update tests that regression test the epiparameter database

epiverse-trace · Sep 13, 2024 · 1dd58f5 · 1dd58f5
1 parent d4b8888
commit 1dd58f5
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Showing 5 changed files with 11 additions and 11 deletions.
diff --git a/tests/testthat/_snaps/parameter_tbl.md b/tests/testthat/_snaps/parameter_tbl.md
@@ -4,7 +4,7 @@
       dist_tbl
     Output
       # Parameter table:
-      # A data frame:    122 x 7
+      # A data frame:    125 x 7
          disease  pathogen epi_distribution prob_distribution author  year sample_size
          <chr>    <chr>    <chr>            <chr>             <chr>  <dbl>       <dbl>
        1 Adenovi~ Adenovi~ incubation peri~ lnorm             Lessl~  2009          14
@@ -17,7 +17,7 @@
        8 Parainf~ Parainf~ incubation peri~ lnorm             Lessl~  2009          11
        9 RSV      RSV      incubation peri~ lnorm             Lessl~  2009          24
       10 Rhinovi~ Rhinovi~ incubation peri~ lnorm             Lessl~  2009          28
-      # i 112 more rows
+      # i 115 more rows
 
 # parameter_tbl works for incubation period with db
 

diff --git a/tests/testthat/_snaps/print.md b/tests/testthat/_snaps/print.md
@@ -3,15 +3,15 @@
     Code
       epiparameter_db()
     Message
-      Returning 122 results that match the criteria (99 are parameterised). 
+      Returning 125 results that match the criteria (100 are parameterised). 
       Use subset to filter by entry variables or single_epiparameter to return a single entry. 
       To retrieve the citation for each use the 'get_citation' function
     Output
-      # List of 122 <epiparameter> objects
+      # List of 125 <epiparameter> objects
       Number of diseases: 23
       > Adenovirus > COVID-19 > Chikungunya > Dengue > Ebola Virus Disease > Hantavirus Pulmonary Syndrome > Human Coronavirus > Influenza > Japanese Encephalitis > MERS > Marburg Virus Disease > Measles > Mpox > Parainfluenza > Pneumonic Plague > RSV > Rhinovirus > Rift Valley Fever > SARS > Smallpox > West Nile Fever > Yellow Fever > Zika Virus Disease
-      Number of epi distributions: 12
-      > generation time > hospitalisation to death > hospitalisation to discharge > incubation period > notification to death > notification to discharge > offspring distribution > onset to death > onset to discharge > onset to hospitalisation > onset to ventilation > serial interval
+      Number of epi distributions: 13
+      > case fatality risk > generation time > hospitalisation to death > hospitalisation to discharge > incubation period > notification to death > notification to discharge > offspring distribution > onset to death > onset to discharge > onset to hospitalisation > onset to ventilation > serial interval
       [[1]]
       Disease: Adenovirus
       Pathogen: Adenovirus
@@ -54,7 +54,7 @@
         meanlog: 0.660
         sdlog: 1.205
       
-      # i 119 more elements
+      # i 122 more elements
       # i Use `print(n = ...)` to see more elements.
       # i Use `parameter_tbl()` to see a summary table of the parameters.
       # i Explore database online at: https://epiverse-trace.github.io/epiparameter/articles/database.html

diff --git a/tests/testthat/test-epiparameter.R b/tests/testthat/test-epiparameter.R
@@ -1263,7 +1263,7 @@ test_that("c.epiparameter works with <epiparameter> & <multi_epiparameter>", {
 test_that("c.multi_epiparameter works with two <multi_epiparameter>s", {
   res <- c(db, db)
   expect_s3_class(res, class = "multi_epiparameter")
-  expect_length(res, 244)
+  expect_length(res, 250)
   expect_s3_class(res[[1]], class = "epiparameter")
 })
 

diff --git a/tests/testthat/test-epiparameter_db.R b/tests/testthat/test-epiparameter_db.R
@@ -208,7 +208,7 @@ test_that(".read_epiparameter_db works as expected", {
   db <- .read_epiparameter_db()
   expect_s3_class(db, class = "multi_epiparameter")
   expect_type(db, type = "list")
-  expect_length(db, 122)
+  expect_length(db, 125)
   expect_true(all(vapply(db, is_epiparameter, FUN.VALUE = logical(1))))
 })
 
@@ -244,7 +244,7 @@ test_that("as.data.frame works for <multi_epiparameter>", {
   db <- suppressMessages(epiparameter_db())
   df <- as.data.frame(db)
   expect_s3_class(df, class = "data.frame")
-  expect_identical(dim(df), c(122L, 10L))
+  expect_identical(dim(df), c(125L, 10L))
   expect_identical(
     colnames(df),
     c("disease", "pathogen", "epi_distribution", "prob_distribution",

diff --git a/tests/testthat/test-parameter_tbl.R b/tests/testthat/test-parameter_tbl.R
@@ -4,7 +4,7 @@ db <- suppressMessages(epiparameter_db())
 test_that("parameter_tbl works as expected supplied with db", {
   dist_tbl <- parameter_tbl(multi_epiparameter = db)
   expect_s3_class(dist_tbl, "data.frame")
-  expect_identical(dim(dist_tbl), c(122L, 7L))
+  expect_identical(dim(dist_tbl), c(125L, 7L))
   expect_named(
     dist_tbl,
     c("disease", "pathogen", "epi_distribution", "prob_distribution",