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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-30 14:50:33 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-30 14:50:33 +0100
commit78884beed74c18c99521b9ceeaa643e13cf94c06 (patch)
treeaf1ebfd975cac837a6bf15c86638299a67a0e017 /tests/testthat/test_nlme.R
parentb3bebc06061cc77b6d549f7b2760afe0b9489bf7 (diff)
Log-Cholesky parameterisation as default in nlme.mmkin
Diffstat (limited to 'tests/testthat/test_nlme.R')
-rw-r--r--tests/testthat/test_nlme.R20
1 files changed, 11 insertions, 9 deletions
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index 4fd8e53f..da994f49 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -38,24 +38,27 @@ test_that("nlme_function works correctly", {
m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
data = grouped_data,
fixed = parent_0 + log_k_parent_sink ~ 1,
- random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
- start = mean_dp)
+ random = pdLogChol(parent_0 + log_k_parent_sink ~ 1),
+ start = mean_dp,
+ control = list("msWarnNoConv" = FALSE))
m_nlme_mkin <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),
data = grouped_data,
fixed = parent_0 + log_k_parent_sink ~ 1,
- random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
- start = mean_dp)
+ random = pdLogChol(parent_0 + log_k_parent_sink ~ 1),
+ start = mean_dp,
+ control = list("msWarnNoConv" = FALSE))
expect_equal(m_nlme_raw$coefficients, m_nlme_mkin$coefficients)
- m_nlme_mmkin <- nlme(f)
+ m_nlme_mmkin <- nlme(f, control = list("msWarnNoConv" = FALSE))
m_nlme_raw_2 <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent),
data = grouped_data,
fixed = parent_0 + log_k_parent ~ 1,
- random = pdDiag(parent_0 + log_k_parent ~ 1),
- start = mean_degparms(f, random = TRUE))
+ random = pdLogChol(parent_0 + log_k_parent ~ 1),
+ start = mean_degparms(f, random = TRUE),
+ control = list("msWarnNoConv" = FALSE))
expect_equal(m_nlme_raw_2$coefficients, m_nlme_mmkin$coefficients)
@@ -84,8 +87,7 @@ test_that("nlme_function works correctly", {
m_nlme_mkin_up_2 <- update(m_nlme_mkin, random = parent_0 ~ 1)
expect_equal(m_nlme_raw_up_2$coefficients, m_nlme_mkin_up_2$coefficients)
- expect_silent(tmp <- update(m_nlme_mkin))
- expect_silent(tmp <- update(m_nlme_mmkin))
+ expect_warning(tmp <- update(m_nlme_mmkin), "Iteration 1, LME step")
geomean_dt50_mmkin <- exp(mean(log((sapply(f, function(x) endpoints(x)$distimes["parent", "DT50"])))))
expect_equal(round(endpoints(m_nlme_mmkin)$distimes["parent", "DT50"]), round(geomean_dt50_mmkin))

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