From 37bffdcfab0ca4e0de638b1a63e808b1d29d3f15 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 28 Feb 2022 14:38:23 +0100 Subject: Add nlmixr tests, reorganize, test intervals() --- tests/testthat/test-dmta.R | 64 ---------------------------------------------- 1 file changed, 64 deletions(-) delete mode 100644 tests/testthat/test-dmta.R (limited to 'tests/testthat/test-dmta.R') 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) -- cgit v1.2.1