From ccc70e82af4ba435f0a71ba1ae4e0e92045c3852 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 5 May 2017 12:46:31 +0200 Subject: Static docs except articles rebuilt with current pkgdown --- docs/reference/mccall81_245T.html | 67 +++++++++++++++++++-------------------- 1 file changed, 32 insertions(+), 35 deletions(-) (limited to 'docs/reference/mccall81_245T.html') diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 4fa32b30..9a681191 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,8 +6,7 @@ - - — mccall81_245T • mkin +Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin @@ -26,12 +25,14 @@ - + + + @@ -71,6 +72,9 @@
  • Performance benefit by using compiled model definitions in mkin
    • +
  • + Calculation of time weighted average concentrations with mkin +
  • @@ -96,8 +100,7 @@
    -

    -

    +

    Datasets on aerobic soil metabolism of 2,4,5-T in six soils

    @@ -106,21 +109,20 @@ extracts.

    - 
    mccall81_245T
    + 
    mccall81_245T

    Format

    -

    A dataframe containing the following variables. -

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

    A dataframe containing the following variables.

    +
    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.

    -
    time
    a numeric vector containing sampling times in days after - treatment
    -
    value
    a numeric vector containing concentrations in percent of applied radioactivity
    -
    soil
    a factor containing the name of the soil
    -

    + mkinmod.

    +
    time

    a numeric vector containing sampling times in days after + treatment

    +
    value

    a numeric vector containing concentrations in percent of applied radioactivity

    +
    soil

    a factor containing the name of the soil

    +

    Source

    @@ -132,16 +134,11 @@ 
      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)
    #> Warning: Optimisation by method Port did not converge.
-#> Convergence code is 1
        summary(fit.1, data = FALSE)
    #> mkin version:    0.9.45.1 
-#> R version:       3.3.3 
-#> Date of fit:     Wed Mar 15 09:44:52 2017 
-#> Date of summary: Wed Mar 15 09:44:52 2017 
-#> 
-#> 
-#> Warning: Optimisation by method Port did not converge.
-#> Convergence code is 1 
-#> 
+    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
+    summary(fit.1, data = FALSE)
    #> mkin version:    0.9.45.2 
+#> R version:       3.4.0 
+#> Date of fit:     Fri May  5 12:45:02 2017 
+#> Date of summary: Fri May  5 12:45:02 2017 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -151,7 +148,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 590 model solutions performed in 3.519 s
+#> Fitted with method Port using 612 model solutions performed in 3.576 s
 #> 
 #> Weighting: none
 #> 
@@ -183,7 +180,7 @@
 #> T245_0               103.9000         NA    NA    NA
 #> log_k_T245_sink       -4.1130         NA    NA    NA
 #> log_k_T245_phenol     -3.6120         NA    NA    NA
-#> log_k_phenol_sink    -26.3900         NA    NA    NA
+#> log_k_phenol_sink    -26.8400         NA    NA    NA
 #> log_k_phenol_anisole  -0.9037         NA    NA    NA
 #> log_k_anisole_sink    -5.0090         NA    NA    NA
 #> 
@@ -198,8 +195,8 @@
 #>                   Estimate   t value    Pr(>t) Lower Upper
 #> T245_0           1.039e+02 4.282e+01 7.236e-20    NA    NA
 #> k_T245_sink      1.636e-02 8.901e-01 1.926e-01    NA    NA
-#> k_T245_phenol    2.701e-02 1.504e+00 7.498e-02    NA    NA
-#> k_phenol_sink    3.457e-12 1.230e-11 5.000e-01    NA    NA
+#> k_T245_phenol    2.701e-02 1.504e+00 7.499e-02    NA    NA
+#> k_phenol_sink    2.212e-12 7.870e-12 5.000e-01    NA    NA
 #> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02    NA    NA
 #> k_anisole_sink   6.679e-03 8.146e+00 9.469e-08    NA    NA
 #> 
@@ -214,7 +211,7 @@
 #>                       ff
 #> T245_sink      3.772e-01
 #> T245_phenol    6.228e-01
-#> phenol_sink    8.534e-12
+#> phenol_sink    5.462e-12
 #> phenol_anisole 1.000e+00
 #> anisole_sink   1.000e+00
 #> 
@@ -228,10 +225,10 @@
   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, data = FALSE)
    #> mkin version:    0.9.45.1 
-#> R version:       3.3.3 
-#> Date of fit:     Wed Mar 15 09:44:54 2017 
-#> Date of summary: Wed Mar 15 09:44:54 2017 
+  summary(fit.2, data = FALSE)
    #> mkin version:    0.9.45.2 
+#> R version:       3.4.0 
+#> Date of fit:     Fri May  5 12:45:04 2017 
+#> Date of summary: Fri May  5 12:45:04 2017 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -241,7 +238,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.449 s
+#> Fitted with method Port using 246 model solutions performed in 1.461 s
 #> 
 #> Weighting: none
 #> 
-- 
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