fix R cmd check issues

Author: jgabry

R/mcmc-diagnostics-nuts.R

@@ -180,7 +180,7 @@ mcmc_nuts_acceptance <-
     }
     hists <- hists +
       dont_expand_y_axis(c(0.005, 0)) +
-      facet_wrap(vars(Parameter), scales = "free") +
+      facet_wrap(vars(.data$Parameter), scales = "free") +
       yaxis_text(FALSE) +
       yaxis_title(FALSE) +
       yaxis_ticks(FALSE) +
@@ -476,7 +476,7 @@ mcmc_nuts_energy <-
     }
 
     graph +
-      facet_wrap(vars(Chain)) +
+      facet_wrap(vars(.data$Chain)) +
       force_axes_in_facets()
   }
 

R/mcmc-diagnostics.R

@@ -519,8 +519,8 @@ drop_NAs_and_warn <- function(x) {
     plot_data <- acf_data(x = x, lags = lags)
 
     if (num_chains(x) > 1) {
-      facet_args$rows <- vars(Chain)
-      facet_args$cols <- vars(Parameter)
+      facet_args$rows <- vars(.data$Chain)
+      facet_args$cols <- vars(.data$Parameter)
       facet_fun <- "facet_grid"
     } else { # 1 chain
       facet_args$facets <- "Parameter"

R/mcmc-distributions.R

@@ -405,13 +405,13 @@ mcmc_violin <- function(
   facet_args[["scales"]] <- facet_args[["scales"]] %||% "free"
   if (!by_chain) {
     if (n_param > 1) {
-      facet_args[["facets"]] <- vars(Parameter)
+      facet_args[["facets"]] <- vars(.data$Parameter)
       graph <- graph + do.call("facet_wrap", facet_args)
     }
   } else {
-    facet_args[["rows"]] <- vars(Chain)
+    facet_args[["rows"]] <- vars(.data$Chain)
     if (n_param > 1) {
-      facet_args[["cols"]] <- vars(Parameter)
+      facet_args[["cols"]] <- vars(.data$Parameter)
     }
     graph <- graph +
       do.call("facet_grid", facet_args) +
@@ -526,7 +526,7 @@ mcmc_violin <- function(
       labs(x = if (violin) "Chain" else levels(data$Parameter),
            y = if (violin) levels(data$Parameter) else NULL)
   } else {
-    facet_args[["facets"]] <- vars(Parameter)
+    facet_args[["facets"]] <- vars(.data$Parameter)
     facet_args[["scales"]] <- facet_args[["scales"]] %||% "free"
     graph <- graph + do.call("facet_wrap", facet_args)
   }

R/mcmc-traces.R

@@ -335,7 +335,7 @@ mcmc_rank_overlay <- function(x,
 
   facet_call <- NULL
   if (n_param > 1) {
-    facet_args$facets <- vars(parameter)
+    facet_args$facets <- vars(.data$parameter)
     facet_args$scales <- facet_args$scales %||% "fixed"
     facet_call <- do.call("facet_wrap", facet_args)
   }
@@ -387,16 +387,16 @@ mcmc_rank_hist <- function(x,
   right_edge <- max(data_boundaries$value_rank)
 
   facet_args[["scales"]] <- facet_args[["scales"]] %||% "fixed"
-  facet_args[["rows"]] <- facet_args[["rows"]] %||% vars(parameter)
-  facet_args[["cols"]] <- facet_args[["cols"]] %||% vars(chain)
 
   # If there is one parameter, put the chains in one row.
   # Otherwise, use a grid.
   if (n_param > 1) {
     facet_f <- facet_grid
-    names(facet_args)[names(facet_args) == "facets"] <- "rows"
+    facet_args[["rows"]] <- facet_args[["rows"]] %||% vars(.data$parameter)
+    facet_args[["cols"]] <- facet_args[["cols"]] %||% vars(.data$chain)
   } else {
     facet_f <- facet_wrap
+    facet_args[["facets"]] <- vars(.data$parameter, .data$chain)
     facet_args[["nrow"]] <- facet_args[["nrow"]] %||% 1
     labeller <- function(x) label_value(x, multi_line = FALSE)
     facet_args[["labeller"]] <- facet_args[["labeller"]] %||% labeller
@@ -528,7 +528,7 @@ mcmc_rank_ecdf <-
   if (n_param == 1) {
     facet_call <- ylab(levels(data$parameter))
   } else {
-    facet_args$facets <- vars(parameter)
+    facet_args$facets <- vars(.data$parameter)
     facet_args$scales <- facet_args$scales %||% "free"
     facet_call <- do.call("facet_wrap", facet_args)
   }
@@ -707,7 +707,7 @@ mcmc_trace_data <- function(x,
   if (n_param == 1) {
     facet_call <- ylab(levels(data$parameter))
   } else {
-    facet_args$facets <- vars(parameter)
+    facet_args$facets <- vars(.data$parameter)
     facet_args$scales <- facet_args$scales %||% "free"
     facet_call <- do.call("facet_wrap", facet_args)
   }

R/ppc-errors.R

@@ -398,11 +398,11 @@ error_hist_facets <-
 
     if (grouped) {
       facet_fun <- "facet_grid"
-      facet_args[["rows"]] <- vars(rep_id)
-      facet_args[["cols"]] <- vars(group)
+      facet_args[["rows"]] <- vars(.data$rep_id)
+      facet_args[["cols"]] <- vars(.data$group)
     } else {
       facet_fun <- "facet_wrap"
-      facet_args[["facets"]] <- vars(rep_id)
+      facet_args[["facets"]] <- vars(.data$rep_id)
     }
     facet_args[["scales"]] <- facet_args[["scales"]] %||% scales_default
 

tests/testthat/test-ppc-distributions.R

@@ -39,7 +39,7 @@ test_that("ppc_dens,pp_hist,ppc_freqpoly,ppc_boxplot return ggplot objects", {
   expect_gg(p <- ppc_hist(y, yrep[1:8, ], binwidth = 3))
   if (utils::packageVersion("ggplot2") >= "3.0.0") {
     facet_var <- vars(rep_label)
-    expect_equal(as.character(p$facet$params$facets[1]), facet_var)
+    expect_equal(p$facet$params$facets[[1]], facet_var[[1]])
   }
 
   # ppd versions