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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-29 20:23:17 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-29 20:23:17 +0100
commitaaa4cab7e0c7212f91147a9789af54b97fe342ca (patch)
tree44605b8b650f032a035dbe5cd7ba6512b351a666 /tests/testthat
parent61b9a4046582da5cf88bd3c04d0d6ca77adc3405 (diff)
Complete starting values in summary for saem.mmkin fits
Also update tests to the changes in mhmkin (see NEWS)
Diffstat (limited to 'tests/testthat')
-rw-r--r--tests/testthat/illparms_hfits_synth_no_ranef_auto.txt4
-rw-r--r--tests/testthat/print_hfits_synth_no_ranef_auto.txt9
-rw-r--r--tests/testthat/summary_hfit_sfo_tc.txt11
-rw-r--r--tests/testthat/summary_saem_dfop_sfo_s.txt15
-rw-r--r--tests/testthat/test_mhmkin.R10
5 files changed, 24 insertions, 25 deletions
diff --git a/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt b/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt
deleted file mode 100644
index a64ed222..00000000
--- a/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt
+++ /dev/null
@@ -1,4 +0,0 @@
- error
-degradation const tc
- SFO sd(parent_0)
- FOMC b.1
diff --git a/tests/testthat/print_hfits_synth_no_ranef_auto.txt b/tests/testthat/print_hfits_synth_no_ranef_auto.txt
deleted file mode 100644
index 9af1cbcd..00000000
--- a/tests/testthat/print_hfits_synth_no_ranef_auto.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-<mhmkin> object
-Status of individual fits:
-
- error
-degradation const tc
- SFO OK OK
- FOMC OK OK
-
-OK: Fit terminated successfully
diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt
index bb5bf6fb..0a61f75f 100644
--- a/tests/testthat/summary_hfit_sfo_tc.txt
+++ b/tests/testthat/summary_hfit_sfo_tc.txt
@@ -17,13 +17,22 @@ Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
-Mean of starting values for individual parameters:
+Starting values for degradation parameters:
parent_0 log_k_parent
101 -3
Fixed degradation parameter values:
None
+Starting values for random effects (square root of initial entries in omega):
+ parent_0 log_k_parent
+parent_0 4 0.0
+log_k_parent 0 0.4
+
+Starting values for error model parameters:
+a.1 b.1
+ 1 1
+
Results:
Likelihood computed by importance sampling
diff --git a/tests/testthat/summary_saem_dfop_sfo_s.txt b/tests/testthat/summary_saem_dfop_sfo_s.txt
index 7c337843..6468ff17 100644
--- a/tests/testthat/summary_saem_dfop_sfo_s.txt
+++ b/tests/testthat/summary_saem_dfop_sfo_s.txt
@@ -22,7 +22,7 @@ Using 300, 100 iterations and 4 chains
Variance model: Two-component variance function
-Mean of starting values for individual parameters:
+Starting values for degradation parameters:
parent_0 k_m1 f_parent_to_m1 k1 k2
1e+02 7e-03 5e-01 1e-01 2e-02
g
@@ -31,6 +31,19 @@ Mean of starting values for individual parameters:
Fixed degradation parameter values:
None
+Starting values for random effects (square root of initial entries in omega):
+ parent_0 k_m1 f_parent_to_m1 k1 k2 g
+parent_0 101 0 0 0 0 0
+k_m1 0 1 0 0 0 0
+f_parent_to_m1 0 0 1 0 0 0
+k1 0 0 0 1 0 0
+k2 0 0 0 0 1 0
+g 0 0 0 0 0 1
+
+Starting values for error model parameters:
+a.1 b.1
+ 1 1
+
Results:
Likelihood computed by importance sampling
diff --git a/tests/testthat/test_mhmkin.R b/tests/testthat/test_mhmkin.R
index 93333ac1..e2339f28 100644
--- a/tests/testthat/test_mhmkin.R
+++ b/tests/testthat/test_mhmkin.R
@@ -46,14 +46,4 @@ test_that("Multiple hierarchical kinetic models can be fitted and diagnosed", {
print(fits_synth_const),
"print_fits_synth_const.txt")
- hfits_no_ranef_auto <- update(hfits, no_random_effect = "auto", auto_ranef_threshold = 2)
-
- expect_known_output(
- print(hfits_no_ranef_auto),
- "print_hfits_synth_no_ranef_auto.txt")
-
- expect_known_output(
- print(illparms(hfits_no_ranef_auto)),
- "illparms_hfits_synth_no_ranef_auto.txt")
-
})

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