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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-09 10:35:59 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-09 10:35:59 +0200 |
| commit | e4e54169ab3961c354f580bc489d150299038367 (patch) | |
| tree | 293790e7db06d0d808ceabc69ee4711294d928b6 /tests/testthat/test_nlme.R | |
| parent | 23461dddcc6a1858f1c9c9052512f22485d08842 (diff) | |
Improve test coverage and fix nlme test
No idea why I had to do more assignments all of a sudden in test_nlme.R
Diffstat (limited to 'tests/testthat/test_nlme.R')
| -rw-r--r-- | tests/testthat/test_nlme.R | 9 |
1 files changed, 5 insertions, 4 deletions
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R index 0d1fcd6d..efbc231a 100644 --- a/tests/testthat/test_nlme.R +++ b/tests/testthat/test_nlme.R @@ -31,6 +31,7 @@ test_that("nlme_function works correctly", { # The following assignment was introduced for nlme as evaluated by testthat # to find the function assign("nlme_f", nlme_f, pos = globalenv()) + assign("sampling_times", sampling_times, pos = globalenv()) m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink), data = grouped_data, @@ -68,7 +69,6 @@ test_that("nlme_function works correctly", { test_that("nlme_function works correctly in other cases", { dt50_in <- c(400, 800, 1200, 1600, 2000) - dt50_in_geomean <- geomean(dt50_in) k_in <- log(2) / dt50_in SFO <- mkinmod(parent = mkinsub("SFO")) pred_sfo <- function(k) { @@ -85,15 +85,16 @@ test_that("nlme_function works correctly in other cases", { names(ds_me_sfo_5) <- paste("Dataset", 1:15) dimnames(ds_me_sfo_5) <- list(Subset = 1:3, DT50 = dt50_in) - f_me_sfo_5 <- mmkin("SFO", ds_me_sfo_5) + f_me_sfo_5 <- mmkin("SFO", ds_me_sfo_5, quiet = TRUE) ds_me_sfo_5_grouped_mkin <- nlme_data(f_me_sfo_5) ds_me_sfo_5_mean_dp <- mean_degparms(f_me_sfo_5) me_sfo_function <- nlme_function(f_me_sfo_5) + assign("me_sfo_function", me_sfo_function, pos = globalenv()) f_nlme_sfo_5_all_mkin <- nlme(value ~ me_sfo_function(name, time, parent_0, log_k_parent_sink), - data = ds_me_sfo_5_grouped, + data = ds_me_sfo_5_grouped_mkin, fixed = parent_0 + log_k_parent_sink ~ 1, random = pdDiag(parent_0 + log_k_parent_sink ~ 1), start = ds_me_sfo_5_mean_dp) @@ -109,7 +110,7 @@ test_that("nlme_function works correctly in other cases", { # With less ideal starting values we get fits with lower AIC (not shown) f_nlme_sfo_5_all_mkin_nostart <- nlme(value ~ me_sfo_function(name, time, parent_0, log_k_parent_sink), - data = ds_me_sfo_5_grouped, + data = ds_me_sfo_5_grouped_mkin, fixed = parent_0 + log_k_parent_sink ~ 1, random = pdDiag(parent_0 + log_k_parent_sink ~ 1), start = c(parent_0 = 100, log_k_parent_sink = log(0.1))) |