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authorJohannes Ranke <jranke@uni-bremen.de>2016-12-08 09:23:22 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2016-12-08 09:26:47 +0100
commit9733b1ae5596228c50b3acdfdd78fe96ab1e0533 (patch)
treee486ce3225a3d2d955940d17c6fec1bd3aca4ab3 /docs/articles/FOCUS_Z.R
parentcc72aa3422eb6cb51b47da32e2cccca6afd4d271 (diff)
Static documentation articles rebuilt by pkgdown::build_articles()
Diffstat (limited to 'docs/articles/FOCUS_Z.R')
-rw-r--r--docs/articles/FOCUS_Z.R108
1 files changed, 92 insertions, 16 deletions
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R
index eacefa90..0d5f0940 100644
--- a/docs/articles/FOCUS_Z.R
+++ b/docs/articles/FOCUS_Z.R
@@ -3,20 +3,96 @@ require(knitr)
opts_chunk$set(engine='R', tidy = FALSE, cache = TRUE)
options(width=70)
-## ----FOCUS_2006_Z_data, echo=TRUE, eval=TRUE------------------------
-require(mkin)
-LOD = 0.5
-FOCUS_2006_Z = data.frame(
- t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
- 42, 61, 96, 124),
- Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8,
- 2.9, 3.5, 5.3, 4.4, 1.2, 0.7),
- Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1,
- 1.6, 0.6, 0.5 * LOD, NA, NA, NA),
- Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5,
- 0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA),
- Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5,
- 25.2, 17.2, 4.8, 4.5, 2.8, 4.4))
-
-FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
+## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6-------------------
+Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
+ Z1 = mkinsub("SFO"))
+m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.2a)
+summary(m.Z.2a, data = FALSE)$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)

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