diff options
| -rw-r--r-- | DESCRIPTION | 7 | ||||
| -rw-r--r-- | NEWS.md | 26 | ||||
| -rw-r--r-- | R/D24_2014.R | 2 | ||||
| -rw-r--r-- | check.log | 16 | ||||
| -rw-r--r-- | man/D24_2014.Rd | 2 | ||||
| -rw-r--r-- | man/saem.Rd | 8 | ||||
| -rw-r--r-- | man/summary.saem.mmkin.Rd | 2 | ||||
| -rw-r--r-- | test.log | 52 | ||||
| -rw-r--r-- | test_dev.log | 69 | ||||
| -rw-r--r-- | tests/testthat/print_mmkin_biphasic_mixed.txt | 4 | ||||
| -rw-r--r-- | tests/testthat/print_nlme_biphasic.txt | 8 | ||||
| -rw-r--r-- | tests/testthat/setup_script.R | 39 | ||||
| -rw-r--r-- | tests/testthat/summary_nlme_biphasic_s.txt | 42 | ||||
| -rw-r--r-- | tests/testthat/test_error_models.R | 1 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 13 | ||||
| -rw-r--r-- | tests/testthat/test_plot.R | 14 |
16 files changed, 187 insertions, 118 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 697aa90d..fa6c1c90 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.50.4 -Date: 2020-12-10 +Date: 2021-01-06 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), @@ -18,9 +18,10 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, particular purpose. Depends: R (>= 2.15.1), parallel Imports: stats, graphics, methods, deSolve, R6, inline (>= 0.3.17), numDeriv, - lmtest, pkgbuild, nlme (>= 3.1-151), purrr, saemix (>= 3.1.9000) + lmtest, pkgbuild, nlme (>= 3.1-151), purrr Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr, - benchmarkme, tibble, stats4 + benchmarkme, tibble, stats4, saemix (>= 3.1.9000) +Additional_repositories: https://jranke.github.io/drat License: GPL LazyLoad: yes LazyData: yes @@ -1,28 +1,36 @@ # mkin 0.9.50.4 (unreleased) -- 'mixed.mmkin' New container for mmkin objects for plotting with the 'plot.mixed.mmkin' method +## General new features - 'mkinmod' models gain arguments 'name' and 'dll_dir' which, in conjunction with a current version of the 'inline' package, make it possible to still use the DLL used for fast ODE solutions with 'deSolve' after saving and restoring the 'mkinmod' object. -- 'f_norm_temp_focus' generic function to normalise time intervals using the FOCUS method, with methods for numeric vectors and 'mkindsg' objects - - 'mkindsg' R6 class for groups of 'mkinds' datasets with metadata -- 'D24_2014' dataset +- 'f_norm_temp_focus' generic function to normalise time intervals using the FOCUS method, with methods for numeric vectors and 'mkindsg' objects + +- 'D24_2014' and 'dimethenamid_2018' datasets - 'focus_soil_moisture' FOCUS default soil moisture data -- 'plot.mixed.mmkin' method used for 'nlme.mmkin' and 'saem.mmkin', both inheriting from 'mixed.mmkin' (currently virtual) - -- 'saem' generic function to fit saemix models, with a generator 'saem.mmkin', summary and plot methods +- 'update' method for 'mmkin' objects - 'transform_odeparms', 'backtransform_odeparms': Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable -- 'update' method for 'mmkin' objects +## Mixed-effects models + +- 'mixed.mmkin' New container for mmkin objects for plotting with the 'plot.mixed.mmkin' method + +- 'plot.mixed.mmkin' method used for 'nlme.mmkin' and 'saem.mmkin', both inheriting from 'mixed.mmkin' (currently virtual) - 'plot', 'summary' and 'print' methods for 'nlme.mmkin' objects -- 'saemix_model', 'saemix_data': Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package +- Add the current development version of the saemix package as a second, optional backend for mixed-effects models + +- DESCRIPTION: Additional_repositories entry pointing to my drat repository on github for a suitable saemix version + +- 'saemix_model', 'saemix_data': Helper functions to fit nonlinear mixed-effects models for mmkin row objects. + +- 'saem' generic function to fit saemix models using 'saemix_model' and 'saemix_data', with a generator 'saem.mmkin', summary and plot methods # mkin 0.9.50.3 (2020-10-08) diff --git a/R/D24_2014.R b/R/D24_2014.R index 0a111e1c..1f2bcc04 100644 --- a/R/D24_2014.R +++ b/R/D24_2014.R @@ -23,6 +23,7 @@ #' \url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812} #' @examples #' print(D24_2014) +#' \dontrun{ #' print(D24_2014$ds[[1]], data = TRUE) #' m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"), #' DCP = mkinsub("SFO", to = "DCA"), @@ -32,4 +33,5 @@ #' DCP = mkinsub("SFO", to = "DCA"), #' DCA = mkinsub("SFO")) #' print(m_D24_2) +#' } "D24_2014" @@ -10,7 +10,8 @@ * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ * checking package namespace information ... OK -* checking package dependencies ... OK +* checking package dependencies ... NOTE +Package suggested but not available for checking: ‘saemix’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK @@ -21,8 +22,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ * checking whether package ‘mkin’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... NOTE -unable to verify current time +* checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK @@ -46,7 +46,8 @@ unable to verify current time * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK -* checking Rd cross-references ... OK +* checking Rd cross-references ... NOTE +Package unavailable to check Rd xrefs: ‘saemix’ * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK @@ -57,7 +58,10 @@ unable to verify current time * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... OK +* checking examples ... NOTE +Examples with CPU (user + system) or elapsed time > 5s + user system elapsed +D24_2014 1.808 3.425 0.986 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -68,7 +72,7 @@ unable to verify current time * checking for detritus in the temp directory ... OK * DONE -Status: 1 NOTE +Status: 3 NOTEs See ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ for details. diff --git a/man/D24_2014.Rd b/man/D24_2014.Rd index 8d0e632c..1afa9596 100644 --- a/man/D24_2014.Rd +++ b/man/D24_2014.Rd @@ -36,6 +36,7 @@ specific pieces of information in the comments. } \examples{ print(D24_2014) +\dontrun{ print(D24_2014$ds[[1]], data = TRUE) m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"), DCP = mkinsub("SFO", to = "DCA"), @@ -46,4 +47,5 @@ m_D24_2 = mkinmod(D24 = mkinsub("DFOP", to = "DCP"), DCA = mkinsub("SFO")) print(m_D24_2) } +} \keyword{datasets} diff --git a/man/saem.Rd b/man/saem.Rd index 775a8e7b..969e9a22 100644 --- a/man/saem.Rd +++ b/man/saem.Rd @@ -57,7 +57,7 @@ automatic choice is not desired} \item{control}{Passed to \link[saemix:saemix]{saemix::saemix}} \item{verbose}{Should we print information about created objects of -type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?} +type \link[saemix:SaemixModel]{saemix::SaemixModel} and \link[saemix:SaemixData]{saemix::SaemixData}?} \item{suppressPlot}{Should we suppress any plotting that is done by the saemix function?} @@ -71,12 +71,12 @@ and the end of the optimisation process?} } \value{ An S3 object of class 'saem.mmkin', containing the fitted -\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The +\link[saemix:SaemixObject]{saemix::SaemixObject} as a list component named 'so'. The object also inherits from 'mixed.mmkin'. -An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object. +An \link[saemix:SaemixModel]{saemix::SaemixModel} object. -An \link[saemix:SaemixData-class]{saemix::SaemixData} object. +An \link[saemix:SaemixData]{saemix::SaemixData} object. } \description{ This function uses \code{\link[saemix:saemix]{saemix::saemix()}} as a backend for fitting nonlinear mixed diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd index 67cb3cbb..4f83489c 100644 --- a/man/summary.saem.mmkin.Rd +++ b/man/summary.saem.mmkin.Rd @@ -27,7 +27,7 @@ included.} \item{digits}{Number of digits to use for printing} } \value{ -The summary function returns a list based on the \link[saemix:SaemixObject-class]{saemix::SaemixObject} +The summary function returns a list based on the \link[saemix:SaemixObject]{saemix::SaemixObject} obtained in the fit, with at least the following additional components \item{saemixversion, mkinversion, Rversion}{The saemix, mkin and R versions used} \item{date.fit, date.summary}{The dates where the fit and the summary were @@ -4,41 +4,47 @@ Testing mkin ✔ | OK F W S | Context ✔ | 5 | AIC calculation ✔ | 2 | Export dataset for reading into CAKE -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] -✔ | 7 | Fitting the SFORB model [3.6 s] -✔ | 5 | Analytical solutions for coupled models [3.3 s] +✔ | 7 | Fitting the SFORB model [4.0 s] +✔ | 5 | Analytical solutions for coupled models [3.6 s] ✔ | 5 | Calculation of Akaike weights -✔ | 14 | Confidence intervals and p-values [1.2 s] -✔ | 14 | Error model fitting [5.6 s] +✔ | 14 | Confidence intervals and p-values [1.4 s] +✔ | 14 | Error model fitting [6.8 s] ✔ | 5 | Time step normalisation -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] -✔ | 1 | Fitting the logistic model [0.2 s] -✔ | 33 1 | Nonlinear mixed effects models [28.7 s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.5 s] +✔ | 1 | Fitting the logistic model [0.3 s] +✔ | 5 3 | Nonlinear mixed-effects models [0.1 s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_mixed.R:143:3): saem results are reproducible for biphasic fits -Reason: Fitting with saemix takes around 10 minutes when using deSolve +Skip (test_mixed.R:4:3): Parent fits using saemix are correctly implemented +Reason: !saemix_available is TRUE + +Skip (test_mixed.R:94:3): Print methods work +Reason: !saemix_available is TRUE + +Skip (test_mixed.R:118:3): saem results are reproducible for biphasic fits +Reason: !saemix_available is TRUE ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Test dataset classes mkinds and mkindsg -✔ | 1 | mkinfit features [0.3 s] -✔ | 10 | Special cases of mkinfit calls [0.3 s] +✔ | 1 | mkinfit features [0.4 s] +✔ | 10 | Special cases of mkinfit calls [0.4 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.4 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7 s] -✔ | 9 | Nonlinear mixed-effects models [8.2 s] -✔ | 16 | Plotting [1.9 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.0 s] +✔ | 9 | Nonlinear mixed-effects models [9.3 s] +✔ | 14 | Plotting [2.0 s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s] -✔ | 4 | Summary [0.1 s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.8 s] +✔ | 4 | Summary [0.2 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s] -✔ | 9 | Hypothesis tests [7.3 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5 s] +✔ | 9 | Hypothesis tests [7.9 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.7 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 71.3 s +Duration: 48.3 s ── Skipped tests ────────────────────────────────────────────────────────────── -● Fitting with saemix takes around 10 minutes when using deSolve (1) +● !saemix_available is TRUE (3) -[ FAIL 0 | WARN 0 | SKIP 1 | PASS 206 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 176 ] diff --git a/test_dev.log b/test_dev.log index c57bb958..df159d1e 100644 --- a/test_dev.log +++ b/test_dev.log @@ -1,37 +1,62 @@ Loading mkin +Loading required package: parallel Testing mkin ✔ | OK F W S | Context -✔ | 4 | AIC calculation +✔ | 5 | AIC calculation ✔ | 2 | Export dataset for reading into CAKE -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s] -✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s] -✔ | 7 | Fitting the SFORB model [3.1 s] -✔ | 5 | Analytical solutions for coupled models [2.8 s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s] +✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] +✔ | 7 | Fitting the SFORB model [3.4 s] +✔ | 5 | Analytical solutions for coupled models [3.1 s] ✔ | 5 | Calculation of Akaike weights -✔ | 10 | Confidence intervals and p-values [0.9 s] -✔ | 14 | Error model fitting [3.8 s] +✔ | 14 | Confidence intervals and p-values [1.2 s] +✔ | 14 | Error model fitting [5.8 s] +✔ | 5 | Time step normalisation ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] -✔ | 1 | Test dataset class mkinds used in gmkin -✔ | 1 | mkinfit features [0.2 s] -✔ | 12 | Special cases of mkinfit calls [0.6 s] +✔ | 5 3 | Nonlinear mixed-effects models [0.1 s] +──────────────────────────────────────────────────────────────────────────────── +Skip (test_mixed.R:4:3): Parent fits using saemix are correctly implemented +Reason: !saemix_available is TRUE + +Skip (test_mixed.R:94:3): Print methods work +Reason: !saemix_available is TRUE + +Skip (test_mixed.R:118:3): saem results are reproducible for biphasic fits +Reason: !saemix_available is TRUE +──────────────────────────────────────────────────────────────────────────────── +✔ | 2 | Test dataset classes mkinds and mkindsg +✔ | 1 | mkinfit features [0.3 s] +✔ | 10 | Special cases of mkinfit calls [0.3 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.3 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.3 s] -✔ | 9 | Nonlinear mixed-effects models [7.3 s] -✔ | 14 | Plotting [1.3 s] +✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [2.2 s] +──────────────────────────────────────────────────────────────────────────────── +Skip (test_nafta.R:25:5): Test data from Appendix B are correctly evaluated +Reason: getRversion() >= "4.1.0" is TRUE + +Skip (test_nafta.R:53:5): Test data from Appendix D are correctly evaluated +Reason: getRversion() >= "4.1.0" is TRUE +──────────────────────────────────────────────────────────────────────────────── +✔ | 9 | Nonlinear mixed-effects models [7.9 s] +✔ | 0 1 | Plotting [0.7 s] +──────────────────────────────────────────────────────────────────────────────── +Skip (test_plot.R:18:3): Plotting mkinfit, mmkin and mixed model objects is reproducible +Reason: getRversion() >= "4.1.0" is TRUE +──────────────────────────────────────────────────────────────────────────────── ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s] -✔ | 4 | Summary +✔ | 4 | Summary [0.1 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.0 s] -✔ | 9 | Hypothesis tests [7.4 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s] +✔ | 9 | Hypothesis tests [7.7 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 36.9 s +Duration: 41.2 s + +── Skipped tests ────────────────────────────────────────────────────────────── +● !saemix_available is TRUE (3) +● getRversion() >= "4.1.0" is TRUE (3) -OK: 162 -Failed: 0 -Warnings: 0 -Skipped: 0 +[ FAIL 0 | WARN 0 | SKIP 6 | PASS 160 ] diff --git a/tests/testthat/print_mmkin_biphasic_mixed.txt b/tests/testthat/print_mmkin_biphasic_mixed.txt index 3d92b120..11e11bfc 100644 --- a/tests/testthat/print_mmkin_biphasic_mixed.txt +++ b/tests/testthat/print_mmkin_biphasic_mixed.txt @@ -21,6 +21,6 @@ OK: No warnings Mean fitted parameters: parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 - 100.700 -6.299 -0.078 -3.094 -3.954 + 100.702 -5.347 -0.078 -2.681 -4.366 g_qlogis - 0.027 + -0.335 diff --git a/tests/testthat/print_nlme_biphasic.txt b/tests/testthat/print_nlme_biphasic.txt index 98895d3a..f86bda76 100644 --- a/tests/testthat/print_nlme_biphasic.txt +++ b/tests/testthat/print_nlme_biphasic.txt @@ -11,19 +11,19 @@ d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) Data: 509 observations of 2 variable(s) grouped in 15 datasets -Log-likelihood: -1343 +Log-likelihood: -1329 Fixed effects: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 - 100.37 -6.23 -0.08 -3.22 -4.10 + 100.43 -5.34 -0.08 -2.90 -4.34 g_qlogis - -0.10 + -0.19 Random effects: Formula: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) Level: ds Structure: Diagonal parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis Residual -StdDev: 1 2e-04 0.3 0.7 0.8 0.3 3 +StdDev: 1 0.1 0.3 0.6 0.5 0.3 3 diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index fd9635d1..2071e05c 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -156,7 +156,7 @@ DFOP_SFO <- mkinmod( m1 = mkinsub("SFO"), quiet = TRUE) dfop_sfo_pop <- list(parent_0 = 100, - k_m1 = 0.002, f_parent_to_m1 = 0.5, + k_m1 = 0.005, f_parent_to_m1 = 0.5, k1 = 0.05, k2 = 0.01, g = 0.5) syn_biphasic_parms <- as.matrix(data.frame( k1 = rlnorm(n_biphasic, log(dfop_sfo_pop$k1), log_sd), @@ -178,19 +178,27 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { }) # Mixed model fits -mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc") -sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix") +saemix_available <- FALSE +if (requireNamespace("saemix", quietly = TRUE)) { + if(packageVersion("saemix") > "3.1.9000") saemix_available <- TRUE +} +mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_cores) +mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores) +mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE, cores = n_cores) +mmkin_biphasic_mixed <- mixed(mmkin_biphasic) -mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE) -dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin") -dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix") dfop_nlme_1 <- nlme(mmkin_dfop_1) - -mmkin_biphasic <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, quiet = TRUE) -mmkin_biphasic_mixed <- mixed(mmkin_biphasic) nlme_biphasic <- nlme(mmkin_biphasic) -saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) -saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) + +if (saemix_available) { + sfo_saem_1 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "saemix") + + dfop_saemix_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin") + dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix") + + saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) + saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) +} ds_uba <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c("name", "time", "value")])) @@ -200,7 +208,10 @@ sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"), dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"), A1 = mkinsub("SFO"), quiet = TRUE) f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba), - ds_uba, quiet = TRUE) + ds_uba, quiet = TRUE, cores = n_cores) f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ]) -f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix") -f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix") + +if (saemix_available) { + f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix") + f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix") +} diff --git a/tests/testthat/summary_nlme_biphasic_s.txt b/tests/testthat/summary_nlme_biphasic_s.txt index f9171748..65aead62 100644 --- a/tests/testthat/summary_nlme_biphasic_s.txt +++ b/tests/testthat/summary_nlme_biphasic_s.txt @@ -17,15 +17,15 @@ Data: Model predictions using solution type analytical -Fitted in test time 0 s using 2 iterations +Fitted in test time 0 s using 3 iterations Variance model: Constant variance Mean of starting values for individual parameters: parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 - 100.70 -6.30 -0.08 -3.09 -3.95 + 100.70 -5.35 -0.08 -2.68 -4.37 g_qlogis - 0.03 + -0.33 Fixed degradation parameter values: value type @@ -34,40 +34,40 @@ m1_0 0 state Results: AIC BIC logLik - 2711 2766 -1343 + 2683 2738 -1329 Optimised, transformed parameters with symmetric confidence intervals: lower est. upper -parent_0 99.5 100.37 101.23 -log_k_m1 -6.5 -6.23 -5.94 -f_parent_qlogis -0.2 -0.08 0.08 -log_k1 -3.6 -3.22 -2.84 -log_k2 -4.5 -4.10 -3.68 -g_qlogis -0.4 -0.10 0.17 +parent_0 99.6 100.43 101.26 +log_k_m1 -5.5 -5.34 -5.18 +f_parent_qlogis -0.3 -0.08 0.09 +log_k1 -3.2 -2.90 -2.60 +log_k2 -4.6 -4.34 -4.07 +g_qlogis -0.5 -0.19 0.08 Correlation: prnt_0 lg_k_1 f_prn_ log_k1 log_k2 -log_k_m1 -0.185 -f_parent_qlogis -0.161 0.405 -log_k1 0.056 -0.014 -0.016 -log_k2 0.025 0.011 -0.004 0.026 -g_qlogis -0.032 -0.046 -0.012 -0.109 -0.103 +log_k_m1 -0.177 +f_parent_qlogis -0.164 0.385 +log_k1 0.108 -0.017 -0.025 +log_k2 0.036 0.054 0.008 0.096 +g_qlogis -0.068 -0.110 -0.030 -0.269 -0.267 Random effects: Formula: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) Level: ds Structure: Diagonal parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis Residual -StdDev: 1 2e-04 0.3 0.7 0.8 0.3 3 +StdDev: 1 0.1 0.3 0.6 0.5 0.3 3 Backtransformed parameters with asymmetric confidence intervals: lower est. upper parent_0 1e+02 1e+02 1e+02 -k_m1 1e-03 2e-03 3e-03 +k_m1 4e-03 5e-03 6e-03 f_parent_to_m1 4e-01 5e-01 5e-01 -k1 3e-02 4e-02 6e-02 -k2 1e-02 2e-02 3e-02 +k1 4e-02 6e-02 7e-02 +k2 1e-02 1e-02 2e-02 g 4e-01 5e-01 5e-01 Resulting formation fractions: @@ -77,5 +77,5 @@ parent_sink 0.5 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -parent 27 105 31 17 42 -m1 352 1171 NA NA NA +parent 26 131 39 13 53 +m1 144 479 NA NA NA diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R index 2a1ffcc1..c11f6712 100644 --- a/tests/testthat/test_error_models.R +++ b/tests/testthat/test_error_models.R @@ -56,6 +56,7 @@ test_that("The default error model algorithm finds the best known AIC values for f_tc_exp_d_3 <- mmkin(c("SFO", "DFOP", "HS"), lapply(experimental_data_for_UBA_2019, function(x) x$data), error_model = "tc", + cores = n_cores, quiet = TRUE) AIC_exp_d_3 <- lapply(f_tc_exp_d_3, AIC) diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 1e96c338..e9af10e6 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -1,6 +1,8 @@ context("Nonlinear mixed-effects models") -test_that("Parent only models can be fitted using nonlinear mixed effects models", { +test_that("Parent fits using saemix are correctly implemented", { + skip_if(!saemix_available) + expect_error(saem(fits), "Only row objects") # Some fits were done in the setup script mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100)) @@ -26,7 +28,7 @@ test_that("Parent only models can be fitted using nonlinear mixed effects models expect_equal(round(s_sfo_s1$confint_back["k_parent", "est."], 3), round(s_sfo_n$confint_back["k_parent", "est."], 3)) - mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc") + mmkin_fomc_1 <- mmkin("FOMC", ds_fomc, quiet = TRUE, error_model = "tc", cores = n_cores) fomc_saem_1 <- saem(mmkin_fomc_1, quiet = TRUE) ci_fomc_s1 <- summary(fomc_saem_1)$confint_back @@ -66,7 +68,7 @@ test_that("Parent only models can be fitted using nonlinear mixed effects models rel_diff_2 <- (s_dfop_s2$confint_back[, "est."] - dfop_pop) / dfop_pop expect_true(all(rel_diff_2 < 0.12)) - mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const") + mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores) hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE) ci_hs_s1 <- summary(hs_saem_1)$confint_back @@ -88,10 +90,12 @@ test_that("Print methods work", { expect_known_output(print(fits, digits = 2), "print_mmkin_parent.txt") expect_known_output(print(mmkin_biphasic_mixed, digits = 2), "print_mmkin_biphasic_mixed.txt") expect_known_output(print(nlme_biphasic, digits = 1), "print_nlme_biphasic.txt") + + skip_if(!saemix_available) expect_known_output(print(sfo_saem_1, digits = 1), "print_sfo_saem_1.txt") }) -test_that("nlme results are reproducible", { +test_that("nlme results are reproducible to some degree", { test_summary <- summary(nlme_biphasic) test_summary$nlmeversion <- "Dummy 0.0 for testing" @@ -111,6 +115,7 @@ test_that("nlme results are reproducible", { test_that("saem results are reproducible for biphasic fits", { + skip_if(!saemix_available) test_summary <- summary(saem_biphasic_s) test_summary$saemixversion <- "Dummy 0.0 for testing" test_summary$mkinversion <- "Dummy 0.0 for testing" diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index 75d401a3..1c95d069 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -35,8 +35,10 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed) vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin) - plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem) - vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s) + if (saemix_available) { + plot_biphasic_saem_s <- function() plot(f_uba_dfop_sfo_saem) + vdiffr::expect_doppelganger("mixed model fit for saem object with saemix transformations", plot_biphasic_saem_s) + } skip_on_travis() @@ -46,10 +48,12 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { #plot_biphasic_mmkin <- function() plot(mixed(mmkin_biphasic)) # Biphasic fits with lots of data and fits have lots of potential for differences plot_biphasic_nlme <- function() plot(nlme_biphasic) - #plot_biphasic_saem_s <- function() plot(saem_biphasic_s) - plot_biphasic_saem_m <- function() plot(saem_biphasic_m) + if (saemix_available) { + #plot_biphasic_saem_s <- function() plot(saem_biphasic_s) + plot_biphasic_saem_m <- function() plot(saem_biphasic_m) - vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_biphasic_saem_m) + vdiffr::expect_doppelganger("mixed model fit for saem object with mkin transformations", plot_biphasic_saem_m) + } # different results when working with eigenvalues plot_errmod_fit_D_obs_eigen <- function() plot_err(fit_D_obs_eigen, sep_obs = FALSE) |