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Removed global variables from argument lists

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This commit is contained in:
Waldir Leoncio 2020-11-19 14:29:37 +01:00
parent 13446958aa
commit 19e212b137
15 changed files with 33 additions and 88 deletions
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6
R/admix1.R
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@ -5,13 +5,9 @@
#' `tietue`should contain the following elements: PARTITION, COUNTS, SUMCOUNTS,
#' alleleCodes, adjprior, popnames, rowsFromInd, data, npops, noalle
#' @param tietue tietue
#' @param PARTITION PARTITION
#' @param COUNTS COUNTS
#' @param SUMCOUNTS SUMCOUNTS
#' @importFrom methods is
#' @export
admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
COUNTS = matrix(NA, 0, 0), SUMCOUNTS = NA) {
admix1 <- function(tietue) {
if (!is.list(tietue)) {
message('Load mixture result file. These are the files in this directory:')
print(list.files())

5
R/computeAllFreqs2.R
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@ -2,11 +2,8 @@
#' @description Lisää a priori jokaista alleelia joka populaation joka lokukseen
#' j 1/noalle(j) verran.
#' @param noalle noalle
#' @param COUNTS counts
#' @param SUMCOUNTS sumcounts
#' @export
computeAllFreqs2 <- function (noalle, COUNTS = matrix(NA, 0, 0),
SUMCOUNTS = NA) {
computeAllFreqs2 <- function (noalle) {
max_noalle <- size(COUNTS, 1)
nloci <- size(COUNTS,2)

4
R/computePersonalAllFreqs.R
View file

@ -7,11 +7,9 @@
#' @param data data
#' @param allFreqs allFreqs
#' @param rowsFromInd rowsFromInd
#' @param COUNTS COUNTS
#' @export
computePersonalAllFreqs <- function(ind, data, allFreqs, rowsFromInd,
COUNTS = matrix(0)) {
computePersonalAllFreqs <- function(ind, data, allFreqs, rowsFromInd) {
nloci <- ifelse(is.na(dim(COUNTS)[2]), 1, dim(COUNTS)[2])
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])

5
R/laskeMuutokset12345.R
View file

@ -7,11 +7,8 @@
#' @param omaFreqs own Freqs?
#' @param osuusTaulu Percentage table?
#' @param logml log maximum likelihood
#' @param COUNTS COUNTS
#' @export
laskeMuutokset4 <- function (
osuus, osuusTaulu, omaFreqs, logml, COUNTS = matrix(0)
) {
laskeMuutokset4 <- function (osuus, osuusTaulu, omaFreqs, logml) {
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
notEmpty <- which(osuusTaulu > 0.005)
muutokset <- zeros(npops)

7
R/poistaLiianPienet.R
View file

@ -5,13 +5,8 @@
#' @param npops npops
#' @param rowsFromInd rowsFromInd
#' @param alaraja alaraja
#' @param PARTITION PARTITION
#' @param COUNTS COUNTS
#' @param SUMCOUNTS SUMCOUNTS
#' @export
poistaLiianPienet <- function (npops, rowsFromInd, alaraja,
PARTITION = matrix(NA, 0, 0), COUNTS = matrix(NA, 0, 0),
SUMCOUNTS = NA) {
poistaLiianPienet <- function (npops, rowsFromInd, alaraja) {
popSize <- zeros(1,npops)
if (npops > 0) {
for (i in 1:npops) {

3
R/simulateAllFreqs.R
View file

@ -2,10 +2,9 @@
#' @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
#' @param COUNTS COUNTS
#' @export
simulateAllFreqs <- function(noalle, COUNTS = matrix(NA, 0, 0)) {
simulateAllFreqs <- function(noalle) {
max_noalle <- size(COUNTS, 1)
nloci <- size(COUNTS, 2)
npops <- size(COUNTS, 3)

3
R/suoritaMuutos.R
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@ -3,9 +3,8 @@
#' @param osuusTaulu Percentage table?
#' @param osuus percentage?
#' @param indeksi index
#' @param COUNTS counts
#' @export
suoritaMuutos <- function (osuusTaulu, osuus, indeksi, COUNTS = matrix(0)) {
suoritaMuutos <- function (osuusTaulu, osuus, indeksi) {
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
i1 <- indeksi %% npops

2
R/viewPartition.R
View file

@ -1,4 +1,4 @@
viewPartition <- function(osuudet, popnames, COUNTS = matrix(0, 0, 0)) {
viewPartition <- function(osuudet, popnames) {
npops <- size(COUNTS, 3)
nind <- size(osuudet,1)

13
man/admix1.Rd
View file

@ -4,21 +4,10 @@
\alias{admix1}
\title{Admixture analysis}
\usage{
admix1(
tietue,
PARTITION = matrix(NA, 0, 0),
COUNTS = matrix(NA, 0, 0),
SUMCOUNTS = NA
)
admix1(tietue)
}
\arguments{
\item{tietue}{tietue}
\item{PARTITION}{PARTITION}
\item{COUNTS}{COUNTS}
\item{SUMCOUNTS}{SUMCOUNTS}
}
\description{
Admixture analysis

6
man/computeAllFreqs2.Rd
View file

@ -4,14 +4,10 @@
\alias{computeAllFreqs2}
\title{Compute all freqs - version 2}
\usage{
computeAllFreqs2(noalle, COUNTS = matrix(NA, 0, 0), SUMCOUNTS = NA)
computeAllFreqs2(noalle)
}
\arguments{
\item{noalle}{noalle}
\item{COUNTS}{counts}
\item{SUMCOUNTS}{sumcounts}
}
\description{
Lisää a priori jokaista alleelia joka populaation joka lokukseen

4
man/computePersonalAllFreqs.Rd
View file

@ -4,7 +4,7 @@
\alias{computePersonalAllFreqs}
\title{Compute Personal Freqs}
\usage{
computePersonalAllFreqs(ind, data, allFreqs, rowsFromInd, COUNTS = matrix(0))
computePersonalAllFreqs(ind, data, allFreqs, rowsFromInd)
}
\arguments{
\item{ind}{ind}
@ -14,8 +14,6 @@ computePersonalAllFreqs(ind, data, allFreqs, rowsFromInd, COUNTS = matrix(0))
\item{allFreqs}{allFreqs}
\item{rowsFromInd}{rowsFromInd}
\item{COUNTS}{COUNTS}
}
\description{
Laskee npops*(rowsFromInd*nloci) taulukon, jonka kutakin

4
man/laskeMuutokset4.Rd
View file

@ -4,7 +4,7 @@
\alias{laskeMuutokset4}
\title{Calculate changes (?)}
\usage{
laskeMuutokset4(osuus, osuusTaulu, omaFreqs, logml, COUNTS = matrix(0))
laskeMuutokset4(osuus, osuusTaulu, omaFreqs, logml)
}
\arguments{
\item{osuus}{Percentages?}
@ -14,8 +14,6 @@ laskeMuutokset4(osuus, osuusTaulu, omaFreqs, logml, COUNTS = matrix(0))
\item{omaFreqs}{own Freqs?}
\item{logml}{log maximum likelihood}
\item{COUNTS}{COUNTS}
}
\description{
Palauttaa npops*npops taulun, jonka alkio (i,j) kertoo, mik?on

15
man/poistaLiianPienet.Rd
View file

@ -4,14 +4,7 @@
\alias{poistaLiianPienet}
\title{Remove too small}
\usage{
poistaLiianPienet(
npops,
rowsFromInd,
alaraja,
PARTITION = matrix(NA, 0, 0),
COUNTS = matrix(NA, 0, 0),
SUMCOUNTS = NA
)
poistaLiianPienet(npops, rowsFromInd, alaraja)
}
\arguments{
\item{npops}{npops}
@ -19,12 +12,6 @@ poistaLiianPienet(
\item{rowsFromInd}{rowsFromInd}
\item{alaraja}{alaraja}
\item{PARTITION}{PARTITION}
\item{COUNTS}{COUNTS}
\item{SUMCOUNTS}{SUMCOUNTS}
}
\description{
Muokkaa tulokset muotoon, jossa outlier yksilöt on poistettu.

4
man/simulateAllFreqs.Rd
View file

@ -4,12 +4,10 @@
\alias{simulateAllFreqs}
\title{Simulate All Frequencies}
\usage{
simulateAllFreqs(noalle, COUNTS = matrix(NA, 0, 0))
simulateAllFreqs(noalle)
}
\arguments{
\item{noalle}{noalle}
\item{COUNTS}{COUNTS}
}
\description{
Lisää jokaista alleelia joka populaation joka lokukseen j1/noalle(j) verran. Näin saatuja counts:eja vastaavista Dirichlet-jakaumista simuloidaan arvot populaatioiden alleelifrekvensseille.

4
man/suoritaMuutos.Rd
View file

@ -4,7 +4,7 @@
\alias{suoritaMuutos}
\title{suoritaMuutos}
\usage{
suoritaMuutos(osuusTaulu, osuus, indeksi, COUNTS = matrix(0))
suoritaMuutos(osuusTaulu, osuus, indeksi)
}
\arguments{
\item{osuusTaulu}{Percentage table?}
@ -12,8 +12,6 @@ suoritaMuutos(osuusTaulu, osuus, indeksi, COUNTS = matrix(0))
\item{osuus}{percentage?}
\item{indeksi}{index}
\item{COUNTS}{counts}
}
\description{
Päivittää osuusTaulun muutoksen jälkeen.