fix

Author: d-morrison

R/sim_pop_data.R

@@ -106,7 +106,7 @@ sim_pop_data <- function(
 
   predpar <-
     curve_params |>
-    filter(.data$antigen_iso %in% antigen_isos) |>
+    dplyr::filter(.data$antigen_iso %in% antigen_isos) |>
     droplevels() |>
     prep_curve_params_for_array() |>
     df_to_array(dim_var_names = c("antigen_iso", "parameter"))

inst/examples/exm-analyze_sims.R

@@ -11,6 +11,8 @@ nrep <- c(50, 200)
 # incidence rate in e
 lambdas <- c(.05, .8)
 
+antibodies <- c("HlyE_IgA", "HlyE_IgG")
+lifespan <- c(0, 10)
 sim_df <-
   sim_pop_data_multi(
     n_cores = n_cores,

inst/examples/exm-autoplot.sim_results.R

@@ -10,7 +10,11 @@
 
   # incidence rate in e
   lambdas <- c(.05, .8)
-
+  antibodies <- c("HlyE_IgA", "HlyE_IgG")
+  dlims <- rbind(
+    "HlyE_IgA" = c(min = 0, max = 0.5),
+    "HlyE_IgG" = c(min = 0, max = 0.5)
+  )
   sim_df <-
     sim_pop_data_multi(
       n_cores = n_cores,

tests/testthat/fixtures/make-test_sim_results.R

@@ -9,7 +9,11 @@ nrep <- c(50, 100, 150, 200)
 
 # incidence rate in e
 lambdas <- c(.05, .1, .15, .2, .5, .8)
-
+antibodies <- c("HlyE_IgA", "HlyE_IgG")
+dlims <- rbind(
+  "HlyE_IgA" = c(min = 0, max = 0.5),
+  "HlyE_IgG" = c(min = 0, max = 0.5)
+)
 sim_df <-
   sim_pop_data_multi(
     n_cores = n_cores,

tests/testthat/test-autoplot.sim_results.R

@@ -11,7 +11,12 @@ test_that("results are consistent", {
 
   # incidence rate in e
   lambdas <- c(.05, .8)
-
+  antibodies <- c("HlyE_IgA", "HlyE_IgG")
+  lifespan <- c(0, 10)
+  dlims <- rbind(
+    "HlyE_IgA" = c(min = 0, max = 0.5),
+    "HlyE_IgG" = c(min = 0, max = 0.5)
+  )
   sim_df <-
     sim_pop_data_multi(
       n_cores = n_cores,