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-rw-r--r--tests/testthat/test_nlme.R9
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)))

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