With saemix 3.0 on CRAN there's no need to check for it in tests

1 files changed, 64 insertions, 0 deletions

diff --git a/tests/testthat/test-dmta.R b/tests/testthat/test-dmta.R
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+++ b/tests/testthat/test-dmta.R
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+local_edition(3)
+
+# Data
+dmta_ds <- lapply(1:7, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL
+
+# mkin
+nlm_dfop <- mmkin("DFOP", dmta_ds)
+nlm_dfop_tc <- mmkin("DFOP", dmta_ds, error_model = "tc")
+parms(nlm_dfop_tc)
+
+# nlme
+nlme_dfop_tc <- nlme(nlm_dfop_tc)
+summary(nlme_dfop_tc)
+intervals(nlme_dfop_tc)
+
+# saemix
+saem_saemix_dfop_tc <- saem(nlm_dfop_tc)
+saem_saemix_dfop_tc$so <- saemix::llgq.saemix(saem_saemix_dfop_tc$so)
+summary(saem_saemix_dfop_tc)
+intervals(saem_saemix_dfop_tc)
+AIC(saem_saemix_dfop_tc$so)
+AIC(saem_saemix_dfop_tc$so, "gq")
+AIC(saem_saemix_dfop_tc$so, "lin")
+saemix::plot(saem_saemix_dfop_tc$so, plot.type = "likelihood")
+saemix::plot(saem_saemix_dfop_tc$so, plot.type = "convergence")
+
+saem_saemix_dfop_tc_1k <- saem(nlm_dfop_tc, nbiter.saemix = c(1000, 100))
+AIC(saem_saemix_dfop_tc_1k$so)
+saemix::plot(saem_saemix_dfop_tc_1k$so, plot.type = "convergence")
+saemix::plot(saem_saemix_dfop_tc_1k$so, plot.type = "likelihood")
+intervals(saem_saemix_dfop_tc_1k)
+
+saem_saemix_dfop_tc_1.5k <- saem(nlm_dfop_tc, nbiter.saemix = c(1500, 100))
+saem_saemix_dfop_tc_1.5k$so <- saemix::llgq.saemix(saem_saemix_dfop_tc_1.5k$so)
+saemix::plot(saem_saemix_dfop_tc_1.5k$so, plot.type = "convergence")
+AIC(saem_saemix_dfop_tc_1.5k$so)
+AIC(saem_saemix_dfop_tc_1.5k$so, "gq")
+intervals(saem_saemix_dfop_tc_1.5k)
+
+# nlmixr saem
+saem_nlmixr_dfop_tc <- nlmixr(nlm_dfop_tc, est = "saem",
+  control = nlmixr::saemControl(nBurn = 300, nEm = 100, nmc = 9, print = 0))
+intervals(saem_nlmixr_dfop_tc)
+summary(saem_nlmixr_dfop_tc)
+AIC(saem_nlmixr_dfop_tc$nm)
+
+saem_nlmixr_dfop_tc_1k <- nlmixr(nlm_dfop_tc, est = "saem",
+  control = nlmixr::saemControl(nBurn = 1000, nEm = 300, nmc = 9, print = 0))
+intervals(saem_nlmixr_dfop_tc_1k)
+summary(saem_nlmixr_dfop_tc_1k)
+AIC(saem_nlmixr_dfop_tc_1k$nm)
+
+focei_nlmixr_dfop_tc <- nlmixr(nlm_dfop_tc, est = "focei")
+intervals(focei_nlmixr_dfop_tc)
+
+AIC(saem_nlmixr_dfop_tc$nm)