diff options
| -rw-r--r-- | DESCRIPTION | 6 | ||||
| -rw-r--r-- | NAMESPACE | 2 | ||||
| -rw-r--r-- | R/simulate_data.R | 16 | ||||
| -rw-r--r-- | man/simulate_data.Rd | 5 | ||||
| -rw-r--r-- | tests/testthat.R | 12 | ||||
| -rw-r--r-- | tests/testthat/test-simulate_data.R | 4 |
6 files changed, 32 insertions, 13 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 34d6b7b..2e67bd8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,3 +8,9 @@ License: GPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 8.0.0 +Imports: + MASS, + stats +Suggests: + testthat (>= 3.0.0) +Config/testthat/edition: 3 @@ -2,3 +2,5 @@ export(simulate_data) importFrom(MASS,mvrnorm) +importFrom(stats,rchisq) +importFrom(stats,runif) diff --git a/R/simulate_data.R b/R/simulate_data.R index 2338805..297b76f 100644 --- a/R/simulate_data.R +++ b/R/simulate_data.R @@ -15,11 +15,12 @@ #' @return A list with X, S and a vector identifying the contaminated rows. #' #' @examples -#' X_obj <- generate_data(n = 10, p = 10) +#' X_obj <- simulate_data(n = 10, p = 10) #' X <- X_obj$X #' S_true <- X_obj$S #' #' @importFrom MASS mvrnorm +#' @importFrom stats rchisq runif #' #' @export simulate_data <- function( @@ -28,8 +29,7 @@ simulate_data <- function( rho = 0.8, contamination = 0, block_fraction = 0.5, - t_df = Inf, - exact_contamination = FALSE + t_df = Inf ){ if(any( rho < 0, @@ -56,7 +56,7 @@ simulate_data <- function( # Regular clean observations Z <- MASS::mvrnorm(n = n, mu = numeric(p), Sigma = Sigma) if(is.finite(t_df)){ - w <- rchisq(n, df = t_df) + w <- stats::rchisq(n, df = t_df) X <- Z / sqrt(w / t_df) }else{ X <- Z @@ -65,15 +65,11 @@ simulate_data <- function( # Contamination - by row outlier_rows <- integer(0) if(contamination > 0){ - if(exact_contamination){ - outlier_rows <- sample.int(n, ceiling(contamination * n)) - }else{ - outlier_rows <- which(runif(n) < contamination) - } + outlier_rows <- which(stats::runif(n) < contamination) if(length(outlier_rows) > 0){ X[outlier_rows, ] <- matrix( - rchisq(length(outlier_rows) * p, df = 1), + stats::rchisq(length(outlier_rows) * p, df = 1), nrow = length(outlier_rows), ncol = p ) diff --git a/man/simulate_data.Rd b/man/simulate_data.Rd index b362518..09ae881 100644 --- a/man/simulate_data.Rd +++ b/man/simulate_data.Rd @@ -10,8 +10,7 @@ simulate_data( rho = 0.8, contamination = 0, block_fraction = 0.5, - t_df = Inf, - exact_contamination = FALSE + t_df = Inf ) } \arguments{ @@ -37,7 +36,7 @@ with the intention of evaluating the performance of covariance or correlation matrix estimators. } \examples{ -X_obj <- generate_data(n = 10, p = 10) +X_obj <- simulate_data(n = 10, p = 10) X <- X_obj$X S_true <- X_obj$S diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..7b29596 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(RSC.analysis) + +test_check("RSC.analysis") diff --git a/tests/testthat/test-simulate_data.R b/tests/testthat/test-simulate_data.R new file mode 100644 index 0000000..9d0cba3 --- /dev/null +++ b/tests/testthat/test-simulate_data.R @@ -0,0 +1,4 @@ +test_that("Returns a true sparse correlation matrix", { + X_obj <- simulate_data(n = 10, p = 10, rho = 0) + expect_equal(X_obj$S, diag(nrow = 10)) +}) |