diff options
| -rw-r--r-- | R/mhmkin.R | 28 | ||||
| -rw-r--r-- | log/check.log | 4 | ||||
| -rw-r--r-- | log/test.log | 38 | ||||
| -rw-r--r-- | man/mhmkin.Rd | 18 | ||||
| -rw-r--r-- | tests/testthat/illparms_hfits_synth_no_ranef_auto.txt | 4 | ||||
| -rw-r--r-- | tests/testthat/print_hfits_synth_no_ranef_auto.txt | 9 | ||||
| -rw-r--r-- | tests/testthat/test_mhmkin.R | 14 |
7 files changed, 85 insertions, 30 deletions
@@ -12,6 +12,13 @@ #' degradation models to the same data #' @param backend The backend to be used for fitting. Currently, only saemix is #' supported +#' @param no_random_effect Default is NULL and will be passed to [saem]. If +#' you specify "auto", random effects are only included if the number +#' of datasets in which the parameter passed the t-test is at least 'auto_ranef_threshold'. +#' Beware that while this may make for convenient model reduction or even +#' numerical stability of the algorithm, it will likely lead to +#' underparameterised models. +#' @param auto_ranef_threshold See 'no_random_effect. #' @param algorithm The algorithm to be used for fitting (currently not used) #' @param \dots Further arguments that will be passed to the nonlinear mixed-effects #' model fitting function. @@ -31,7 +38,7 @@ #' @author Johannes Ranke #' @seealso \code{\link{[.mhmkin}} for subsetting [mhmkin] objects #' @export -mhmkin <- function(objects, backend = "saemix", algorithm = "saem", ...) { +mhmkin <- function(objects, ...) { UseMethod("mhmkin") } @@ -43,7 +50,8 @@ mhmkin.mmkin <- function(objects, ...) { #' @export #' @rdname mhmkin -mhmkin.list <- function(objects, backend = "saemix", +mhmkin.list <- function(objects, backend = "saemix", algorithm = "saem", + no_random_effect = NULL, auto_ranef_threshold = 3, ..., cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL) { @@ -94,7 +102,19 @@ mhmkin.list <- function(objects, backend = "saemix", deg_index <- w[1] error_index <- w[2] mmkin_row <- objects[[error_index]][deg_index, ] - res <- try(do.call(backend_function, args = c(list(mmkin_row), dot_args))) + if (identical(no_random_effect, "auto")) { + ip <- illparms(mmkin_row) + ipt <- table(unlist(lapply(as.list(ip), strsplit, ", "))) + no_ranef <- names(ipt)[which((length(ds) - ipt) <= auto_ranef_threshold)] + transparms <- rownames(mmkin_row[[1]]$start_transformed) + bparms <- rownames(mmkin_row[[1]]$start) + names(transparms) <- bparms + no_ranef_trans <- transparms[no_ranef] + } else { + no_ranef_trans <- no_random_effect + } + res <- try(do.call(backend_function, + args = c(list(mmkin_row), dot_args, list(no_random_effect = no_ranef_trans)))) return(res) } @@ -207,7 +227,7 @@ anova.mhmkin <- function(object, ..., if (identical(model.names, "auto")) { model.names <- outer(rownames(object), colnames(object), paste) } - rlang::inject(anova(!!!(object), method = method, test = test, + rlang::inject(anova(!!!(object), method = method, test = test, model.names = model.names)) } diff --git a/log/check.log b/log/check.log index 3fea2ec6..d8225158 100644 --- a/log/check.log +++ b/log/check.log @@ -57,12 +57,12 @@ 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 ... [36s/46s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK -* checking re-building of vignette outputs ... OK +* checking re-building of vignette outputs ... [26s/41s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK diff --git a/log/test.log b/log/test.log index 611b66b6..95d50017 100644 --- a/log/test.log +++ b/log/test.log @@ -1,57 +1,57 @@ 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 [31.9s] +✔ | 1 12 | Dimethenamid data from 2018 [33.0s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.6s] ✔ | 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 [0.3s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 8 | Batch fitting and diagnosing hierarchical kinetic models [14.5s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [26.9s] ✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.4s] -✔ | 3 | mkinfit features [0.7s] -✔ | 8 | mkinmod model generation and printing [0.2s] +✔ | 10 | Special cases of mkinfit calls [0.6s] +✔ | 3 | mkinfit features [0.8s] +✔ | 8 | mkinmod model generation and printing [0.3s] ✔ | 3 | Model predictions with mkinpredict [0.4s] -✔ | 7 | Multistart method for saem.mmkin models [36.2s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.4s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] -✔ | 16 | Plotting [10.0s] +✔ | 7 | Multistart method for saem.mmkin models [44.7s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.8s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.9s] +✔ | 16 | Plotting [10.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 37 | saemix parent models [71.4s] +✔ | 1 37 | saemix parent models [76.1s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_saemix_parent.R:153:3): 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 [1.5s] ✔ | 11 | Processing of residue series -✔ | 7 | Fitting the SFORB model [3.7s] +✔ | 7 | 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) [2.2s] -✔ | 9 | Hypothesis tests [8.1s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +✔ | 9 | Hypothesis tests [8.4s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 206.7 s +Duration: 237.3 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) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 3 | PASS 263 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 265 ] diff --git a/man/mhmkin.Rd b/man/mhmkin.Rd index 1a6e3869..597fa8ac 100644 --- a/man/mhmkin.Rd +++ b/man/mhmkin.Rd @@ -9,13 +9,16 @@ \title{Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models} \usage{ -mhmkin(objects, backend = "saemix", algorithm = "saem", ...) +mhmkin(objects, ...) \method{mhmkin}{mmkin}(objects, ...) \method{mhmkin}{list}( objects, backend = "saemix", + algorithm = "saem", + no_random_effect = NULL, + auto_ranef_threshold = 3, ..., cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL @@ -31,13 +34,22 @@ degradation models to the same data, but using different error models. Alternatively, a single \link{mmkin} object containing fits of several degradation models to the same data} +\item{\dots}{Further arguments that will be passed to the nonlinear mixed-effects +model fitting function.} + \item{backend}{The backend to be used for fitting. Currently, only saemix is supported} \item{algorithm}{The algorithm to be used for fitting (currently not used)} -\item{\dots}{Further arguments that will be passed to the nonlinear mixed-effects -model fitting function.} +\item{no_random_effect}{Default is NULL and will be passed to \link{saem}. If +you specify "auto", random effects are only included if the number +of datasets in which the parameter passed the t-test is at least 'auto_ranef_threshold'. +Beware that while this may make for convenient model reduction or even +numerical stability of the algorithm, it will likely lead to +underparameterised models.} + +\item{auto_ranef_threshold}{See 'no_random_effect.} \item{cores}{The number of cores to be used for multicore processing. This is only used when the \code{cluster} argument is \code{NULL}. On Windows diff --git a/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt b/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt new file mode 100644 index 00000000..a64ed222 --- /dev/null +++ b/tests/testthat/illparms_hfits_synth_no_ranef_auto.txt @@ -0,0 +1,4 @@ + 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 new file mode 100644 index 00000000..9af1cbcd --- /dev/null +++ b/tests/testthat/print_hfits_synth_no_ranef_auto.txt @@ -0,0 +1,9 @@ +<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/test_mhmkin.R b/tests/testthat/test_mhmkin.R index 9fd29c50..93333ac1 100644 --- a/tests/testthat/test_mhmkin.R +++ b/tests/testthat/test_mhmkin.R @@ -38,12 +38,22 @@ test_that("Multiple hierarchical kinetic models can be fitted and diagnosed", { expect_known_output(print(test_summary, digits = 1), "summary_hfit_sfo_tc.txt") - # It depends on the platform exactly which of the - # SFO datasets fail to converge with FOMC + # It depends on the platform exactly which of the datasets fail to converge + # with FOMC, because they were generated to be SFO skip_on_travis() expect_known_output( 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") + }) |