From 73e8e8d875087c9d12964f2bc8f57408c1cd8d5b Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 4 Jun 2019 14:53:42 +1000
Subject: [PATCH] Add suggested package checks to examples

---
 R/BASiCS-simulate.R                   |  4 +++-
 R/mfa-estimate.R                      | 10 ++++++----
 R/mfa-simulate.R                      |  4 +++-
 R/pheno-estimate.R                    | 12 +++++++-----
 R/pheno-simulate.R                    |  5 +++--
 R/sparseDC-estimate.R                 | 18 ++++++++++--------
 R/sparseDC-simulate.R                 |  5 +++--
 R/zinb-simulate.R                     |  4 +++-
 man/BASiCSSimulate.Rd                 |  4 +++-
 man/mfaEstimate.Rd                    | 10 ++++++----
 man/mfaSimulate.Rd                    |  4 +++-
 man/phenoEstimate.Rd                  | 12 +++++++-----
 man/phenoSimulate.Rd                  |  5 +++--
 man/sparseDCEstimate.Rd               | 18 ++++++++++--------
 man/sparseDCSimulate.Rd               |  5 +++--
 man/zinbSimulate.Rd                   |  4 +++-
 tests/testthat/test-BASiCS-simulate.R |  2 +-
 17 files changed, 77 insertions(+), 49 deletions(-)

diff --git a/R/BASiCS-simulate.R b/R/BASiCS-simulate.R
index 743f48f..f2f40da 100644
--- a/R/BASiCS-simulate.R
+++ b/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, ...) {
 
diff --git a/R/mfa-estimate.R b/R/mfa-estimate.R
index 62aa212..1ff363c 100644
--- a/R/mfa-estimate.R
+++ b/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")
diff --git a/R/mfa-simulate.R b/R/mfa-simulate.R
index 8f6a7a2..eb7e1d1 100644
--- a/R/mfa-simulate.R
+++ b/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, ...) {
 
diff --git a/R/pheno-estimate.R b/R/pheno-estimate.R
index cccf02f..b7ee6e8 100644
--- a/R/pheno-estimate.R
+++ b/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")
diff --git a/R/pheno-simulate.R b/R/pheno-simulate.R
index 56c2e99..8e068a3 100644
--- a/R/pheno-simulate.R
+++ b/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, ...) {
diff --git a/R/sparseDC-estimate.R b/R/sparseDC-estimate.R
index b4b02ea..99c8b7c 100644
--- a/R/sparseDC-estimate.R
+++ b/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()) {
diff --git a/R/sparseDC-simulate.R b/R/sparseDC-simulate.R
index 6b410ed..5aa9a4e 100644
--- a/R/sparseDC-simulate.R
+++ b/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(),
diff --git a/R/zinb-simulate.R b/R/zinb-simulate.R
index 7ebefa2..83da973 100644
--- a/R/zinb-simulate.R
+++ b/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
diff --git a/man/BASiCSSimulate.Rd b/man/BASiCSSimulate.Rd
index 635d549..acdfb16 100644
--- a/man/BASiCSSimulate.Rd
+++ b/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
diff --git a/man/mfaEstimate.Rd b/man/mfaEstimate.Rd
index c8ad13e..9bf1521 100644
--- a/man/mfaEstimate.Rd
+++ b/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
+}
 }
diff --git a/man/mfaSimulate.Rd b/man/mfaSimulate.Rd
index ec2a98e..016bb04 100644
--- a/man/mfaSimulate.Rd
+++ b/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
diff --git a/man/phenoEstimate.Rd b/man/phenoEstimate.Rd
index 1c102ba..7a46a24 100644
--- a/man/phenoEstimate.Rd
+++ b/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
+}
 }
diff --git a/man/phenoSimulate.Rd b/man/phenoSimulate.Rd
index 34f5efb..24c43a8 100644
--- a/man/phenoSimulate.Rd
+++ b/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
diff --git a/man/sparseDCEstimate.Rd b/man/sparseDCEstimate.Rd
index 72671dc..cbfdbe8 100644
--- a/man/sparseDCEstimate.Rd
+++ b/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
+}
 }
diff --git a/man/sparseDCSimulate.Rd b/man/sparseDCSimulate.Rd
index 4c1f341..c88ac8d 100644
--- a/man/sparseDCSimulate.Rd
+++ b/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
diff --git a/man/zinbSimulate.Rd b/man/zinbSimulate.Rd
index 17c6611..ab3d227 100644
--- a/man/zinbSimulate.Rd
+++ b/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{
diff --git a/tests/testthat/test-BASiCS-simulate.R b/tests/testthat/test-BASiCS-simulate.R
index 98d6cad..081ada5 100644
--- a/tests/testthat/test-BASiCS-simulate.R
+++ b/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()))
 })
-- 
GitLab