Add nlmixr tests, reorganize, test intervals()

1 files changed, 0 insertions, 64 deletions

diff --git a/tests/testthat/test-dmta.R b/tests/testthat/test-dmta.R
deleted file mode 100644
index 12bbcb8e..00000000
--- a/tests/testthat/test-dmta.R
+++ /dev/null
@@ -1,64 +0,0 @@
-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)