diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | build.log | 2 | ||||
| -rw-r--r-- | man/mmkin.Rd | 5 | ||||
| -rw-r--r-- | test.log | 28 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 | ||||
| -rw-r--r-- | tests/testthat/test_nlme.R | 63 |
6 files changed, 89 insertions, 15 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 1aa5cac2..a9d0e939 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 0.9.49.9 -Date: 2020-03-31 +Version: 0.9.49.10 +Date: 2020-04-07 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), @@ -6,5 +6,5 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.49.9.tar.gz’ +* building ‘mkin_0.9.49.10.tar.gz’ diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 4bf07370..99895400 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -32,8 +32,9 @@ for parallel execution.} \item{\dots}{Further arguments that will be passed to \code{\link{mkinfit}}.} } \value{ -A matrix of \code{\link{mkinfit}} objects that can be indexed using - the model and dataset names as row and column indices. +A two-dimensional \code{\link{array}} of \code{\link{mkinfit}} + objects that can be indexed using the model names for the first index (row index) + and the dataset names for the second index (column index). } \description{ This function calls \code{\link{mkinfit}} on all combinations of models and @@ -6,15 +6,25 @@ Testing mkin ✔ | 4 | Calculation of FOCUS chi2 error levels [2.2 s] ✔ | 4 | Fitting the SFORB model [1.7 s] ✔ | 5 | Calculation of Akaike weights -✔ | 10 | Confidence intervals and p-values [9.6 s] -✔ | 14 | Error model fitting [38.4 s] -✔ | 6 | Test fitting the decline of metabolites from their maximum [0.7 s] +✔ | 10 | Confidence intervals and p-values [9.4 s] +✔ | 14 | Error model fitting [37.5 s] +✔ | 6 | Test fitting the decline of metabolites from their maximum [0.8 s] ✔ | 1 | Fitting the logistic model [0.9 s] ✔ | 1 | Test dataset class mkinds used in gmkin -✔ | 12 | Special cases of mkinfit calls [2.2 s] +✔ | 12 | Special cases of mkinfit calls [2.3 s] ✔ | 9 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.3 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.2 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s] +✖ | 0 1 | Nonlinear mixed-effects models [1.3 s] +──────────────────────────────────────────────────────────────────────────────── +test_nlme.R:37: error: nlme_function works correctly +konnte Funktion "nlme_f" nicht finden +Backtrace: + 1. nlme::nlme(...) tests/testthat/test_nlme.R:37:2 + 2. nlme::nlme.formula(...) + 3. [ base::eval(...) ] with 1 more call + 5. [ base::eval(...) ] with 1 more call +──────────────────────────────────────────────────────────────────────────────── ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s] ✔ | 3 | Summary ✔ | 11 | Plotting [0.6 s] @@ -22,17 +32,17 @@ Testing mkin ✔ | 2 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s] -✔ | 7 1 | Hypothesis tests [32.5 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.0 s] +✔ | 7 1 | Hypothesis tests [31.9 s] ──────────────────────────────────────────────────────────────────────────────── test_tests.R:60: skip: We can do a likelihood ratio test using an update specification Reason: This errors out if called by testthat while it works in a normal R session ──────────────────────────────────────────────────────────────────────────────── ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 112.1 s +Duration: 111.4 s OK: 138 -Failed: 0 +Failed: 1 Warnings: 0 Skipped: 1 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index fe5e481a..f492a57f 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2020-04-01 +Date: 2020-04-07 Optimiser: IRLS [Data] diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R new file mode 100644 index 00000000..b3c41f00 --- /dev/null +++ b/tests/testthat/test_nlme.R @@ -0,0 +1,63 @@ +context("Nonlinear mixed-effects models") + +test_that("nlme_function works correctly", { + + sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) + m_SFO <- mkinmod(parent = mkinsub("SFO")) + d_SFO_1 <- mkinpredict(m_SFO, + c(k_parent_sink = 0.1), + c(parent = 98), sampling_times) + d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time") + d_SFO_2 <- mkinpredict(m_SFO, + c(k_parent_sink = 0.05), + c(parent = 102), sampling_times) + d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time") + d_SFO_3 <- mkinpredict(m_SFO, + c(k_parent_sink = 0.02), + c(parent = 103), sampling_times) + d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time") + + d1 <- add_err(d_SFO_1, function(value) 3, n = 1, seed = 123456) + d2 <- add_err(d_SFO_2, function(value) 2, n = 1, seed = 234567) + d3 <- add_err(d_SFO_3, function(value) 4, n = 1, seed = 345678) + ds <- c(d1 = d1, d2 = d2, d3 = d3) + + f <- mmkin("SFO", ds, cores = 1, quiet = TRUE) + + mean_dp <- mean_degparms(f) + grouped_data <- nlme_data(f) + nlme_f <- nlme_function(f) + + m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink), + data = grouped_data, + fixed = parent_0 + log_k_parent_sink ~ 1, + random = pdDiag(parent_0 + log_k_parent_sink ~ 1), + start = mean_dp) + + m_nlme_mkin <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink), + data = grouped_data, + fixed = parent_0 + log_k_parent_sink ~ 1, + random = pdDiag(parent_0 + log_k_parent_sink ~ 1), + start = mean_dp) + + expect_equal(m_nlme_raw$coefficients, m_nlme_mkin$coefficients) + + m_nlme_raw_up_1 <- update(m_nlme_raw, random = log_k_parent_sink ~ 1) + # The following two calls give an error although they should + # do the same as the call above + # The error occurs in the evaluation of the modelExpression in the + # call to .C(fit_nlme, ...) + # m_nlme_mkin_up_1 <- update(m_nlme_mkin, random = log_k_parent_sink ~ 1) + # m_nlme_mkin <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink), + # data = grouped_data, + # fixed = parent_0 + log_k_parent_sink ~ 1, + # random = log_k_parent_sink ~ 1, + # start = mean_dp) + + m_nlme_raw_up_2 <- update(m_nlme_raw, random = parent_0 ~ 1) + m_nlme_mkin_up_2 <- update(m_nlme_mkin, random = parent_0 ~ 1) + expect_equal(m_nlme_raw_up_2$coefficients, m_nlme_mkin_up_2$coefficients) + + # update(m_nlme_mkin) # works + +}) |