From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Jan 2023 06:22:04 +0100 Subject: Prebuilt PDF vignettes, summary_listing --- vignettes/web_only/FOCUS_Z.R | 115 +++++++ vignettes/web_only/FOCUS_Z.html | 278 ++++++++++------ vignettes/web_only/benchmarks.R | 114 +++++++ vignettes/web_only/benchmarks.html | 193 +++++++++-- vignettes/web_only/compiled_models.R | 65 ++++ vignettes/web_only/compiled_models.html | 230 +++++++------ vignettes/web_only/dimethenamid_2018.R | 152 +++++++++ vignettes/web_only/dimethenamid_2018.html | 365 +++++++++++++++------ .../figure-html/f_parent_mkin_dfop_const-1.png | Bin 58608 -> 57786 bytes .../f_parent_mkin_dfop_const_test-1.png | Bin 58777 -> 57786 bytes .../figure-html/f_parent_mkin_dfop_tc_test-1.png | Bin 60062 -> 59396 bytes .../figure-html/f_parent_mkin_sfo_const-1.png | Bin 56694 -> 55982 bytes .../figure-html/f_parent_saemix_sfo_tc-1.png | Bin 28655 -> 28538 bytes .../figure-html/plot_parent_nlme-1.png | Bin 59194 -> 59192 bytes vignettes/web_only/mkin_benchmarks.rda | Bin 1650 -> 1722 bytes 15 files changed, 1193 insertions(+), 319 deletions(-) create mode 100644 vignettes/web_only/FOCUS_Z.R create mode 100644 vignettes/web_only/benchmarks.R create mode 100644 vignettes/web_only/compiled_models.R create mode 100644 vignettes/web_only/dimethenamid_2018.R (limited to 'vignettes/web_only') diff --git a/vignettes/web_only/FOCUS_Z.R b/vignettes/web_only/FOCUS_Z.R new file mode 100644 index 00000000..0c19794e --- /dev/null +++ b/vignettes/web_only/FOCUS_Z.R @@ -0,0 +1,115 @@ +## ---- 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/FOCUS_Z.html b/vignettes/web_only/FOCUS_Z.html index 035b8f84..4601f2b4 100644 --- a/vignettes/web_only/FOCUS_Z.html +++ b/vignettes/web_only/FOCUS_Z.html @@ -27,14 +27,11 @@ document.addEventListener('DOMContentLoaded', function(e) { } }); - - + @@ -1874,6 +1947,9 @@ $(document).ready(function () { - + - + - + code{white-space: pre-wrap;} + span.smallcaps{font-variant: small-caps;} + span.underline{text-decoration: underline;} + div.column{display: inline-block; vertical-align: top; width: 50%;} + div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;} + ul.task-list{list-style: none;} + + + @@ -1711,6 +1748,9 @@ $(document).ready(function () { -