diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | NEWS.md | 12 | ||||
| -rw-r--r-- | log/check.log | 4 | ||||
| -rw-r--r-- | log/test.log | 36 |
4 files changed, 27 insertions, 27 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index bb9ae3a5..de0fab86 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.2.0 -Date: 2022-11-01 +Date: 2022-11-16 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", @@ -1,5 +1,11 @@ # mkin 1.2.0 (unreleased) +- 'R/saem.R': 'logLik', 'update' and 'anova' methods for 'saem.mmkin' objects. + +- 'R/saem.R': Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions. + +- 'R/status.R': New generic to show status information for fit array objects with methods for 'mmkin', 'mhmkin' and 'multistart' objects. + - 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel. - 'R/mhmkin.R': 'anova.mhmkin' for conveniently comparing the resulting fits. @@ -8,12 +14,6 @@ - 'R/multistart.R': New method for testing multiple start parameters for hierarchical model fits, with function 'llhist' and new generic 'parplot' for diagnostics, and new generics 'which.best' and 'best' for extracting the fit with the highest likelihood -- 'R/saem.R': 'logLik', 'update' and 'anova' methods for 'saem.mmkin' objects. - -- 'R/saem.R': Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions. - -- 'R/status.R': New generic to show status information for fit array objects with methods for 'mmkin', 'mhmkin' and 'multistart' objects. - - 'R/summary.mmkin.R': Summary method for mmkin objects. - 'R/saem.R': Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported. diff --git a/log/check.log b/log/check.log index 3fea2ec6..7aa4610c 100644 --- a/log/check.log +++ b/log/check.log @@ -41,7 +41,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [14s/14s] OK +* checking R code for possible problems ... [18s/18s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -57,7 +57,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [15s/15s] OK +* checking examples ... [20s/20s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK diff --git a/log/test.log b/log/test.log index eb8d6b9a..b305bf58 100644 --- a/log/test.log +++ b/log/test.log @@ -1,22 +1,22 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.7s] +✔ | 5 | Analytical solutions for coupled models [3.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.1s] -✔ | 1 12 | Dimethenamid data from 2018 [37.5s] +✔ | 1 12 | Dimethenamid data from 2018 [34.5s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:98'): 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 [5.5s] +✔ | 14 | Error model fitting [5.3s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.7s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s] +✔ | 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 [0.3s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [27.2s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.6s] ✔ | 1 12 | Nonlinear mixed-effects models [0.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits @@ -24,30 +24,30 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls [0.6s] -✔ | 3 | mkinfit features [0.8s] +✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 9 | Multistart method for saem.mmkin models [45.7s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.7s] -✔ | 9 | Nonlinear mixed-effects models with nlme [10.3s] -✔ | 16 | Plotting [11.4s] +✔ | 9 | Multistart method for saem.mmkin models [40.2s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.5s] +✔ | 16 | Plotting [10.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [75.4s] +✔ | 1 36 | saemix parent models [69.8s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [4.2s] +✔ | 10 | Fitting the SFORB model [3.9s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s] -✔ | 9 | Hypothesis tests [9.6s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +✔ | 9 | Hypothesis tests [8.5s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 245.9 s +Duration: 225.9 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) |