Add three functions to facilitate the use of nlme

2 files changed, 0 insertions, 176 deletions

diff --git a/vignettes/web_only/FOCUS_Z.R b/vignettes/web_only/FOCUS_Z.R
deleted file mode 100644
index 0c19794e..00000000
--- a/vignettes/web_only/FOCUS_Z.R
+++ /dev/null
@@ -1,115 +0,0 @@
-## ---- include = FALSE---------------------------------------------------------
-require(knitr)
-options(digits = 5)
-opts_chunk$set(engine='R', tidy = FALSE)
-
-## ---- echo = TRUE, fig = TRUE, fig.width = 8, fig.height = 7------------------
-library(mkin, quietly = TRUE)
-LOD = 0.5
-FOCUS_2006_Z = data.frame(
-  t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
-        42, 61, 96, 124),
-  Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8,
-         2.9, 3.5, 5.3, 4.4, 1.2, 0.7),
-  Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1,
-         1.6, 0.6, 0.5 * LOD, NA, NA, NA),
-  Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5,
-         0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA),
-  Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5,
-         25.2, 17.2, 4.8, 4.5, 2.8, 4.4))
-
-FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
-
-## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6-----------------------------
-Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
-                Z1 = mkinsub("SFO"))
-m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.2a)
-summary(m.Z.2a, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6-----------------------------
-Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
-                   Z1 = mkinsub("SFO"),
-                   use_of_ff = "max")
-
-m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.2a.ff)
-summary(m.Z.2a.ff, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6-----------------------------
-Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-               Z1 = mkinsub("SFO"), use_of_ff = "max")
-m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.3)
-summary(m.Z.3, data = FALSE)$bpar
-
-## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7-----------------------------
-Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-               Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-               Z2 = mkinsub("SFO"), use_of_ff = "max")
-m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.5)
-
-## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8-----------------------------
-Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-                   Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                   Z2 = mkinsub("SFO", "Z3"),
-                   Z3 = mkinsub("SFO"),
-                   use_of_ff = "max")
-m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
-                     parms.ini = m.Z.5$bparms.ode,
-                     quiet = TRUE)
-plot_sep(m.Z.FOCUS)
-summary(m.Z.FOCUS, data = FALSE)$bpar
-endpoints(m.Z.FOCUS)
-
-## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8-----------------------------
-Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFORB"))
-m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.mkin.1)
-summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
-
-## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8-----------------------------
-Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO"))
-m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-plot_sep(m.Z.mkin.3)
-
-## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8----------------------------
-Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFO"))
-m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
-                      parms.ini = m.Z.mkin.3$bparms.ode,
-                      quiet = TRUE)
-plot_sep(m.Z.mkin.4)
-
-## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8----------------------------
-Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFORB"))
-m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
-                      parms.ini = m.Z.mkin.4$bparms.ode[1:4],
-                      quiet = TRUE)
-plot_sep(m.Z.mkin.5)
-
-## ----FOCUS_2006_Z_fits_11a, echo=TRUE-----------------------------------------
-m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
-                       parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
-                                     k_Z3_bound_free = 0),
-                       fixed_parms = "k_Z3_bound_free",
-                       quiet = TRUE)
-plot_sep(m.Z.mkin.5a)
-
-## ----FOCUS_2006_Z_fits_11b, echo=TRUE-----------------------------------------
-mkinparplot(m.Z.mkin.5a)
-
-## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE-------------------------------
-endpoints(m.Z.mkin.5a)
-
diff --git a/vignettes/web_only/compiled_models.R b/vignettes/web_only/compiled_models.R
deleted file mode 100644
index 691037ec..00000000
--- a/vignettes/web_only/compiled_models.R
+++ /dev/null
@@ -1,61 +0,0 @@
-## ---- include = FALSE---------------------------------------------------------
-library(knitr)
-opts_chunk$set(tidy = FALSE, cache = FALSE)
-
-## ----check_gcc, eval = FALSE--------------------------------------------------
-#  pkgbuild::has_compiler()
-
-## ----Rprofile, eval = FALSE---------------------------------------------------
-#  Sys.setenv(PATH = paste("C:/Rtools/bin", Sys.getenv("PATH"), sep=";"))
-
-## ----HOME, eval = FALSE-------------------------------------------------------
-#  Sys.getenv("HOME")
-
-## ----create_SFO_SFO-----------------------------------------------------------
-library("mkin", quietly = TRUE)
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-
-## ----benchmark_SFO_SFO, fig.height = 3, message = FALSE, warning = FALSE------
-if (require(rbenchmark)) {
-  b.1 <- benchmark(
-    "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
-                                      solution_type = "deSolve",
-                                      use_compiled = FALSE, quiet = TRUE),
-    "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D,
-                                 solution_type = "eigen", quiet = TRUE),
-    "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
-                                  solution_type = "deSolve", quiet = TRUE),
-    replications = 3)
-  print(b.1)
-  factor_SFO_SFO <- round(b.1["1", "relative"])
-} else {
-  factor_SFO_SFO <- NA
-  print("R package rbenchmark is not available")
-}
-
-## ----benchmark_FOMC_SFO, fig.height = 3, warning = FALSE----------------------
-if (require(rbenchmark)) {
-  FOMC_SFO <- mkinmod(
-    parent = mkinsub("FOMC", "m1"),
-    m1 = mkinsub( "SFO"))
-
-  b.2 <- benchmark(
-    "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
-                                      use_compiled = FALSE, quiet = TRUE),
-    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
-    replications = 3)
-  print(b.2)
-  factor_FOMC_SFO <- round(b.2["1", "relative"])
-} else {
-  factor_FOMC_SFO <- NA
-  print("R package benchmark is not available")
-}
-
-## ----sessionInfo, echo = FALSE------------------------------------------------
-cat(utils::capture.output(utils::sessionInfo())[1:3], sep = "\n")
-if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
-  cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
-}
-