Use html_vignette for FOCUS_D vignette, fix addressv0.9.46.3

Static documentation articles rebuilt by pkgdown::build_articles()

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)