ) {
   # Replacing original file reading code with greedyMix()

R/handleData.R

@@ -8,7 +8,6 @@
 #' code to the smallest code that is larger than any code in use. After this,
 #' the function changes the allele codes so that one locus j
 #' codes get values between? 1, ..., Noah (j).
-#' @export
 handleData <- function(raw_data) {
   # Alkuper?isen datan viimeinen sarake kertoo, milt?yksil?lt?
   # kyseinen rivi on per?isin. Funktio tutkii ensin, ett?montako

R/handlePopData.R

@@ -4,7 +4,6 @@
 #' codes so that the codes for one locus have values between 1 and noalle[j].
 #' Before this change, an allele whose code is zero is changed.
 #' @param raw_data raw data
-#' @export
 handlePopData <- function(raw_data) {
   # Alkuperäisen datan viimeinen sarake kertoo, milt?yksilölt?
   # kyseinen rivi on peräisin. Funktio muuttaa alleelikoodit

R/initPopNames.R

@@ -1,7 +1,6 @@
 #' @title Initialize Pop Names
 #' @param nameFile nameFile
 #' @param indexFile indexFile
-#' @export
 initPopNames <- function(nameFile, indexFile) {
   # Palauttaa tyhj<68>n, mik<69>li nimitiedosto ja indeksitiedosto
   #  eiv<69>t olleet yht?pitki?

R/learn_partition_modified.R

@@ -1,5 +1,4 @@
 #' @title Learn partition (modified)
-#' @export
 #' @param ordered ordered
 #' @return part
 #' @description This function is called only if some individual has less than

R/learn_simple_partition.R

@@ -3,7 +3,6 @@
 #' @param fii fii
 #' @description Goes through all the ways to divide the points into two or
 #' three groups. Chooses the partition which obtains highest logml.
-#' @export
 learn_simple_partition <- function(ordered_points, fii) {
   npoints <- length(ordered_points)
 

R/linkage.R

@@ -13,7 +13,6 @@
 #' that BAPS should use this function instead of the base one, so this is why
 #' this function is part of this package (instead of a MATLAB-replicating
 #' package such as matlab2r)
-#' @export
 linkage <- function(Y, method = "co") {
   k <- size(Y)[1]
   n <- size(Y)[2]

R/logml2String.R

@@ -2,7 +2,6 @@
 #' @description Returns a string representation of a logml
 #' @param logml input Logml
 #' @return String version of logml
-#' @export
 logml2String <- function(logml) {
   # Palauttaa logml:n string-esityksen.
   mjono <- "       "

R/lueGenePopData.R

@@ -2,7 +2,6 @@
 #' @description Reads GenePop-formatted data
 #' @param tiedostonNimi Name of the file
 #' @return list containing data and popnames
-#' @export
 lueGenePopData <- function(tiedostonNimi) {
   fid <- readLines(tiedostonNimi)
   line <- fid[1] # ensimmäinen rivi

R/lueGenePopDataPop.R

@@ -3,7 +3,6 @@
 #' group. popnames are as before.
 #' @param tiedostonNimi Name of the file
 #' @return List containing data and popnames
-#' @export
 lueGenePopDataPop <- function(tiedostonNimi) {
   # Data annetaan muodossa, jossa viimeinen sarake kertoo ryhmän.
   # popnames on kuten ennenkin.

R/lueNimi.R

@@ -2,7 +2,6 @@
 #' @description Returns the part of the line from the beginning that is before the comma. Useful for returning the name of a GenePop area
 #' @param line line
 #' @return nimi
-#' @export
 lueNimi <- function(line) {
   # ==========================================================================
   # Validation

R/noIndex.R

@@ -5,7 +5,6 @@
 #' @return puredata: a data contains no index column.
 #' @param data data
 #' @param noalle noalle
-#' @export
 noIndex <- function(data, noalle) {
   limit <- ifelse(is(noalle, "matrix"), ncol(noalle), length(noalle))
   if (size(data, 2) == limit + 1) {

R/ownNum2Str.R

@@ -2,7 +2,6 @@
 #' @description Converts numbers to strings
 #' @param number number
 #' @note On Matlab, if number is NaN the output is 'NaN'. Here, the output will be an error. Also, the function belo expects "number" to have length one, whereas Matlab accepts vectors.
-#' @export
 ownNum2Str <- function(number) {
   absolute <- abs(number)
   if (absolute < 1000) {

R/poistaLiianPienet.R

@@ -5,7 +5,6 @@
 #' @param npops npops
 #' @param rowsFromInd rowsFromInd
 #' @param alaraja alaraja
-#' @export
 poistaLiianPienet <- function(npops, rowsFromInd, alaraja) {
   popSize <- zeros(1, npops)
   if (npops > 0) {

R/proportion2str.R

@@ -3,7 +3,6 @@
 #' @return a 4-mark presentation of proportion
 #' @note The `round` function in R, being ISO-compliant, rounds 8.5 to 8. The
 #' Matlab equivalent rounds it to 9.
-#' @export
 proportion2str <- function(prob) {
   if (abs(prob) < 1e-3) {
     str <- "0.00"

R/randdir.R

@@ -1,10 +1,9 @@
 #' @title Generates random numbers
 #' @return vector of length `nc` with r.v. realizations from Gamma(rate=1)
-#' @examples randdir(matrix(c(10, 30, 60), 3), 3)
+#' @examples rBAPS:::randdir(matrix(c(10, 30, 60), 3), 3)
 #' @param counts shape parameter
 #' @param nc number of rows on output
 #' @seealso randga
-#' @export
 randdir <- function(counts, nc) {
   svar <- zeros(nc, 1)
   for (i in 1:nc) {

R/rivinSisaltamienMjonojenLkm.R

@@ -2,7 +2,6 @@
 #' @param line line number
 #' @return count
 #' @description Returns the number of queues contained in the line. There must be a space between the queues.
-#' @export
 rivinSisaltamienMjonojenLkm <- function(line) {
   # Palauttaa line:n sis<69>lt<6C>mien mjonojen lukum<75><6D>r<EFBFBD>n.
   # Mjonojen v<>liss?t<>ytyy olla v<>lily<6C>nti.

R/selvitaDigitFormat.R

@@ -1,7 +1,6 @@
 #' @title Find out the Digit Format
 #' @param line the first line after the "pop" word from data in Genepop format. #  @note Function clarified based on the line format whether the alleles of the data are given using 2 or 3 numbers.
 #' @return df
-#' @export
 selvitaDigitFormat <- function(line) {
   # line on ensimm<6D>inen pop-sanan j<>lkeinen rivi
   # Genepop-formaatissa olevasta datasta. funktio selvitt<74><74>

R/simulateAllFreqs.R

@@ -2,8 +2,6 @@
 #' @description Lisää jokaista alleelia joka populaation joka lokukseen j1/noalle(j) verran. Näin saatuja counts:eja vastaavista Dirichlet-jakaumista simuloidaan arvot populaatioiden alleelifrekvensseille.
 #' Add each allele to each locus in each population by j 1 / noalle(j). The Dirichlet distributions corresponding to the counts thus obtained simulate values for the allele frequencies of the populations.
 #' @param noalle noalle
-#' @export
-
 simulateAllFreqs <- function(noalle) {
   if (isGlobalEmpty(COUNTS)) {
     max_noalle <- 0

R/simulateIndividuals.R

@@ -6,8 +6,6 @@
 #' @param allfreqs allfreqs
 #' @param pop pop
 #' @param missing_level missing_level
-#' @export
-
 simulateIndividuals <- function(n, rowsFromInd, allfreqs, pop, missing_level) {
   nloci <- size(allfreqs, 2)
 

R/simuloiAlleeli.R

@@ -5,8 +5,6 @@
 #' @param allfreqs allfreqa
 #' @param pop pop
 #' @param loc loc
-#' @export
-
 simuloiAlleeli <- function(allfreqs, pop, loc) {
   if (length(dim(allfreqs)) == 0) {
     freqs <- 1

R/suoritaMuutos.R

@@ -3,7 +3,6 @@
 #' @param osuusTaulu Percentage table?
 #' @param osuus percentage?
 #' @param indeksi index
-#' @export
 suoritaMuutos <- function(osuusTaulu, osuus, indeksi) {
   if (isGlobalEmpty(COUNTS)) {
     npops <- 1

R/takeLine.R

@@ -3,7 +3,6 @@
 #' @param description description
 #' @param width width
 #' @return newline
-#' @export
 takeLine <- function(description, width) {
   # Returns one line from the description: line ends to the first
   # space after width:th mark.

R/testaaKoordinaatit.R

@@ -3,7 +3,6 @@
 #' @param coordinates coordinates
 #' @param interactive prompt user for relevant questions during execution
 #' @return a list of defectives ("viallinen") and coordinates
-#' @export
 testaaKoordinaatit <- function(ninds, coordinates, interactive = TRUE) {
  # Testaa onko koordinaatit kunnollisia.
  # modified by Lu Cheng, 05.12.2012

R/testaaOnkoKunnollinenBapsData.R

@@ -2,7 +2,6 @@
 #' @description Test if loaded BAPS data is proper
 #' @param data dataset
 #' @return ninds
-#' @export
 testaaOnkoKunnollinenBapsData <- function(data) {
   # Tarkastaa onko viimeisess?sarakkeessa kaikki
   # luvut 1,2,...,n johonkin n:<3A><>n asti.

R/testaaPop.R

@@ -3,7 +3,6 @@
 #' @param rivi Line
 #' @return pal = 1 if the line starts with one of the following
 # letter combinations: Pop, pop, POP. In all others cases, pal = 0
-#' @export
 testaaPop <- function(rivi) {
   # pal=1, mik<69>li rivi alkaa jollain seuraavista
   # kirjainyhdistelmist? Pop, pop, POP. Kaikissa muissa

R/writeMixtureInfo.R

@@ -10,7 +10,6 @@
 #' @param partitionSummary partitionSummary
 #' @param popnames popnames
 #' @param fixedK fixedK
-#' @export
 writeMixtureInfo <- function(
   logml, rowsFromInd, data, adjprior, priorTerm, outPutFile, inputFile,
   partitionSummary, popnames, fixedK

R/writeMixtureInfoPop.R

@@ -10,7 +10,6 @@
 #' @param partitionSummary partitionSummary
 #' @param popnames popnames
 #' @param fixedK fixedK
-#' @export
 writeMixtureInfoPop <- function(logml, rows, data, adjprior, priorTerm,
                                 outPutFile, inputFile, partitionSummary,
                                 popnames, fixedK) {

man/randdir.Rd

@@ -18,7 +18,7 @@ vector of length `nc` with r.v. realizations from Gamma(rate=1)
 Generates random numbers
 }
 \examples{
-randdir(matrix(c(10, 30, 60), 3), 3)
+rBAPS:::randdir(matrix(c(10, 30, 60), 3), 3)
 }
 \seealso{
 randga