Add set_nd_nq previously in pfm

pfm depends on mkin anyways, so reexporting set_nd_nq and
set_nd_nq_focus in pfm should provide reasonable continuity.

1 files changed, 46 insertions, 14 deletions

diff --git a/log/test.log b/log/test.log
index efa30d17..73fbfcf2 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,24 +1,55 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.4s]
+✔ |         5 | Analytical solutions for coupled models [3.3s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [31.9s]
+✔ |     1  12 | Dimethenamid data from 2018 [32.2s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [4.9s]
+✔ |        14 | Error model fitting [5.1s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.4s]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |         7 | Batch fitting and diagnosing hierarchical kinetic models [14.5s]
-✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
+✖ | 1       6 | Batch fitting and diagnosing hierarchical kinetic models [14.5s]
 ────────────────────────────────────────────────────────────────────────────────
+Failure (test_mhmkin.R:41:3): Multiple hierarchical kinetic models can be fitted and diagnosed
+Results have changed from known value recorded in 'summary_hfit_sfo_tc.txt'.
+
+     old                           | new                               
+[45] ""                            | ""                            [45]
+[46] "Variance model:"             | "Variance model:"             [46]
+[47] "    est. lower upper"        | "    est. lower upper"        [47]
+[48] "a.1 0.91  0.64  1.17"        - "a.1 0.90  0.64  1.17"        [48]
+[49] "b.1 0.05  0.04  0.06"        | "b.1 0.05  0.04  0.06"        [49]
+[50] ""                            | ""                            [50]
+[51] "Backtransformed parameters:" | "Backtransformed parameters:" [51]
+────────────────────────────────────────────────────────────────────────────────
+✖ | 1   1  11 | Nonlinear mixed-effects models [0.3s]
+────────────────────────────────────────────────────────────────────────────────
+Failure (test_mixed.R:8:3): Print methods work
+Results have changed from known value recorded in 'print_sfo_saem_1.txt'.
+
+old[7:19] vs new[7:19]
+  ""
+  "Likelihood computed by importance sampling"
+  "   AIC  BIC logLik"
+- "  1311 1315   -649"
++ "  1312 1316   -650"
+  ""
+  "Fitted parameters:"
+  "            estimate lower upper"
+- "parent_0       1e+02 99.13 1e+02"
++ "parent_0       1e+02 99.28 1e+02"
+  "k_parent       4e-02  0.03 4e-02"
+  "a.1            9e-01  0.75 1e+00"
+and 3 more ...
+
 Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
@@ -26,25 +57,26 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |        10 | Special cases of mkinfit calls [0.4s]
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.8s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.3s]
-✔ |        16 | Plotting [10.0s]
+✔ |         3 | Model predictions with mkinpredict [0.4s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.9s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.6s]
+✔ |        16 | Plotting [10.2s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        28 | saemix parent models [180.2s]
+✔ |        28 | saemix parent models [181.5s]
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
-✔ |         7 | Fitting the SFORB model [3.6s]
+✔ |        11 | Processing of residue series
+✔ |         7 | Fitting the SFORB model [3.7s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
-✔ |         9 | Hypothesis tests [7.8s]
+✔ |         9 | Hypothesis tests [8.3s]
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 277.4 s
+Duration: 280.7 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
 • Fitting with saemix takes around 10 minutes when using deSolve (1)
 
-[ FAIL 0 | WARN 0 | SKIP 2 | PASS 235 ]
+[ FAIL 2 | WARN 0 | SKIP 2 | PASS 244 ]