Make VGAM a suggested package

DESCRIPTION

@@ -31,7 +31,6 @@ Imports:
     Rtsne,
     fpc,
     ape,
-    VGAM,
     pbapply,
     igraph,
     RANN,
@@ -101,6 +100,7 @@ Collate:
 RoxygenNote: 6.0.1
 Suggests:
     gdata,
+    VGAM,
     testthat,
     loomR,
     phateR,

NAMESPACE

@@ -303,8 +303,6 @@ importFrom(ROCR,performance)
 importFrom(ROCR,prediction)
 importFrom(Rcpp,evalCpp)
 importFrom(Rtsne,Rtsne)
-importFrom(VGAM,tobit)
-importFrom(VGAM,vgam)
 importFrom(ape,as.phylo)
 importFrom(ape,drop.tip)
 importFrom(ape,nodelabels)

R/differential_expression_internal.R

@@ -94,14 +94,14 @@ DifferentialTobit <- function(x1, x2, lower = 1, upper = Inf) {
 #internal function to run Tobit DE test
 #credit to Cole Trapnell for this
 #
-#' @importFrom VGAM vgam tobit
 #' @importFrom stats as.formula
 #
-TobitFitter <- function(x, modelFormulaStr, lower = 1, upper = Inf){
+TobitFitter <- function(x, modelFormulaStr, lower = 1, upper = Inf) {
+  PackageCheck('VGAM')
   tryCatch(
-    expr = return(suppressWarnings(expr = vgam(
+    expr = return(suppressWarnings(expr = VGAM::vgam(
       formula = as.formula(object = modelFormulaStr),
-      family = tobit(Lower = lower, Upper = upper),
+      family = VGAM::tobit(Lower = lower, Upper = upper),
       data = x
     ))),
     #warning = function(w) { FM_fit },

R/utilities_internal.R

@@ -621,9 +621,31 @@ LengthCheck <- function(values, cutoff = 0) {
 #
 MaxN <- function(x, N = 2){
   len <- length(x)
-  if(N > len) {
+  if (N > len) {
     warning('N greater than length(x).  Setting N=length(x)')
     N <- length(x)
   }
   sort(x, partial = len - N + 1)[len - N + 1]
 }
+
+# Check the existence of a package
+#
+# @param ... Package names
+# @param error If true, throw an error if the package doesn't exist
+#
+# @return Invisibly returns boolean denoting if the package is installed
+#
+#' @importFrom utils installed.packages
+#
+PackageCheck <- function(..., error = TRUE) {
+  pkgs <- unlist(x = c(...), use.names = FALSE)
+  package.installed <- pkgs %in% rownames(x = installed.packages())
+  if (error && any(!package.installed)) {
+    stop(
+      "Cannot find ",
+      paste(pkgs[!package.installed], collapse = ', '),
+      "; please install"
+    )
+  }
+  invisible(x = package.installed)
+}