From e05656d57668688b971c28e32b4cfd4d3eac4662 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 13:03:50 +0200 Subject: Correct and rebuild docs - Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown --- docs/articles/web_only/FOCUS_Z.html | 39 +++++++++++++++++++++---------------- 1 file changed, 22 insertions(+), 17 deletions(-) (limited to 'docs/articles/web_only/FOCUS_Z.html') diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 8f3fe97e..aed1debc 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -7,8 +7,9 @@ Example evaluation of FOCUS dataset Z • mkin - - + + + @@ -82,13 +83,14 @@ +

Example evaluation of FOCUS dataset Z

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -102,18 +104,18 @@

The data

The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report (FOCUS Work Group on Degradation Kinetics 2014, 354).

-
library(mkin, quietly = TRUE)
+
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,
+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,
+  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,
+  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,
+  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,
+  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)

@@ -130,7 +132,7 @@
 ## with value of zero were removed from the data
plot_sep(m.Z.2a)

-
summary(m.Z.2a, data = FALSE)$bpar
+
summary(m.Z.2a, data = FALSE)$bpar
##             Estimate se_notrans    t value     Pr(>t)    Lower    Upper
 ## Z0_0      9.7015e+01   3.393176 2.8591e+01 6.4352e-21 91.66556 102.3642
 ## k_Z0_sink 7.2231e-10   0.225254 3.2067e-09 5.0000e-01  0.00000      Inf
@@ -148,7 +150,7 @@
 ## with value of zero were removed from the data
plot_sep(m.Z.2a.ff)

-
summary(m.Z.2a.ff, data = FALSE)$bpar
+
summary(m.Z.2a.ff, data = FALSE)$bpar
##            Estimate se_notrans t value     Pr(>t)    Lower    Upper
 ## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642
 ## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600
@@ -166,7 +168,7 @@
 ## value of zero were removed from the data
plot_sep(m.Z.3)

-
summary(m.Z.3, data = FALSE)$bpar
+
summary(m.Z.3, data = FALSE)$bpar
##       Estimate se_notrans t value     Pr(>t)    Lower    Upper
 ## Z0_0  97.01488   2.597342  37.352 2.0106e-24 91.67597 102.3538
 ## k_Z0   2.23601   0.146904  15.221 9.1477e-15  1.95354   2.5593
@@ -201,7 +203,7 @@
 ## 5$bparms.ode, : Observations with value of zero were removed from the data
plot_sep(m.Z.FOCUS)

-
summary(m.Z.FOCUS, data = FALSE)$bpar
+
summary(m.Z.FOCUS, data = FALSE)$bpar
##             Estimate se_notrans t value     Pr(>t)     Lower      Upper
 ## Z0_0       96.838607   1.994273 48.5584 4.0283e-42 92.826626 100.850589
 ## k_Z0        2.215405   0.118459 18.7018 1.0415e-23  1.989465   2.467003
@@ -241,7 +243,7 @@
 ## with value of zero were removed from the data
plot_sep(m.Z.mkin.1)

-
summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
+
summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
##                            Z0_0 log_k_Z0_Z1 log_k_Z1_Z2 log_k_Z2_sink
 ## Z0_0                 3.8375e+00  5.4918e-03  3.0584e-02    1.2969e-01
 ## log_k_Z0_Z1          5.4918e-03  2.7613e-03 -1.8820e-04    2.6634e-04
@@ -312,7 +314,7 @@
 

 
The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized  is excessively small, it seems reasonable to fix it to zero.

 
m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
-                       parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
+                       parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
                                      k_Z3_bound_free = 0),
                        fixed_parms = "k_Z3_bound_free",
                        quiet = TRUE)

@@ -372,17 +374,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ -- cgit v1.2.1