Merge pull request #16 from poissonconsulting/covr-tests

fixes #15 getting covr to run by skipping tests

tests/testthat/test-predict-growth.R

@@ -27,6 +27,8 @@ test_that("bb_predict_growth estimate works", {
 })
 
 test_that("bb_predict_growth multiple years each and one year common", {
+  skip_on_covr()
+
   survival <- bboudata::bbousurv_a
   survival <- survival[survival$Year %in% 2002:2003, ]
 
@@ -44,6 +46,8 @@ test_that("bb_predict_growth multiple years each and one year common", {
 })
 
 test_that("bb_predict_growth 1 year each and no years common", {
+  skip_on_covr()
+
   survival <- bboudata::bbousurv_a
   survival <- survival[survival$Year %in% c(2002, 2004), ]
 

tests/testthat/test-zzzfit-recruitment-ml.R

@@ -1,5 +1,7 @@
 test_that("recruitment default works", {
   skip_on_ci()
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   fit <- bb_fit_recruitment_ml(
     data = x,
@@ -16,6 +18,8 @@ test_that("recruitment default works", {
 
 test_that("recruitment fixed year works", {
   skip_on_ci()
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   fit <- bb_fit_recruitment_ml(
     data = x,
@@ -33,6 +37,8 @@ test_that("recruitment fixed year works", {
 
 test_that("can change fixed adult_female_proportion", {
   skip_on_ci()
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   fit <- bb_fit_recruitment_ml(
     data = x,
@@ -50,6 +56,8 @@ test_that("can change fixed adult_female_proportion", {
 
 test_that("can change fixed yearling_female_proportion", {
   skip_on_ci()
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   x$Yearlings[5:10] <- 1
   fit <- bb_fit_recruitment_ml(
@@ -69,6 +77,8 @@ test_that("can change fixed yearling_female_proportion", {
 test_that("can estimate adult_female_proportion", {
   # minor number rounding differences in fixed year estimates
   skip_on_ci()
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   fit <- bb_fit_recruitment_ml(
     data = x,
@@ -86,6 +96,8 @@ test_that("can estimate adult_female_proportion", {
 
 test_that("can set inits", {
   skip_on_ci()
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
 
   inits <- list(

tests/testthat/test-zzzfit-recruitment.R

@@ -1,4 +1,6 @@
 test_that("recruitment default works", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   set.seed(101)
   fit <- bb_fit_recruitment(
@@ -16,6 +18,8 @@ test_that("recruitment default works", {
 })
 
 test_that("recruitment can set caribou year", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   set.seed(101)
   fit <- bb_fit_recruitment(
@@ -33,6 +37,8 @@ test_that("recruitment can set caribou year", {
 })
 
 test_that("recruitment fixed works", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   set.seed(101)
   fit <- bb_fit_recruitment(
@@ -51,6 +57,8 @@ test_that("recruitment fixed works", {
 })
 
 test_that("recruitment trend works", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   set.seed(101)
   fit <- bb_fit_recruitment(
@@ -70,6 +78,8 @@ test_that("recruitment trend works", {
 })
 
 test_that("can change fixed adult_female_proportion", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   set.seed(101)
   fit <- bb_fit_recruitment(
@@ -88,6 +98,8 @@ test_that("can change fixed adult_female_proportion", {
 })
 
 test_that("can estimate adult_female_proportion", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   set.seed(101)
   fit <- bb_fit_recruitment(
@@ -106,6 +118,8 @@ test_that("can estimate adult_female_proportion", {
 })
 
 test_that("can change fixed yearling_female_proportion", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   x$Yearlings[5:10] <- 1
   set.seed(101)
@@ -125,6 +139,8 @@ test_that("can change fixed yearling_female_proportion", {
 })
 
 test_that("can set priors", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   set.seed(101)
 
@@ -162,6 +178,8 @@ test_that("can set priors", {
 })
 
 test_that("fails with wrong prior", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   wrong_prior <- list(bInterce = 1)
   expect_chk_error(bb_fit_recruitment(x, nthin = 1L, priors = wrong_prior, quiet = TRUE), "Names in `priors` must match 'adult_female_proportion_alpha', 'adult_female_proportion_beta', 'b0_mu', 'b0_sd', 'bAnnual_sd', 'bYear_mu', 'bYear_sd' or 'sAnnual_rate', not 'bInterce'.")
@@ -173,6 +191,8 @@ test_that("fails with multiple populations", {
 })
 
 test_that("can set niters", {
+  skip_on_covr()
+
   x <- bboudata::bbourecruit_a
   set.seed(101)
   fit <- bb_fit_recruitment(

tests/testthat/test-zzzfit-survival-ml.R

@@ -1,4 +1,6 @@
 test_that("survival default works", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   fit <- bb_fit_survival_ml(
     data = x,
@@ -15,6 +17,8 @@ test_that("survival default works", {
 
 test_that("survival fixed works", {
   skip_on_ci()
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
 
   fit <- bb_fit_survival_ml(
@@ -32,6 +36,8 @@ test_that("survival fixed works", {
 })
 
 test_that("can exclude year effect", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   fit <- bb_fit_survival_ml(
     data = x,
@@ -49,6 +55,8 @@ test_that("can exclude year effect", {
 })
 
 test_that("year trend works", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   fit <- bb_fit_survival_ml(
     data = x,
@@ -66,6 +74,8 @@ test_that("year trend works", {
 })
 
 test_that("year trend only works", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   fit <- bb_fit_survival_ml(
     data = x,
@@ -85,6 +95,8 @@ test_that("year trend only works", {
 test_that("can include_uncertain_morts", {
   # produces NaN se for some terms
   skip_on_ci()
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   x$MortalitiesUncertain <- pmin(x$StartTotal - x$MortalitiesCertain, rbinom(nrow(x), prob = 0.1, size = 1))
   fit <- bb_fit_survival_ml(
@@ -102,6 +114,8 @@ test_that("can include_uncertain_morts", {
 })
 
 test_that("can set inits", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
 
   inits <- list(
@@ -130,6 +144,8 @@ test_that("fails with multiple populations", {
 })
 
 test_that("works with less than 12 months", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_c
   x <- x[!x$Month %in% 12, ]
   fit <- bb_fit_survival_ml(

tests/testthat/test-zzzfit-survival.R

@@ -1,4 +1,6 @@
 test_that("survival default works", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   set.seed(101)
   fit <- bb_fit_survival(
@@ -15,6 +17,8 @@ test_that("survival default works", {
 })
 
 test_that("survival year start works", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   set.seed(101)
   fit <- bb_fit_survival(
@@ -35,6 +39,8 @@ test_that("survival year start works", {
 })
 
 test_that("survival fixed works", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   set.seed(101)
   fit <- bb_fit_survival(
@@ -53,6 +59,8 @@ test_that("survival fixed works", {
 })
 
 test_that("survival year trend + random works", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   set.seed(101)
   fit <- bb_fit_survival(
@@ -71,6 +79,8 @@ test_that("survival year trend + random works", {
 })
 
 test_that("survival year trend only", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   set.seed(101)
   fit <- bb_fit_survival(
@@ -89,6 +99,8 @@ test_that("survival year trend only", {
 })
 
 test_that("can include_uncertain_morts", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   set.seed(101)
   x$MortalitiesUncertain <- pmin(x$StartTotal - x$MortalitiesCertain, rbinom(nrow(x), prob = 0.1, size = 1))
@@ -107,6 +119,8 @@ test_that("can include_uncertain_morts", {
 })
 
 test_that("can set priors", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   set.seed(101)
   priors <- c(b0_mu = 10, b0_sd = 0.5)
@@ -145,6 +159,8 @@ test_that("fails with multiple populations", {
 })
 
 test_that("can set niters", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_a
   set.seed(101)
   fit <- bb_fit_survival(
@@ -165,6 +181,8 @@ test_that("can set niters", {
 
 
 test_that("works with less than 12 months", {
+  skip_on_covr()
+
   x <- bboudata::bbousurv_c
   x <- x[!x$Month %in% 12, ]
   set.seed(101)