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-rw-r--r--NEWS.md2
-rw-r--r--R/saem.R27
-rw-r--r--log/test.log22
-rw-r--r--tests/testthat/test_saemix_parent.R15
4 files changed, 39 insertions, 27 deletions
diff --git a/NEWS.md b/NEWS.md
index 55462fd3..64700704 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
# mkin 1.1.2
+- 'R/saem.R': Implement and test saemix transformations for HS.
+
- 'R/convergence.R': New generic to show convergence information with a method for 'mmin' objects.
- 'R/illparms.R': New generic to show ill-defined parameters with methods for 'mkinfit' and 'mmkin' objects.
diff --git a/R/saem.R b/R/saem.R
index 36997ad7..d2240ea5 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -252,7 +252,7 @@ saemix_model <- function(object, solution_type = "auto", transformations = c("mk
}
degparms_fixed <- object[[1]]$bparms.fixed
- # Transformations are done in the degradation function
+ # Transformations are done in the degradation function by default
transform.par = rep(0, length(degparms_optim))
odeini_optim_parm_names <- grep('_0$', names(degparms_optim), value = TRUE)
@@ -339,13 +339,24 @@ saemix_model <- function(object, solution_type = "auto", transformations = c("mk
}
}
if (parent_type == "HS") {
- model_function <- function(psi, id, xidep) {
- tb <- exp(psi[id, 4])
- t <- xidep[, "time"]
- k1 = exp(psi[id, 2])
- psi[id, 1] * ifelse(t <= tb,
- exp(- k1 * t),
- exp(- k1 * tb) * exp(- exp(psi[id, 3]) * (t - tb)))
+ if (transformations == "mkin") {
+ model_function <- function(psi, id, xidep) {
+ tb <- exp(psi[id, 4])
+ t <- xidep[, "time"]
+ k1 <- exp(psi[id, 2])
+ psi[id, 1] * ifelse(t <= tb,
+ exp(- k1 * t),
+ exp(- k1 * tb) * exp(- exp(psi[id, 3]) * (t - tb)))
+ }
+ } else {
+ model_function <- function(psi, id, xidep) {
+ tb <- exp(psi[id, 4])
+ t <- xidep[, "time"]
+ psi[id, 1] * ifelse(t <= tb,
+ exp(- psi[id, 2] * t),
+ exp(- psi[id, 2] * tb) * exp(- psi[id, 3] * (t - tb)))
+ }
+ transform.par = c(0, 1, 1, 1)
}
}
}
diff --git a/log/test.log b/log/test.log
index 266a566f..776b6f49 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,13 +1,11 @@
-ℹ Loading mkin
-Loading required package: parallel
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [3.2s]
+✔ | 5 | Analytical solutions for coupled models [3.3s]
✔ | 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 [31.6s]
+✔ | 1 12 | Dimethenamid data from 2018 [32.0s]
────────────────────────────────────────────────────────────────────────────────
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
@@ -16,7 +14,7 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
✔ | 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]
+✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s]
✔ | 1 | Fitting the logistic model [0.2s]
✔ | 1 12 | Nonlinear mixed-effects models [0.2s]
────────────────────────────────────────────────────────────────────────────────
@@ -28,13 +26,13 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 3 | mkinfit features [0.7s]
✔ | 8 | mkinmod model generation and printing [0.2s]
✔ | 3 | Model predictions with mkinpredict [0.4s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s]
-✔ | 16 | Plotting [10.6s]
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.8s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [9.1s]
+✔ | 16 | Plotting [10.7s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 25 | saemix parent models [172.9s]
+✔ | 27 | saemix parent models [178.6s]
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
-✔ | 7 | Fitting the SFORB model [3.7s]
+✔ | 7 | Fitting the SFORB model [3.6s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary [0.2s]
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
@@ -42,10 +40,10 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 255.9 s
+Duration: 263.0 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 2 | PASS 225 ]
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 227 ]
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index 731228d9..7f550999 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -10,6 +10,7 @@ test_that("Parent fits using saemix are correctly implemented", {
sfo_saem_2 <- saem(mmkin_sfo_1, quiet = TRUE, transformations = "mkin")
sfo_saem_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters")
+ expect_equal(endpoints(sfo_saem_1), endpoints(sfo_saem_2), tol = 0.01)
s_sfo_s1 <- summary(sfo_saem_1)
s_sfo_s2 <- summary(sfo_saem_2)
@@ -76,20 +77,20 @@ test_that("Parent fits using saemix are correctly implemented", {
mmkin_hs_1 <- mmkin("HS", ds_hs, quiet = TRUE, error_model = "const", cores = n_cores)
hs_saem_1 <- saem(mmkin_hs_1, quiet = TRUE)
+ hs_saem_2 <- saem(mmkin_hs_1, quiet = TRUE, transformations = "mkin")
+ expect_equal(endpoints(hs_saem_1), endpoints(hs_saem_2), tol = 0.01)
ci_hs_s1 <- summary(hs_saem_1)$confint_back
hs_pop <- as.numeric(hs_pop)
- # expect_true(all(ci_hs_s1[, "lower"] < hs_pop)) # k1 is overestimated
+ #expect_true(all(ci_hs_s1[, "lower"] < hs_pop)) # k1 is overestimated
expect_true(all(ci_hs_s1[, "upper"] > hs_pop))
mmkin_hs_2 <- update(mmkin_hs_1, state.ini = 100, fixed_initials = "parent")
- hs_saem_2 <- saem(mmkin_hs_2, quiet = TRUE)
- ci_hs_s2 <- summary(hs_saem_2)$confint_back
+ hs_saem_3 <- saem(mmkin_hs_2, quiet = TRUE)
+ ci_hs_s3 <- summary(hs_saem_3)$confint_back
- #expect_true(all(ci_hs_s2[, "lower"] < hs_pop[2:4])) # k1 again overestimated
- expect_true(all(ci_hs_s2[, "upper"] > hs_pop[2:4]))
-
- # HS would likely benefit from implemenation of transformations = "saemix"
+ #expect_true(all(ci_hs_s3[, "lower"] < hs_pop[2:4])) # k1 again overestimated
+ expect_true(all(ci_hs_s3[, "upper"] > hs_pop[2:4]))
})
test_that("We can also use mkin solution methods for saem", {

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