Batch processing for hierarchical fits

- 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.

- 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects.

- 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects.

tests: Use 2 cores on travis, should work according to docs

1 files changed, 11 insertions, 10 deletions

diff --git a/log/test.log b/log/test.log
index 67ba8841..8be4a512 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,11 +1,11 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.3s]
+✔ |         5 | Analytical solutions for coupled models [3.4s]
 ✔ |         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 [32.9s]
+✔ |     1  12 | Dimethenamid data from 2018 [32.4s]
 ────────────────────────────────────────────────────────────────────────────────
 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
@@ -16,6 +16,7 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ✔ |        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]
+✔ |         5 | Batch fitting and diagnosing hierarchical kinetic models [14.5s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.2s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
@@ -27,23 +28,23 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.4s]
 ✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.8s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.3s]
-✔ |        16 | Plotting [10.6s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.7s]
+✔ |        16 | Plotting [10.1s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        28 | saemix parent models [182.2s]
+✔ |        28 | saemix parent models [181.2s]
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
-✔ |         7 | Fitting the SFORB model [3.9s]
+✔ |         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 [7.7s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
+✔ |         9 | Hypothesis tests [7.8s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 266.8 s
+Duration: 279.6 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 228 ]
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 233 ]