prepare for tibble 3.0

pierucci · Mar 6, 2020 · 4a32145 · 4a32145
1 parent 7adeb94
commit 4a32145
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Showing 7 changed files with 18 additions and 16 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -146,6 +146,7 @@ export(status_cluster)
 export(use_cluster)
 export(use_distribution)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,anti_join)
 importFrom(dplyr,as.tbl)
 importFrom(dplyr,as_data_frame)
 importFrom(dplyr,bind_rows)

diff --git a/R/heemod.R b/R/heemod.R
@@ -24,7 +24,7 @@
 #' @importFrom dplyr ungroup
 #' @importFrom dplyr mutate_if
 #' @importFrom dplyr funs
-#' @importFrom dplyr antijoin
+#' @importFrom dplyr anti_join
 #' 
 #' @importFrom plyr ldply
 #' @importFrom plyr ddply

diff --git a/R/part_surv.R b/R/part_surv.R
@@ -417,8 +417,8 @@ make_part_surv_from_small_tibble <- function(st, state_names){
   stopifnot(length(pfs_row) == 1,
             length(os_row) == 1
   )
-  define_part_surv(pfs = st[[pfs_row, "fit"]],
-                   os = st[[os_row, "fit"]],
+  define_part_surv(pfs = st[["fit"]][[pfs_row]],
+                   os = st[["fit"]][[os_row]],
                    state_names = state_names)
 }
 

diff --git a/R/sensitivity_define.R b/R/sensitivity_define.R
@@ -57,8 +57,8 @@ define_dsa_ <- function(par_names, low_dots, high_dots) {
     all(par_names == names(low_dots)),
     all(par_names == names(high_dots))
   )
-  dots <- interleave(low_dots, high_dots)
-
+  dots <- interleave(low_dots, high_dots) 
+  class(dots) <- c("list")
   if (any(duplicated(par_names))) {
     stop("Some names are duplicated.")
   }
@@ -73,6 +73,7 @@ define_dsa_ <- function(par_names, low_dots, high_dots) {
     })
   }
 
+
   clean_null <- function(x) {
     Map(
       function(el) if (is.null(el)) NA else el,

diff --git a/man/look_up.Rd b/man/look_up.Rd
diff --git a/tests/testthat/test_parameters.R b/tests/testthat/test_parameters.R
@@ -75,12 +75,12 @@ test_that(
       a = 2,
       b = a * markov_cycle
     )
-    e_par1 <- heemod:::eval_parameters(
+    e_par1 <- eval_parameters(
       par1, 10
     )
     expect_output(
       str(e_par1),
-      "10 obs\\. of  5 variables"
+      "\\[10 × 5\\]"
     )
     expect_equal(
       get_parameter_names(e_par1),

diff --git a/tests/testthat/test_part_surv.R b/tests/testthat/test_part_surv.R
@@ -295,10 +295,10 @@ test_that("we can run construct_part_surv_tib",
             )
             for_A <- dplyr::filter(explicit_dist_part_surv, .strategy == "A")
             for_B <- dplyr::filter(explicit_dist_part_surv, .strategy == "B")
-            expect_equal(round(compute_surv(for_A[[1, "part_surv"]]$pfs, 1), 4), 0.0332)
-            expect_equal(round(compute_surv(for_A[[1, "part_surv"]]$os, 1), 4), 0.0150)
-            expect_equal(round(compute_surv(for_B[[1, "part_surv"]]$pfs, 1), 4), 0.0472)
-            expect_equal(round(compute_surv(for_B[[1, "part_surv"]]$os, 1), 4), 0.0213)
+            expect_equal(round(compute_surv(for_A[["part_surv"]][[1]]$pfs, 1), 4), 0.0332)
+            expect_equal(round(compute_surv(for_A[["part_surv"]][[1]]$os, 1), 4), 0.0150)
+            expect_equal(round(compute_surv(for_B[["part_surv"]][[1]]$pfs, 1), 4), 0.0472)
+            expect_equal(round(compute_surv(for_B[["part_surv"]][[1]]$os, 1), 4), 0.0213)
 
             use_fits <- read_file(system.file("tabular/surv",
                                               "use_fits_mixed.csv",
@@ -314,13 +314,13 @@ test_that("we can run construct_part_surv_tib",
                                                        "ProgressiveDisease", 
                                                        "Terminal", "Death")
               )
-            expect_identical(class(mixed_dist_part_surv[[1, "part_surv"]]$os),
+            expect_identical(class(mixed_dist_part_surv[["part_surv"]][[1]]$os),
                              "lazy")
-            expect_identical(lazyeval::lazy_eval(mixed_dist_part_surv[[1, "part_surv"]]$pfs),
+            expect_identical(lazyeval::lazy_eval(mixed_dist_part_surv[["part_surv"]][[1]]$pfs),
                              'define_survival(distribution = "exp", rate = 1/100)')
-            expect_identical(class(lazyeval::lazy_eval(mixed_dist_part_surv[[1, "part_surv"]]$os)),
+            expect_identical(class(lazyeval::lazy_eval(mixed_dist_part_surv[["part_surv"]][[1]]$os)),
                              "flexsurvreg")
-            prob <- compute_surv(lazyeval::lazy_eval(mixed_dist_part_surv[[1, "part_surv"]]$os), 1)
+            prob <- compute_surv(lazyeval::lazy_eval(mixed_dist_part_surv[["part_surv"]][[1]]$os), 1)
             expect_equal(round(prob, 5), 0.00213)
                       })