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-rw-r--r--R/summary.nlme.mmkin.R2
-rw-r--r--R/summary.nlmixr.mmkin.R2
-rw-r--r--R/summary.saem.mmkin.R2
-rw-r--r--test.log20
-rw-r--r--tests/testthat/summary_nlme_biphasic_s.txt12
-rw-r--r--tests/testthat/summary_saem_biphasic_s.txt12
-rw-r--r--tests/testthat/test_dmta.R49
7 files changed, 73 insertions, 26 deletions
diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R
index b42d5d7b..be7f0441 100644
--- a/R/summary.nlme.mmkin.R
+++ b/R/summary.nlme.mmkin.R
@@ -200,7 +200,7 @@ print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
if (nrow(x$confint_trans) > 1) {
corr <- x$corFixed
class(corr) <- "correlation"
- print(corr, title = "\nCorrelation:", ...)
+ print(corr, title = "\nCorrelation:", rdig = digits, ...)
}
cat("\n") # Random effects
diff --git a/R/summary.nlmixr.mmkin.R b/R/summary.nlmixr.mmkin.R
index a023f319..94d4ed93 100644
--- a/R/summary.nlmixr.mmkin.R
+++ b/R/summary.nlmixr.mmkin.R
@@ -211,7 +211,7 @@ print.summary.nlmixr.mmkin <- function(x, digits = max(3, getOption("digits") -
if (nrow(x$confint_trans) > 1) {
corr <- x$corFixed
class(corr) <- "correlation"
- print(corr, title = "\nCorrelation:", ...)
+ print(corr, title = "\nCorrelation:", rdig = digits, ...)
}
cat("\nRandom effects (omega):\n")
diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index 204cb46f..fa52a579 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -229,7 +229,7 @@ print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3)
if (nrow(x$confint_trans) > 1) {
corr <- x$corFixed
class(corr) <- "correlation"
- print(corr, title = "\nCorrelation:", ...)
+ print(corr, title = "\nCorrelation:", rdig = digits, ...)
}
cat("\nRandom effects:\n")
diff --git a/test.log b/test.log
index 5a9e0034..5c8f1802 100644
--- a/test.log
+++ b/test.log
@@ -3,12 +3,12 @@ Loading required package: parallel
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.5s]
+✔ | 5 | Analytical solutions for coupled models [3.4s]
✔ | 5 | Calculation of Akaike weights
✔ | 2 | Export dataset for reading into CAKE
✔ | 12 | Confidence intervals and p-values [1.0s]
-⠋ | 1 | Dimethenamid data from 2018, parent fits
-✔ | 24 | Dimethenamid data from 2018, parent fits [36.7s]
+⠋ | 1 | Dimethenamid data from 2018
+✔ | 24 | Dimethenamid data from 2018 [37.1s]
✔ | 14 | Error model fitting [6.8s]
✔ | 5 | Time step normalisation
✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s]
@@ -24,22 +24,22 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 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 [0.3s]
+✔ | 3 | Model predictions with mkinpredict [0.4s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [9.4s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [9.0s]
✔ | 16 | Plotting [1.5s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 23 | saemix_parent [29.2s]
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.7s]
-✔ | 7 | Fitting the SFORB model [4.4s]
+✔ | 23 | saemix_parent [29.0s]
+✔ | 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]
-✔ | 9 | Hypothesis tests [9.5s]
+✔ | 9 | Hypothesis tests [9.4s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 115.5 s
+Duration: 115.2 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting with saemix takes around 10 minutes when using deSolve (1)
diff --git a/tests/testthat/summary_nlme_biphasic_s.txt b/tests/testthat/summary_nlme_biphasic_s.txt
index 86049775..03ef49a6 100644
--- a/tests/testthat/summary_nlme_biphasic_s.txt
+++ b/tests/testthat/summary_nlme_biphasic_s.txt
@@ -46,12 +46,12 @@ log_k2 -4.7 -4.5 -4.35
g_qlogis -0.4 -0.1 0.17
Correlation:
- prnt_0 lg_k_1 f_prn_ log_k1 log_k2
-log_k_m1 -0.167
-f_parent_qlogis -0.145 0.380
-log_k1 0.170 0.005 -0.026
-log_k2 0.083 0.168 0.032 0.365
-g_qlogis -0.088 -0.170 -0.044 -0.472 -0.631
+ pr_0 l__1 f_p_ lg_1 lg_2
+log_k_m1 -0.2
+f_parent_qlogis -0.1 0.4
+log_k1 0.2 0.0 0.0
+log_k2 0.1 0.2 0.0 0.4
+g_qlogis -0.1 -0.2 0.0 -0.5 -0.6
Random effects:
Formula: list(parent_0 ~ 1, log_k_m1 ~ 1, f_parent_qlogis ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt
index 4569099f..b30e35b8 100644
--- a/tests/testthat/summary_saem_biphasic_s.txt
+++ b/tests/testthat/summary_saem_biphasic_s.txt
@@ -47,12 +47,12 @@ k2 1.2e-02 9.6e-03 1.4e-02
g 4.6e-01 4.1e-01 5.1e-01
Correlation:
- prnt_0 k_m1 f_p__1 k1 k2
-k_m1 -0.172
-f_parent_to_m1 -0.144 0.383
-k1 0.132 -0.007 -0.024
-k2 0.044 0.138 0.030 0.197
-g -0.067 -0.212 -0.061 -0.404 -0.531
+ prn_0 k_m1 f___1 k1 k2
+k_m1 -0.17
+f_parent_to_m1 -0.14 0.38
+k1 0.13 -0.01 -0.02
+k2 0.04 0.14 0.03 0.20
+g -0.07 -0.21 -0.06 -0.40 -0.53
Random effects:
est. lower upper
diff --git a/tests/testthat/test_dmta.R b/tests/testthat/test_dmta.R
index 3437966f..46a4fdcc 100644
--- a/tests/testthat/test_dmta.R
+++ b/tests/testthat/test_dmta.R
@@ -1,4 +1,4 @@
-context("Dimethenamid data from 2018, parent fits")
+context("Dimethenamid data from 2018")
# Data
dmta_ds <- lapply(1:7, function(i) {
@@ -91,6 +91,7 @@ test_that("Different backends get consistent results for DFOP tc, dimethenamid d
backtransform_odeparms(ints_nlme$reStruct$ds[, "upper"], dmta_dfop$mkinmod)))
# Variance function
+ skip_on_travis() # For some reason this fails on Travis
# saemix vs. nlme
expect_true(all(ints_saemix[[3]][, "est."] >
ints_nlme$varStruct[, "lower"]))
@@ -118,3 +119,49 @@ test_that("Different backends get consistent results for DFOP tc, dimethenamid d
expect_true(ints_nlmixr_focei[[3]]["rsd_high", "est."] <
ints_nlme$varStruct["prop", "upper"])
})
+
+# Model definition from the 2020 paper https://doi.org/10.3390/environments8080071
+# But note the data are different, as we did not pool the data from the same soils
+# for the paper
+# The model is called DFOP-SFO3+ in the paper
+dfop_sfo3p <- mkinmod(
+ DMTA = mkinsub("DFOP", c("M23", "M27", "M31")),
+ M23 = mkinsub("SFO"),
+ M27 = mkinsub("SFO"),
+ M31 = mkinsub("SFO", "M27", sink = FALSE),
+ quiet = TRUE
+)
+dfop_sfo3 <- mkinmod(
+ DMTA = mkinsub("DFOP", c("M23", "M27", "M31")),
+ M23 = mkinsub("SFO"),
+ M27 = mkinsub("SFO"),
+ M31 = mkinsub("SFO"),
+ quiet = TRUE
+)
+
+# The following is work in progress
+#dmta_dfop_sfo3p_tc <- mmkin(list("DFOP-SFO3+" = dfop_sfo3p),
+# dmta_ds, error_model = "tc", quiet = TRUE)
+# The Borstel dataset give false convergence
+#dmta_dfop_sfo3_tc <- mmkin(list("DFOP-SFO3" = dfop_sfo3),
+# dmta_ds, error_model = "tc", quiet = TRUE)
+# We get convergence in all soils
+
+#test_that("Different backends get consistent results for DFOP-SFO3+, dimethenamid data", {
+
+ # nlme needs some help to converge
+# nlme_dfop_sfo3p_tc <- nlme(dmta_dfop_sfo3p_tc,
+# control = list(pnlsMaxIter = 30, tolerance = 3e-3))
+# ints_nlme_dfop_sfo3p_tc <- intervals(nlme_dfop_sfo3p_tc, which = "fixed")
+
+ # saemix does not succeed with these data, we get problems
+ # with the deSolve solutions, depending on the seed:
+ # Error in lsoda(y, times, func, parms, ...) :
+ # illegal input detected before taking any integration steps - see
+ # written message
+ # or:
+ # Error in out[available, var] : (subscript) logical subscript too long
+ #saem_saemix_dfop_sfo3p_tc <- saem(dmta_dfop_sfo3p_tc)
+
+#})
+

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