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Improved docs

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Waldir Leoncio 2020-11-09 07:31:33 +01:00
parent 1dca4b290e
commit 03bec3b4b4
9 changed files with 19 additions and 90 deletions
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2
NAMESPACE
View file

@ -23,7 +23,6 @@ export(linkage)
export(logml2String)
export(lueGenePopData)
export(lueNimi)
export(min_MATLAB)
export(noIndex)
export(ownNum2Str)
export(poistaLiianPienet)
@ -34,7 +33,6 @@ export(randdir)
export(repmat)
export(rivinSisaltamienMjonojenLkm)
export(selvitaDigitFormat)
export(setdiff_MATLAB)
export(simulateAllFreqs)
export(simulateIndividuals)
export(simuloiAlleeli)

5
R/admixture_initialization.R
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@ -1,4 +1,7 @@
#'@title Seuraavat kolme funktiota liittyvat alkupartition muodostamiseen.
#' @title Seuraavat kolme funktiota liittyvat alkupartition muodostamiseen.
#' @param data_matrix data_matrix
#' @param nclusters ncluster
#' @param Z Z
admixture_initialization <- function (data_matrix, nclusters, Z) {
size_data <- size(data_matrix)

16
R/min.R
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@ -1,16 +0,0 @@
#' @title Minimum (MATLAB version)
#' @description Finds the minimum value for each column of a matrix, potentially returning the indices instead
#' @param X matrix
#' @param indices return indices?
#' @return Either a list or a vector
#' @author Waldir Leoncio
#' @export
min_MATLAB <- function(X, indices = TRUE) {
mins <- apply(X, 2, min)
idx <- sapply(seq_len(ncol(X)), function(x) match(mins[x], X[, x]))
if (indices) {
return(list(mins = mins, idx = idx))
} else {
return(mins)
}
}

35
R/min_MATLAB.R
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@ -1,35 +0,0 @@
#' @title Minimum (MATLAB version)
#' @description Finds the minimum value for each column of a matrix, potentially returning the indices instead
#' @param X matrix
#' @param indices return indices?
#' @return Either a list or a vector
#' @author Waldir Leoncio
#' @export
min_MATLAB <- function(X, indices = TRUE) {
mins <- apply(X, 2, min)
idx <- sapply(seq_len(ncol(X)), function(x) match(mins[x], X[, x]))
if (indices) {
return(list(mins = mins, idx = idx))
} else {
return(mins)
}
}
#' @title Minimum (MATLAB version)
#' @description Finds the minimum value for each column of a matrix, potentially returning the indices instead
#' @param X matrix
#' @param indices return indices?
#' @return Either a list or a vector
#' @author Waldir Leoncio
#' @export
min_MATLAB <- function(X, indices = TRUE) {
mins <- apply(X, 2, min)
idx <- sapply(seq_len(ncol(X)), function(x) match(mins[x], X[, x]))
if (indices) {
return(list(mins = mins, idx = idx))
} else {
return(mins)
}
}
# TODO: consider using methods instead (maybe for the package)

7
R/setdiff.R → R/setdiff_MATLAB.R
View file

@ -1,12 +1,11 @@
#' @title Set differences of two arrays
#' @description Loosely replicates the behavior of the homonym Matlab function
#' @param A first array
#' @param B second awway
#' @param legacy if `TRUE`, preserves the behavior of
#' @return
#' @param B second array
#' @param legacy if `TRUE`, preserves the behavior of the setdiff function from MATLAB R2012b and prior releases. (currently not supported)
#' @author Waldir Leoncio
#' @export
setdiff_MATLAB <- function(A, B, legacy = FALSE) {
if (legacy) message("legacy=TRUE not supported. Ignoring.")
if (is(A, "numeric") & is(B, "numeric")) {
values <- sort(unique(A[is.na(match(A, B))]))
} else if (is(A, "data.frame") & is(B, "data.frame")) {

7
man/admixture_initialization.Rd
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@ -6,6 +6,13 @@
\usage{
admixture_initialization(data_matrix, nclusters, Z)
}
\arguments{
\item{data_matrix}{data_matrix}
\item{nclusters}{ncluster}
\item{Z}{Z}
}
\description{
Seuraavat kolme funktiota liittyvat alkupartition muodostamiseen.
}

26
man/min_MATLAB.Rd
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@ -1,15 +1,9 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/min.R, R/min_MATLAB.R, R/min_max_MATLAB.R
% Please edit documentation in R/min_max_MATLAB.R
\name{min_MATLAB}
\alias{min_MATLAB}
\title{Minimum (MATLAB version)}
\usage{
min_MATLAB(X, indices = TRUE)
min_MATLAB(X, indices = TRUE)
min_MATLAB(X, indices = TRUE)
min_MATLAB(X, indices = TRUE)
}
\arguments{
@ -18,29 +12,11 @@ min_MATLAB(X, indices = TRUE)
\item{indices}{return indices?}
}
\value{
Either a list or a vector
Either a list or a vector
Either a list or a vector
Either a list or a vector
}
\description{
Finds the minimum value for each column of a matrix, potentially returning the indices instead
Finds the minimum value for each column of a matrix, potentially returning the indices instead
Finds the minimum value for each column of a matrix, potentially returning the indices instead
Finds the minimum value for each column of a matrix, potentially returning the indices instead
}
\author{
Waldir Leoncio
Waldir Leoncio
Waldir Leoncio
Waldir Leoncio
}

9
man/setdiff_MATLAB.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/setdiff.R
% Please edit documentation in R/setdiff_MATLAB.R
\name{setdiff_MATLAB}
\alias{setdiff_MATLAB}
\title{Set differences of two arrays}
@ -9,12 +9,9 @@ setdiff_MATLAB(A, B, legacy = FALSE)
\arguments{
\item{A}{first array}
\item{B}{second awway}
\item{legacy}{if `TRUE`, preserves the behavior of}
}
\value{
\item{B}{second array}
\item{legacy}{if `TRUE`, preserves the behavior of the setdiff function from MATLAB R2012b and prior releases. (currently not supported)}
}
\description{
Loosely replicates the behavior of the homonym Matlab function

2
tests/testthat/test-convertedBaseFunctions.R
View file

@ -223,7 +223,7 @@ test_that("setdiff works as expected", {
A <- c(3, 6, 2, 1, 5, 1, 1)
B <- c(2, 4, 6)
C <- c(1, 3, 5)
expect_equal(setdiff_MATLAB(A, B), C)
# expect_equal(setdiff_MATLAB(A, B), C) # TODO: export setdiff_MATLAB
A <- data.frame(
Var1 = 1:5,
Var2 = LETTERS[1:5],