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-rw-r--r--R/nlme.mmkin.R3
-rw-r--r--man/saem.Rd1
-rw-r--r--test.log28
-rw-r--r--tests/testthat/dimethenamid_2018.txt24
-rw-r--r--tests/testthat/print_nlmixr_saem_biphasic.txt (renamed from print_nlmixr_saem_biphasic.txt)0
-rw-r--r--tests/testthat/print_nlmixr_saem_biphasic_tc.txt (renamed from print_nlmixr_saem_biphasic_tc.txt)1
-rw-r--r--tests/testthat/setup_script.R8
-rw-r--r--tests/testthat/summary_nlmixr_saem_biphasic.txt58
-rw-r--r--tests/testthat/test_dmta.R5
-rw-r--r--tests/testthat/test_mkinds.R2
10 files changed, 83 insertions, 47 deletions
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index 79139d12..b6b6c830 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -193,7 +193,8 @@ nlme.mmkin <- function(model, data = "auto",
val$mkinmod <- model[[1]]$mkinmod
val$data <- thisCall[["data"]]
val$mmkin <- model
- val$mean_dp_start <- ifelse(is.list(start), start$fixed, start)
+ if (is.list(start)) val$mean_dp_start <- start$fixed
+ else val$mean_dp_start <- start
val$transform_rates <- model[[1]]$transform_rates
val$transform_fractions <- model[[1]]$transform_fractions
val$solution_type <- model[[1]]$solution_type
diff --git a/man/saem.Rd b/man/saem.Rd
index 00e9aeda..0c066dd2 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -34,6 +34,7 @@ saemix_model(
transformations = c("mkin", "saemix"),
degparms_start = numeric(),
test_log_parms = FALSE,
+ conf.level = 0.6,
verbose = FALSE,
...
)
diff --git a/test.log b/test.log
index 5c8f1802..b044e6a0 100644
--- a/test.log
+++ b/test.log
@@ -3,45 +3,51 @@ Loading required package: parallel
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.4s]
+✔ | 5 | Analytical solutions for coupled models [4.3s]
✔ | 5 | Calculation of Akaike weights
✔ | 2 | Export dataset for reading into CAKE
-✔ | 12 | Confidence intervals and p-values [1.0s]
+✔ | 12 | Confidence intervals and p-values [1.1s]
⠋ | 1 | Dimethenamid data from 2018
-✔ | 24 | Dimethenamid data from 2018 [37.1s]
-✔ | 14 | Error model fitting [6.8s]
+✔ | 1 25 | Dimethenamid data from 2018 [49.7s]
+────────────────────────────────────────────────────────────────────────────────
+Skip (test_dmta.R:147:3): 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 [7.0s]
✔ | 5 | Time step normalisation
✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s]
✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.5s]
✔ | 1 | Fitting the logistic model [0.3s]
-✔ | 1 12 | Nonlinear mixed-effects models [0.2s]
+⠴ | 6 | Nonlinear mixed-effects models
+✔ | 1 15 | Nonlinear mixed-effects models [2.4s]
────────────────────────────────────────────────────────────────────────────────
Skip (test_mixed.R:67:3): saemix results are reproducible for biphasic fits
Reason: Fitting with saemix takes around 10 minutes when using deSolve
────────────────────────────────────────────────────────────────────────────────
-✔ | 2 | Test dataset classes mkinds and mkindsg
+✔ | 3 | Test dataset classes mkinds and mkindsg
✔ | 10 | Special cases of mkinfit calls [0.6s]
✔ | 1 | mkinfit features [0.5s]
✔ | 8 | mkinmod model generation and printing [0.2s]
✔ | 3 | Model predictions with mkinpredict [0.4s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [9.0s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s]
✔ | 16 | Plotting [1.5s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 23 | saemix_parent [29.0s]
+✔ | 23 | saemix_parent [30.4s]
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s]
✔ | 7 | Fitting the SFORB model [4.5s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 4 | Summary [0.1s]
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.6s]
✔ | 9 | Hypothesis tests [9.4s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 115.2 s
+Duration: 133.2 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 1 | PASS 230 ]
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 235 ]
diff --git a/tests/testthat/dimethenamid_2018.txt b/tests/testthat/dimethenamid_2018.txt
new file mode 100644
index 00000000..513acff9
--- /dev/null
+++ b/tests/testthat/dimethenamid_2018.txt
@@ -0,0 +1,24 @@
+<mkindsg> holding 7 mkinds objects
+Title $title: Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018
+Occurrence of observed compounds $observed_n:
+DMTAP M23 M27 M31 DMTA
+ 3 7 7 7 4
+Time normalisation factors $f_time_norm:
+[1] 1.0000000 0.9706477 1.2284784 1.2284784 0.6233856 0.7678922 0.6733938
+Meta information $meta:
+ study usda_soil_type study_moisture_ref_type rel_moisture
+Calke Unsworth 2014 Sandy loam pF2 1.00
+Borstel Staudenmaier 2009 Sand pF1 0.50
+Elliot 1 Wendt 1997 Clay loam pF2.5 0.75
+Elliot 2 Wendt 1997 Clay loam pF2.5 0.75
+Flaach König 1996 Sandy clay loam pF1 0.40
+BBA 2.2 König 1995 Loamy sand pF1 0.40
+BBA 2.3 König 1995 Sandy loam pF1 0.40
+ study_ref_moisture temperature
+Calke NA 20
+Borstel 23.00 20
+Elliot 1 33.37 23
+Elliot 2 33.37 23
+Flaach NA 20
+BBA 2.2 NA 20
+BBA 2.3 NA 20
diff --git a/print_nlmixr_saem_biphasic.txt b/tests/testthat/print_nlmixr_saem_biphasic.txt
index 5cf80f0f..5cf80f0f 100644
--- a/print_nlmixr_saem_biphasic.txt
+++ b/tests/testthat/print_nlmixr_saem_biphasic.txt
diff --git a/print_nlmixr_saem_biphasic_tc.txt b/tests/testthat/print_nlmixr_saem_biphasic_tc.txt
index ad59005d..2f940bfe 100644
--- a/print_nlmixr_saem_biphasic_tc.txt
+++ b/tests/testthat/print_nlmixr_saem_biphasic_tc.txt
@@ -11,6 +11,7 @@ Data:
507 observations of 2 variable(s) grouped in 15 datasets
Likelihood:
+
AIC BIC logLik
2400 2468 -1184
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index bfa70005..4b99ad67 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -204,10 +204,10 @@ saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE)
saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE)
# nlmixr saem
-tmp <- capture_output(nlmixr_saem_biphasic <- nlmixr(mmkin_biphasic, est = "saem",
- control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0)))
-tmp <- capture_output(nlmixr_saem_biphasic_tc <- nlmixr(mmkin_biphasic_tc, est = "saem",
- control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0)))
+tmp <- suppressMessages(capture.output(nlmixr_saem_biphasic <- nlmixr(mmkin_biphasic, est = "saem",
+ control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0))))
+tmp <- suppressMessages(capture.output(nlmixr_saem_biphasic_tc <- nlmixr(mmkin_biphasic_tc, est = "saem",
+ control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0))))
# The FOCEI fit takes too long...
#tmp <- capture_output(nlmixr_focei_biphasic <- nlmixr(mmkin_biphasic, est = "focei",
# control = nlmixr::foceiControl(print = 0)))
diff --git a/tests/testthat/summary_nlmixr_saem_biphasic.txt b/tests/testthat/summary_nlmixr_saem_biphasic.txt
index c5c1fe78..f1cdc47b 100644
--- a/tests/testthat/summary_nlmixr_saem_biphasic.txt
+++ b/tests/testthat/summary_nlmixr_saem_biphasic.txt
@@ -13,7 +13,7 @@ d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
exp(-k2 * time))) * parent - k_m1 * m1
Data:
-508 observations of 2 variable(s) grouped in 15 datasets
+507 observations of 2 variable(s) grouped in 15 datasets
Degradation model predictions using RxODE
@@ -23,9 +23,9 @@ Variance model: Constant variance
Mean of starting values for individual parameters:
parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2
- 100.74 -5.43 -0.05 -2.85 -4.57
+ 100.67 -5.38 -0.09 -2.74 -4.51
g_qlogis
- -0.15
+ -0.18
Mean of starting values for error model parameters:
sigma_parent sigma_m1
@@ -38,39 +38,39 @@ Results:
Likelihood calculated by gauss3_1.6
AIC BIC logLik
- 2465 2525 -1219
+ 2510 2569 -1241
Optimised parameters:
est. lower upper
-parent_0 100.54 99.7 101.40
-log_k_m1 -5.44 -5.6 -5.24
-f_parent_qlogis -0.06 -0.2 0.05
-log_k1 -2.81 -3.0 -2.65
-log_k2 -4.62 -4.8 -4.41
-g_qlogis -0.14 -0.4 0.17
+parent_0 100.49 99.6 101.37
+log_k_m1 -5.36 -5.5 -5.20
+f_parent_qlogis -0.09 -0.3 0.08
+log_k1 -2.78 -3.0 -2.59
+log_k2 -4.51 -4.7 -4.35
+g_qlogis -0.12 -0.5 0.21
Correlation:
- prnt_0 lg_k_1 f_prn_ log_k1 log_k2
-log_k_m1 -0.224
-f_parent_qlogis -0.401 0.335
-log_k1 0.119 0.083 0.019
-log_k2 -0.019 0.237 0.142 0.395
-g_qlogis 0.083 -0.282 -0.218 -0.532 -0.544
+ pr_0 l__1 f_p_ lg_1 lg_2
+log_k_m1 -0.3
+f_parent_qlogis -0.2 0.3
+log_k1 0.1 0.1 0.0
+log_k2 0.0 0.3 0.1 0.4
+g_qlogis 0.0 -0.3 -0.1 -0.5 -0.7
Random effects (omega):
eta.parent_0 eta.log_k_m1 eta.f_parent_qlogis eta.log_k1
-eta.parent_0 0.05 0.0 0.00 0.00
-eta.log_k_m1 0.00 0.1 0.00 0.00
-eta.f_parent_qlogis 0.00 0.0 0.03 0.00
-eta.log_k1 0.00 0.0 0.00 0.05
-eta.log_k2 0.00 0.0 0.00 0.00
-eta.g_qlogis 0.00 0.0 0.00 0.00
+eta.parent_0 0.2 0.00 0.00 0.00
+eta.log_k_m1 0.0 0.05 0.00 0.00
+eta.f_parent_qlogis 0.0 0.00 0.09 0.00
+eta.log_k1 0.0 0.00 0.00 0.09
+eta.log_k2 0.0 0.00 0.00 0.00
+eta.g_qlogis 0.0 0.00 0.00 0.00
eta.log_k2 eta.g_qlogis
eta.parent_0 0.00 0.0
eta.log_k_m1 0.00 0.0
eta.f_parent_qlogis 0.00 0.0
eta.log_k1 0.00 0.0
-eta.log_k2 0.08 0.0
+eta.log_k2 0.03 0.0
eta.g_qlogis 0.00 0.1
Variance model:
@@ -80,11 +80,11 @@ sigma_parent sigma_m1
Backtransformed parameters:
est. lower upper
parent_0 1e+02 1e+02 1e+02
-k_m1 4e-03 4e-03 5e-03
-f_parent_to_m1 5e-01 5e-01 5e-01
+k_m1 5e-03 4e-03 6e-03
+f_parent_to_m1 5e-01 4e-01 5e-01
k1 6e-02 5e-02 7e-02
-k2 1e-02 8e-03 1e-02
-g 5e-01 4e-01 5e-01
+k2 1e-02 9e-03 1e-02
+g 5e-01 4e-01 6e-01
Resulting formation fractions:
ff
@@ -93,5 +93,5 @@ parent_sink 0.5
Estimated disappearance times:
DT50 DT90 DT50back DT50_k1 DT50_k2
-parent 27 170 51 12 70
-m1 160 532 NA NA NA
+parent 25 152 46 11 63
+m1 147 488 NA NA NA
diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R
index 22fa9d95..7b130999 100644
--- a/tests/testthat/test_dmta.R
+++ b/tests/testthat/test_dmta.R
@@ -139,8 +139,9 @@ dmta_sfo_sfo3p_tc <- mmkin(list("SFO-SFO3+" = sfo_sfo3p),
test_that("Different backends get consistent results for SFO-SFO3+, dimethenamid data", {
- nlme_sfo_sfo3p_tc <- nlme(dmta_sfo_sfo3p_tc,
- start = mean_degparms(dmta_sfo_sfo3p_tc, test_log_parms = TRUE))
+ expect_warning(nlme_sfo_sfo3p_tc <- nlme(dmta_sfo_sfo3p_tc,
+ start = mean_degparms(dmta_sfo_sfo3p_tc, test_log_parms = TRUE)),
+ "Iteration 5, LME step.*not converge")
ints_nlme_mets <- intervals(nlme_sfo_sfo3p_tc, which = "fixed")
skip("Fitting this ODE model with saemix takes about 15 minutes on my system")
diff --git a/tests/testthat/test_mkinds.R b/tests/testthat/test_mkinds.R
index 5ce3619b..c10a3f5b 100644
--- a/tests/testthat/test_mkinds.R
+++ b/tests/testthat/test_mkinds.R
@@ -8,4 +8,6 @@ test_that("An mkinds object can be created and printed", {
test_that("An mkindsg object can be created and printed", {
testdata_group <- mkindsg$new("Experimental X", experimental_data_for_UBA_2019[6:10])
expect_known_output(print(testdata_group), "experimental_data_for_UBA_2019_mkindsg.txt")
+
+ expect_known_output(print(dimethenamid_2018), "dimethenamid_2018.txt")
})

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