diff options
Diffstat (limited to 'docs/articles/FOCUS_Z.R')
| -rw-r--r-- | docs/articles/FOCUS_Z.R | 32 |
1 files changed, 27 insertions, 5 deletions
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R index 5fc8f123..5c70b57e 100644 --- a/docs/articles/FOCUS_Z.R +++ b/docs/articles/FOCUS_Z.R @@ -1,3 +1,25 @@ +## ----include=FALSE-------------------------------------------------- +require(knitr) +opts_chunk$set(engine='R', tidy = FALSE, cache = TRUE) +options(width=70) + +## ----FOCUS_2006_Z_data, echo=TRUE, eval=TRUE------------------------ +require(mkin) +LOD = 0.5 +FOCUS_2006_Z = data.frame( + t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21, + 42, 61, 96, 124), + Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8, + 2.9, 3.5, 5.3, 4.4, 1.2, 0.7), + Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1, + 1.6, 0.6, 0.5 * LOD, NA, NA, NA), + Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5, + 0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA), + Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5, + 25.2, 17.2, 4.8, 4.5, 2.8, 4.4)) + +FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z) + ## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6------------------- Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"), Z1 = mkinsub("SFO")) @@ -32,9 +54,9 @@ plot_sep(m.Z.5) Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), - Z3 = mkinsub("SFO"), + Z3 = mkinsub("SFO"), use_of_ff = "max") -m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, +m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, quiet = TRUE) plot_sep(m.Z.FOCUS) @@ -62,7 +84,7 @@ 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, +m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.3$bparms.ode, quiet = TRUE) plot_sep(m.Z.mkin.4) @@ -72,13 +94,13 @@ Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), Z3 = mkinsub("SFORB")) -m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, +m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.4$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, +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", |