diff options
Diffstat (limited to 'docs/articles/FOCUS_Z.R')
| -rw-r--r-- | docs/articles/FOCUS_Z.R | 33 |
1 files changed, 16 insertions, 17 deletions
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R index 5c70b57e..a77441cf 100644 --- a/docs/articles/FOCUS_Z.R +++ b/docs/articles/FOCUS_Z.R @@ -1,10 +1,9 @@ -## ----include=FALSE-------------------------------------------------- +## ---- include = FALSE---------------------------------------------------- require(knitr) -opts_chunk$set(engine='R', tidy = FALSE, cache = TRUE) -options(width=70) +opts_chunk$set(engine='R', tidy = FALSE) -## ----FOCUS_2006_Z_data, echo=TRUE, eval=TRUE------------------------ -require(mkin) +## ---- echo = TRUE, fig = TRUE, fig.width = 8, fig.height = 7------------- +library(mkin, quiet = 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, @@ -20,14 +19,14 @@ FOCUS_2006_Z = data.frame( FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z) -## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6------------------- +## ----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)$bpar -## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6------------------- +## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6------------------------ Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"), Z1 = mkinsub("SFO"), use_of_ff = "max") @@ -36,21 +35,21 @@ m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.2a.ff) summary(m.Z.2a.ff, data = FALSE)$bpar -## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6------------------- +## ----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)$bpar -## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7------------------- +## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7------------------------ Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO"), use_of_ff = "max") m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.5) -## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8------------------- +## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8------------------------ Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), @@ -63,7 +62,7 @@ plot_sep(m.Z.FOCUS) summary(m.Z.FOCUS, data = FALSE)$bpar endpoints(m.Z.FOCUS) -## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8------------------- +## ----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"), @@ -72,14 +71,14 @@ 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)$cov.unscaled -## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8------------------- +## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8------------------------ Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO")) m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.3) -## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8------------------ +## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8----------------------- Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), @@ -89,7 +88,7 @@ m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.4) -## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8------------------ +## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8----------------------- Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE), Z1 = mkinsub("SFO", "Z2", sink = FALSE), Z2 = mkinsub("SFO", "Z3"), @@ -99,7 +98,7 @@ m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.5) -## ----FOCUS_2006_Z_fits_11a, echo=TRUE------------------------------- +## ----FOCUS_2006_Z_fits_11a, echo=TRUE------------------------------------ m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.5$bparms.ode[1:7], k_Z3_bound_free = 0), @@ -107,9 +106,9 @@ m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, quiet = TRUE) plot_sep(m.Z.mkin.5a) -## ----FOCUS_2006_Z_fits_11b, echo=TRUE------------------------------- +## ----FOCUS_2006_Z_fits_11b, echo=TRUE------------------------------------ mkinparplot(m.Z.mkin.5a) -## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE--------------------- +## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE-------------------------- endpoints(m.Z.mkin.5a) |