Complete starting values in summary for saem.mmkin fits

Also update tests to the changes in mhmkin (see NEWS)

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")
-
 })