From 194659fcaccdd1ee37851725b8c72e99daa3a8cf Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 10 Apr 2019 10:17:35 +0200 Subject: Adapt tests, vignettes and examples - Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit --- docs/reference/mccall81_245T.html | 75 ++++++++++++++++++++------------------- 1 file changed, 38 insertions(+), 37 deletions(-) (limited to 'docs/reference/mccall81_245T.html') diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 47fa6482..a336a840 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -65,7 +65,7 @@ mkin - 0.9.48.1 + 0.9.49.4 @@ -141,10 +141,10 @@

Format

A dataframe containing the following variables.

-
name

the name of the compound observed. Note that T245 is used as +

name

the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is a legitimate object name in R, which is necessary for specifying models using - mkinmod.

+ mkinmod.

time

a numeric vector containing sampling times in days after treatment

value

a numeric vector containing concentrations in percent of applied radioactivity

@@ -160,23 +160,24 @@

Examples

  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
                          phenol = list(type = "SFO", to = "anisole"),
-                         anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
-    summary(fit.1)$bpar
#> Warning: Could not estimate covariance matrix; singular system.
#>                      Estimate   se_notrans      t value       Pr(>t) Lower
-#> T245_0           1.038550e+02 2.4256088519 4.281607e+01 7.235908e-20    NA
-#> k_T245_sink      1.636106e-02 0.0183803090 8.901408e-01 1.925667e-01    NA
-#> k_T245_phenol    2.700936e-02 0.0179604385 1.503825e+00 7.498498e-02    NA
-#> k_phenol_sink    1.286034e-11 0.2810970202 4.575054e-11 5.000000e-01    NA
-#> k_phenol_anisole 4.050581e-01 0.1608928349 2.517564e+00 1.075371e-02    NA
-#> k_anisole_sink   6.678742e-03 0.0008199239 8.145563e+00 9.469402e-08    NA
-#>                  Upper
-#> T245_0              NA
-#> k_T245_sink         NA
-#> k_T245_phenol       NA
-#> k_phenol_sink       NA
-#> k_phenol_anisole    NA
-#> k_anisole_sink      NA
    endpoints(fit.1)
#> $ff
+                         anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
    summary(fit.1)$bpar
#> Warning: NaNs wurden erzeugt
#>                      Estimate   se_notrans   t value       Pr(>t)        Lower
+#> T245_0           1.038550e+02 2.1508106806 48.286460 3.542223e-18 99.246062186
+#> k_T245_sink      1.636106e-02          NaN       NaN          NaN  0.012661557
+#> k_T245_phenol    2.700936e-02          NaN       NaN          NaN  0.024487315
+#> k_phenol_sink    1.054519e-10          NaN       NaN          NaN  0.000000000
+#> k_phenol_anisole 4.050581e-01 0.1053797258  3.843795 7.969973e-04  0.218013983
+#> k_anisole_sink   6.678742e-03 0.0006205825 10.762053 9.427693e-09  0.005370739
+#> sigma            2.514628e+00 0.3383657682  7.431685 1.054052e-06  1.706607296
+#>                         Upper
+#> T245_0           1.084640e+02
+#> k_T245_sink      2.114150e-02
+#> k_T245_phenol    2.979116e-02
+#> k_phenol_sink             Inf
+#> k_phenol_anisole 7.525759e-01
+#> k_anisole_sink   8.305299e-03
+#> sigma            3.322649e+00
    endpoints(fit.1)
#> $ff
 #>      T245_sink    T245_phenol    phenol_sink phenol_anisole   anisole_sink 
-#>   3.772401e-01   6.227599e-01   3.174937e-11   1.000000e+00   1.000000e+00 
+#>   3.772401e-01   6.227599e-01   2.603376e-10   1.000000e+00   1.000000e+00 
 #> 
 #> $SFORB
 #> logical(0)
@@ -185,26 +186,26 @@
 #>               DT50      DT90
 #> T245     15.982025  53.09114
 #> phenol    1.711229   5.68458
-#> anisole 103.784093 344.76330
-#> 
    # No convergence, no covariance matrix ...
-    # k_phenol_sink is really small, therefore fix it to zero
+#> anisole 103.784092 344.76329
+#> 
    # k_phenol_sink is really small, therefore fix it to zero
     fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
                    parms.ini = c(k_phenol_sink = 0),
-                   fixed_parms = "k_phenol_sink", quiet = TRUE)
-    summary(fit.2)$bpar
#>                      Estimate   se_notrans   t value       Pr(>t)        Lower
-#> T245_0           1.038550e+02 2.3517950656 44.159900 6.461715e-21 98.932670927
-#> k_T245_sink      1.636106e-02 0.0021685502  7.544701 1.978480e-07  0.012397413
-#> k_T245_phenol    2.700936e-02 0.0013511301 19.990199 1.606634e-14  0.024324422
-#> k_phenol_anisole 4.050581e-01 0.1238660786  3.270129 2.013627e-03  0.213574853
-#> k_anisole_sink   6.678742e-03 0.0007468908  8.942059 1.543812e-08  0.005284957
+                   fixed_parms = "k_phenol_sink", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
    summary(fit.2)$bpar
#>                      Estimate   se_notrans   t value       Pr(>t)        Lower
+#> T245_0           1.038550e+02 2.1623652988 48.028441 4.993105e-19 99.271024566
+#> k_T245_sink      1.636106e-02 0.0019676253  8.315129 1.673677e-07  0.012679144
+#> k_T245_phenol    2.700936e-02 0.0012421965 21.743225 1.314080e-13  0.024500318
+#> k_phenol_anisole 4.050581e-01 0.1177235385  3.440757 1.679236e-03  0.218746681
+#> k_anisole_sink   6.678743e-03 0.0006829745  9.778904 1.872891e-08  0.005377084
+#> sigma            2.514628e+00 0.3790944250  6.633250 2.875782e-06  1.710983655
 #>                         Upper
-#> T245_0           1.087774e+02
-#> k_T245_sink      2.159195e-02
-#> k_T245_phenol    2.999066e-02
-#> k_phenol_anisole 7.682180e-01
-#> k_anisole_sink   8.440105e-03
    endpoints(fit.1)
#> $ff
+#> T245_0           1.084390e+02
+#> k_T245_sink      2.111217e-02
+#> k_T245_phenol    2.977534e-02
+#> k_phenol_anisole 7.500550e-01
+#> k_anisole_sink   8.295501e-03
+#> sigma            3.318272e+00
    endpoints(fit.1)
#> $ff
 #>      T245_sink    T245_phenol    phenol_sink phenol_anisole   anisole_sink 
-#>   3.772401e-01   6.227599e-01   3.174937e-11   1.000000e+00   1.000000e+00 
+#>   3.772401e-01   6.227599e-01   2.603376e-10   1.000000e+00   1.000000e+00 
 #> 
 #> $SFORB
 #> logical(0)
@@ -213,8 +214,8 @@
 #>               DT50      DT90
 #> T245     15.982025  53.09114
 #> phenol    1.711229   5.68458
-#> anisole 103.784093 344.76330
-#>
+#> anisole 103.784092 344.76329 +#>
plot_sep(fit.2)