Fix missing ggplot2 namespace

tesselle · Nov 25, 2019 · 8765578 · 8765578
1 parent 70962f8
commit 8765578
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Showing 5 changed files with 31 additions and 12 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -57,11 +57,25 @@ exportMethods(test_fit)
 exportMethods(turnover)
 importFrom(ca,ca)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,coord_fixed)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_rect)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_path)
 importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_tile)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_size_area)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_x_discrete)
 importFrom(ggplot2,scale_x_log10)
+importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,scale_y_discrete)
+importFrom(ggplot2,scale_y_log10)
+importFrom(ggplot2,theme)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,new)

diff --git a/R/index-diversity.R b/R/index-diversity.R
@@ -85,7 +85,7 @@ simulate_diversity <- function(x, method, prob = NULL,
   }
   loop_args <- list(X = sample_sizes, FUN = sim,
                     n = n, prob = prob, level = level, method = method, ...)
-  loop_fun <- if (requireNamespace("pbapply", quietly = TRUE)) {
+  loop_fun <- if (interactive() && requireNamespace("pbapply", quietly = TRUE)) {
     pbapply::pblapply
   } else {
     lapply

diff --git a/R/index-richness.R b/R/index-richness.R
@@ -39,6 +39,7 @@ setMethod(
     .RichnessIndex(
       id = object[["id"]],
       index = index,
+      size = rowSums(object),
       method = method
     )
   }

diff --git a/R/plot-diversity.R b/R/plot-diversity.R
@@ -28,17 +28,21 @@ setMethod(
         type = ifelse(sim_stacked[["ind"]] == "mean", "mean", "conf. int.")
       )
       sim <- stats::na.omit(sim)
-      gg_sim <- geom_path(mapping = aes(x = .data$size, y = .data$values,
-                                        colour = .data$type, group = .data$ind),
-                          data = sim, inherit.aes = FALSE)
+      gg_sim <- ggplot2::geom_path(
+        mapping = ggplot2::aes(x = .data$size, y = .data$values,
+                               colour = .data$type, group = .data$ind),
+        data = sim, inherit.aes = FALSE
+      )
     }
 
     # ggplot
-    ggplot(data = count,
-           mapping = aes(x = .data$x, y = .data$y, label = .data$label)) +
-      geom_point() +
+    ggplot2::ggplot(data = count,
+                    mapping = ggplot2::aes(x = .data$x, y = .data$y,
+                                           label = .data$label)) +
+      ggplot2::geom_point() +
       gg_sim +
-      scale_x_log10() +
-      labs(x = "Sample size", y = object[["method"]], colour = "Simulation")
+      ggplot2::scale_x_log10() +
+      ggplot2::labs(x = "Sample size", y = object[["method"]],
+                    colour = "Simulation")
   }
 )
diff --git a/R/refine.R b/R/refine.R
@@ -96,7 +96,7 @@ boot_hull <- function(x, margin = 1, n = 1000, axes = c(1, 2), ...) {
     return(as.data.frame(hull))
   }
 
-  loop_fun <- if (requireNamespace("pbapply", quietly = TRUE)) {
+  loop_fun <- if (interactive() && requireNamespace("pbapply", quietly = TRUE)) {
     pbapply::pbapply
   } else {
     apply
@@ -210,7 +210,7 @@ boot_date <- function(x, model, margin = 1, n = 1000, keep = ncol(x),
     return(distrib)
   }
 
-  loop_fun <- if (requireNamespace("pbapply", quietly = TRUE)) {
+  loop_fun <- if (interactive() && requireNamespace("pbapply", quietly = TRUE)) {
     pbapply::pbapply
   } else {
     apply
@@ -292,7 +292,7 @@ jack_date <- function(x, model, keep = ncol(x), level = 0.95, ...) {
     return(stats::coef(fit))
   }
 
-  loop_fun <- if (requireNamespace("pbapply", quietly = TRUE)) {
+  loop_fun <- if (interactive() && requireNamespace("pbapply", quietly = TRUE)) {
     pbapply::pblapply
   } else {
     lapply