Merge pull request #59 from n8thangreen/dev

bug fix plot

R/ceac_plot_graph.R

@@ -133,7 +133,7 @@ ceac_ggplot <- function(he,
   graph_params <- helper_ggplot_params(he, graph_params)
   legend_params <- make_legend_ggplot(he, pos_legend)
   theme_add <- purrr::keep(extra_params, is.theme)
-  
+
   ggplot(data_psa, aes(x = .data$k, y = .data$ceac)) +
     geom_line(aes(linetype = .data$comparison,
                   linewidth = factor(.data$comparison),
@@ -151,9 +151,9 @@ ceac_ggplot <- function(he,
     scale_color_manual("",
                        labels = graph_params$labels,
                        values = graph_params$line$color) +
-    scale_size_manual("",
-                      labels = graph_params$labels,
-                      values = graph_params$line$size)
+    scale_linewidth_manual("",
+                           labels = graph_params$labels,
+                           values = graph_params$line$size)
 }
 
 

man-roxygen/args-comparison.R

@@ -1,5 +1,5 @@
 #' @param comparison Selects the comparator, in case of more than two
 #'                   interventions being analysed. Default as NULL plots all the comparisons
 #'                   together. Any subset of the possible comparisons can be selected (e.g.,
-#'                   \code{comparison=c(1,3)} or \code{comparison=2}).
+#'                   `comparison=c(1,3)` or `comparison=2`).
 

man-roxygen/args-graph.R

@@ -1,4 +1,4 @@
 #' @param graph A string used to select the graphical engine to use for
-#'              plotting. Should (partial-)match the three options \code{"base"},
-#'              \code{"ggplot2"} or \code{"plotly"}. Default value is \code{"base"}.
-#'              Not all plotting functions have a \code{"plotly"} implementation yet.
+#'              plotting. Should (partial-)match the three options `"base"`,
+#'              `"ggplot2"` or `"plotly"`. Default value is `"base"`.
+#'              Not all plotting functions have a `"plotly"` implementation yet.

man-roxygen/args-he.R

@@ -1,2 +1,2 @@
-#' @param he A \code{bcea} object containing the results of the Bayesian
+#' @param he A `bcea` object containing the results of the Bayesian
 #'           modelling and the economic evaluation.

man-roxygen/args-pos.R

@@ -1,10 +1,10 @@
 #' @param pos Parameter to set the position of the legend (only relevant for
 #'            multiple interventions, ie more than 2 interventions being compared).
 #'            Can be given in form
-#'            of a string \code{(bottom|top)(right|left)} for base graphics and
-#'            \code{bottom|top|left|right} for ggplot2. It can be a two-elements vector,
+#'            of a string `(bottom|top)(right|left)` for base graphics and
+#'            `bottom|top|left|right` for ggplot2. It can be a two-elements vector,
 #'            which specifies the relative position on the x and y axis respectively, or
-#'            alternatively it can be in form of a logical variable, with \code{FALSE}
-#'            indicating to use the default position and \code{TRUE} to place it on the
+#'            alternatively it can be in form of a logical variable, with `FALSE`
+#'            indicating to use the default position and `TRUE` to place it on the
 #'            bottom of the plot.
 

tests/testthat/test-bcea.R

@@ -9,7 +9,7 @@
 
 test_that("input errors", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata/ce.RData"))
 
   expect_dims_error <- function(x, y) {
     expect_error(
@@ -60,7 +60,7 @@ test_that("input errors", {
 
 test_that("basic return", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   res <- 
     bcea(e = eff,
@@ -187,7 +187,7 @@ test_that("jags, bugs, stan methods", {
 
 test_that("k and wtp arguments", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   m <- bcea(eff, cost, plot = FALSE)
 
@@ -205,7 +205,7 @@ test_that("k and wtp arguments", {
 
 test_that("using e and c still works", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   e <- eff
   c <- cost
@@ -218,7 +218,7 @@ test_that("using e and c still works", {
 
 test_that("named reference", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   expect_equal(bcea(eff, cost, ref = 1, interventions = c("a", "b")),
                bcea(eff, cost, ref = "a", interventions = c("a", "b")))

tests/testthat/test-bcea_setters.R

@@ -5,7 +5,7 @@
 
 test_that("setKmax", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   m <- bcea(e = eff,
             c = cost,
@@ -23,7 +23,7 @@ test_that("setKmax", {
 
 test_that("setReferenceGroup", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   m <- bcea(e = eff,
             c = cost,
@@ -40,7 +40,7 @@ test_that("setReferenceGroup", {
 
 test_that("setComparison", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   m_r1 <- bcea(e = eff,
                c = cost,

tests/testthat/test-ceac_plot_ggplot.R

@@ -3,7 +3,8 @@
 # library(purrr)
 
 test_that("ceac.plot_ggplot draws correctly", {
-  load("ce.RData")
+  load(test_path("testdata", "ce.RData"))
+
   he <- BCEA::bcea(eff, cost)
 
   ceac_plot <- ceac.plot(he, graph = "ggplot2", title = "my title")

tests/testthat/test-compute_U.R

@@ -6,7 +6,7 @@
 
 test_that("compute_U", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   # single wtp
 

tests/testthat/test-compute_ol.R

@@ -8,7 +8,7 @@
 
 test_that("simple data input parameters", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   # only one intervention
   # limiting case
@@ -66,7 +66,7 @@ test_that("simple data input parameters", {
 
 test_that("call via bcea", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   res <- 
     bcea(e = eff,

tests/testthat/test-compute_vi.R

@@ -8,7 +8,7 @@
 
 test_that("simple data", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   # only one intervention
   # limiting case
@@ -50,7 +50,7 @@ test_that("simple data", {
 
 test_that("call via bcea", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   res <- 
     bcea(e = eff,
@@ -86,7 +86,7 @@ test_that("errors in dimensions", {
 
 test_that("using sim_table", {
 
-  load(test_path("ce.RData"))
+  load(test_path("testdata", "ce.RData"))
 
   res <- 
     bcea(e = eff,

tests/testthat/test-eib_plot_ggplot.R

@@ -7,7 +7,8 @@
 
 
 test_that("eib.plot_ggplot draws correctly", {
-  load("ce.RData")
+  load(test_path("testdata", "ce.RData"))
+
   he <- BCEA::bcea(eff, cost)
 
   eib_plot <- eib.plot(he, graph = "ggplot2", title = "my title")