Add suggested package checks to examples

R/BASiCS-simulate.R

@@ -25,7 +25,9 @@
 #' Code: \url{https://github.com/catavallejos/BASiCS}
 #'
 #' @examples
-#' sim <- BASiCSSimulate()
+#' if (requireNamespace("BASiCS", quietly = TRUE)) {
+#'     sim <- BASiCSSimulate()
+#' }
 #' @export
 BASiCSSimulate <- function(params = newBASiCSParams(), verbose = TRUE, ...) {
 

R/mfa-estimate.R

@@ -16,11 +16,13 @@
 #'
 #' @examples
 #' # Load example data
-#' library(scater)
-#' data("sc_example_counts")
+#' if (requireNamespace("mfa", quietly = TRUE)) {
+#'     library(scater)
+#'     data("sc_example_counts")
 #'
-#' params <- mfaEstimate(sc_example_counts)
-#' params
+#'     params <- mfaEstimate(sc_example_counts)
+#'     params
+#' }
 #' @export
 mfaEstimate <- function(counts, params = newMFAParams()) {
     UseMethod("mfaEstimate")

R/mfa-simulate.R

@@ -27,7 +27,9 @@
 #' Code: \url{https://github.com/kieranrcampbell/mfa}
 #'
 #' @examples
-#' sim <- mfaSimulate()
+#' if (requireNamespace("mfa", quietly = TRUE)) {
+#'     sim <- mfaSimulate()
+#' }
 #' @export
 mfaSimulate <- function(params = newMFAParams(), verbose = TRUE, ...) {
 

R/pheno-estimate.R

@@ -15,12 +15,14 @@
 #' @return PhenoParams object containing the estimated parameters.
 #'
 #' @examples
-#' # Load example data
-#' library(scater)
-#' data("sc_example_counts")
+#' if (requireNamespace("phenopath", quietly = TRUE)) {
+#'     # Load example data
+#'     library(scater)
+#'     data("sc_example_counts")
 #'
-#' params <- phenoEstimate(sc_example_counts)
-#' params
+#'     params <- phenoEstimate(sc_example_counts)
+#'     params
+#' }
 #' @export
 phenoEstimate <- function(counts, params = newPhenoParams()) {
     UseMethod("phenoEstimate")

R/pheno-simulate.R

@@ -29,8 +29,9 @@
 #' Code: \url{https://github.com/kieranrcampbell/phenopath}
 #'
 #' @examples
-#' sim <- phenoSimulate()
-#'
+#' if (requireNamespace("phenopath", quietly = TRUE)) {
+#'     sim <- phenoSimulate()
+#' }
 #' @export
 #' @importFrom SingleCellExperiment SingleCellExperiment
 phenoSimulate <- function(params = newPhenoParams(), verbose = TRUE, ...) {

R/sparseDC-estimate.R

@@ -24,16 +24,18 @@
 #' @return SparseParams object containing the estimated parameters.
 #'
 #' @examples
-#' # Load example data
-#' library(scater)
-#' data("sc_example_counts")
+#' if (requireNamespace("SparseDC", quietly = TRUE)) {
+#'     # Load example data
+#'     library(scater)
+#'     data("sc_example_counts")
 #'
-#' set.seed(1)
-#' conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
+#'     set.seed(1)
+#'     conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
 #'
-#' params <- sparseDCEstimate(sc_example_counts[1:500, ], conditions,
-#'                            nclusters = 3)
-#' params
+#'     params <- sparseDCEstimate(sc_example_counts[1:500, ], conditions,
+#'                                nclusters = 3)
+#'     params
+#' }
 #' @export
 sparseDCEstimate <- function(counts, conditions, nclusters, norm = TRUE,
                              params = newSparseDCParams()) {

R/sparseDC-simulate.R

@@ -31,8 +31,9 @@
 #' Paper: \url{10.1093/nar/gkx1113}
 #'
 #' @examples
-#' sim <- sparseDCSimulate()
-#'
+#' if (requireNamespace("SparseDC", quietly = TRUE)) {
+#'     sim <- sparseDCSimulate()
+#' }
 #' @export
 #' @importFrom SingleCellExperiment SingleCellExperiment
 sparseDCSimulate <- function(params = newSparseDCParams(),

R/zinb-simulate.R

@@ -30,7 +30,9 @@
 #' Code: \url{https://github.com/drisso/zinbwave}
 #'
 #' @examples
-#' sim <- zinbSimulate()
+#' if (requireNamespace("zinbwave", quietly = TRUE)) {
+#'     sim <- zinbSimulate()
+#' }
 #'
 #' @export
 #' @importFrom SingleCellExperiment SingleCellExperiment

man/BASiCSSimulate.Rd

@@ -28,7 +28,9 @@ See \code{\link[BASiCS]{BASiCS_Sim}} for more details of how the simulation
 works.
 }
 \examples{
-sim <- BASiCSSimulate()
+if (requireNamespace("BASiCS", quietly = TRUE)) {
+    sim <- BASiCSSimulate()
+}
 }
 \references{
 Vallejos CA, Marioni JC, Richardson S. BASiCS: Bayesian Analysis of

man/mfaEstimate.Rd

@@ -33,9 +33,11 @@ details on the parameters.
 }
 \examples{
 # Load example data
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("mfa", quietly = TRUE)) {
+    library(scater)
+    data("sc_example_counts")
 
-params <- mfaEstimate(sc_example_counts)
-params
+    params <- mfaEstimate(sc_example_counts)
+    params
+}
 }

man/mfaSimulate.Rd

@@ -29,7 +29,9 @@ output from log-expression to counts and returns a
 how the simulation works.
 }
 \examples{
-sim <- mfaSimulate()
+if (requireNamespace("mfa", quietly = TRUE)) {
+    sim <- mfaSimulate()
+}
 }
 \references{
 Campbell KR, Yau C. Probabilistic modeling of bifurcations in single-cell

man/phenoEstimate.Rd

@@ -32,10 +32,12 @@ input data. The total number of genes is evenly divided into the four types.
 See \code{\link{PhenoParams}} for more details on the parameters.
 }
 \examples{
-# Load example data
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("phenopath", quietly = TRUE)) {
+    # Load example data
+    library(scater)
+    data("sc_example_counts")
 
-params <- phenoEstimate(sc_example_counts)
-params
+    params <- phenoEstimate(sc_example_counts)
+    params
+}
 }

man/phenoSimulate.Rd

@@ -31,8 +31,9 @@ See \code{\link[phenopath]{simulate_phenopath}} and the PhenoPath paper for
 more details about how the simulation works.
 }
 \examples{
-sim <- phenoSimulate()
-
+if (requireNamespace("phenopath", quietly = TRUE)) {
+    sim <- phenoSimulate()
+}
 }
 \references{
 Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic

man/sparseDCEstimate.Rd

@@ -46,14 +46,16 @@ input data. The counts are preprocessed using
 See \code{\link{SparseDCParams}} for more details on the parameters.
 }
 \examples{
-# Load example data
-library(scater)
-data("sc_example_counts")
+if (requireNamespace("SparseDC", quietly = TRUE)) {
+    # Load example data
+    library(scater)
+    data("sc_example_counts")
 
-set.seed(1)
-conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
+    set.seed(1)
+    conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
 
-params <- sparseDCEstimate(sc_example_counts[1:500, ], conditions,
-                           nclusters = 3)
-params
+    params <- sparseDCEstimate(sc_example_counts[1:500, ], conditions,
+                               nclusters = 3)
+    params
+}
 }

man/sparseDCSimulate.Rd

@@ -31,8 +31,9 @@ See \code{\link[SparseDC]{sim_data}} and the SparseDC paper for
 more details about how the simulation works.
 }
 \examples{
-sim <- sparseDCSimulate()
-
+if (requireNamespace("SparseDC", quietly = TRUE)) {
+    sim <- sparseDCSimulate()
+}
 }
 \references{
 Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic

man/zinbSimulate.Rd

@@ -28,7 +28,9 @@ See \code{\link[zinbwave]{zinbSim}} and the ZINB-WaVE paper for
 more details about how the simulation works.
 }
 \examples{
-sim <- zinbSimulate()
+if (requireNamespace("zinbwave", quietly = TRUE)) {
+    sim <- zinbSimulate()
+}
 
 }
 \references{

tests/testthat/test-BASiCS-simulate.R

@@ -2,5 +2,5 @@ context("BASiCS simulation")
 
 test_that("BASiCS simulation output is valid", {
     skip_if_not_installed("BASiCS")
-    expect_true(validObject(sparseDCSimulate()))
+    expect_true(validObject(BASiCSSimulate()))
 })