diff --git a/.Rbuildignore b/.Rbuildignore index fc194f2..b137c2f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -2,4 +2,5 @@ LICENSE TODO.md matlab CHANGELOG.md -CITATION.cff \ No newline at end of file +CITATION.cff +.travis.yml \ No newline at end of file diff --git a/R/poistaLiianPienet.R b/R/poistaLiianPienet.R index 685a8f1..bc7f608 100644 --- a/R/poistaLiianPienet.R +++ b/R/poistaLiianPienet.R @@ -5,6 +5,9 @@ #' @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), diff --git a/R/simulateIndividuals.R b/R/simulateIndividuals.R index e6326d4..94878aa 100644 --- a/R/simulateIndividuals.R +++ b/R/simulateIndividuals.R @@ -1,6 +1,11 @@ #' @title Simulate individuals #' @description simulate n individuals from population pop, such that -#' proportion "missing_level" of the alleles are present. +#' proportion "missing_level" of the alleles are present. +#' @param n n +#' @param rowsFromInd rowsFromInd +#' @param allfreqs allfreqs +#' @param pop pop +#' @param missing_level missing_level #' @export simulateIndividuals <- function(n, rowsFromInd, allfreqs, pop, missing_level) { diff --git a/R/simuloiAlleeli.R b/R/simuloiAlleeli.R index 955684a..a1ec88a 100644 --- a/R/simuloiAlleeli.R +++ b/R/simuloiAlleeli.R @@ -1,6 +1,9 @@ #' @title simuloiAlleeli #' @description Simuloi populaation pop lokukseen loc alleelin. #' @note This function is (only?) called by `simulateIndividuals()`. Therefore, exporting it is probably unnecessary. +#' @param allfreqs allfreqa +#' @param pop pop +#' @param loc loc #' @export simuloiAlleeli <- function(allfreqs, pop, loc) { @@ -18,7 +21,7 @@ simuloiAlleeli <- function(allfreqs, pop, loc) { # allfreqs[, loc], # allfreqs[, loc, pop] # ) - + cumsumma <- cumsum(freqs) arvo <- runif(1) diff --git a/man/poistaLiianPienet.Rd b/man/poistaLiianPienet.Rd index 1e48921..46ea2f7 100644 --- a/man/poistaLiianPienet.Rd +++ b/man/poistaLiianPienet.Rd @@ -19,6 +19,12 @@ 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. diff --git a/man/simulateIndividuals.Rd b/man/simulateIndividuals.Rd index 782cdd9..c8ab401 100644 --- a/man/simulateIndividuals.Rd +++ b/man/simulateIndividuals.Rd @@ -6,6 +6,17 @@ \usage{ simulateIndividuals(n, rowsFromInd, allfreqs, pop, missing_level) } +\arguments{ +\item{n}{n} + +\item{rowsFromInd}{rowsFromInd} + +\item{allfreqs}{allfreqs} + +\item{pop}{pop} + +\item{missing_level}{missing_level} +} \description{ simulate n individuals from population pop, such that proportion "missing_level" of the alleles are present. diff --git a/man/simuloiAlleeli.Rd b/man/simuloiAlleeli.Rd index cd19dd0..6ff761e 100644 --- a/man/simuloiAlleeli.Rd +++ b/man/simuloiAlleeli.Rd @@ -6,6 +6,13 @@ \usage{ simuloiAlleeli(allfreqs, pop, loc) } +\arguments{ +\item{allfreqs}{allfreqa} + +\item{pop}{pop} + +\item{loc}{loc} +} \description{ Simuloi populaation pop lokukseen loc alleelin. }