From 49ebe44092d2033f548c901ea406619713583103 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 7 Feb 2020 07:23:06 +0100 Subject: Update Makefile, update FOCUS URL --- docs/reference/FOCUS_2006.html | 43 ++++++++++++++++--------------- docs/reference/FOCUS_2006_Z.html | 43 ++++++++++++++++--------------- docs/reference/UBA_model_gallery.html | 38 ++++++++++++++------------- docs/reference/gmkin.html | 34 +++++++++++++++---------- docs/reference/gmkinws.html | 48 +++++++++++++++++++++-------------- docs/reference/index.html | 23 ++++++++++++----- 6 files changed, 133 insertions(+), 96 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html index 9066d83..15068de 100644 --- a/docs/reference/FOCUS_2006.html +++ b/docs/reference/FOCUS_2006.html @@ -8,21 +8,25 @@ Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report — FOCUS_2006 • gmkin + + - + + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,6 +43,7 @@ + @@ -49,6 +54,7 @@ + @@ -73,7 +79,7 @@ - @@ -106,6 +111,7 @@ +
@@ -117,64 +123,61 @@
-

An gmkinws object with data taken from FOCUS (2006), Appendix 3. This is the the workspace that is loaded into gmkin by default.

- 
FOCUS_2006
- + +

Format

A list named FOCUS_2006 containing the components needed to populate the gmkin user interface.

-

Source

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://focus.jrc.ec.europa.eu/dk

- + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

Examples

- 
  
# NOT RUN {
-  save(FOCUS_2006, file = "FOCUS_2006.RData")
+    
  if (FALSE) {
+  save(FOCUS_2006, file = "FOCUS_2006.RData")
   # Now you can load the file "FOCUS_2006.RData" from gmkin,
   # restoring the workspace that is loaded at startup.
-
-# }

+  }
+ + + diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html index 8df70a6..6901f59 100644 --- a/docs/reference/FOCUS_2006_Z.html +++ b/docs/reference/FOCUS_2006_Z.html @@ -8,21 +8,25 @@ Example gmkin workspace for Dataset Z from the FOCUS Kinetics report — FOCUS_2006_Z • gmkin + + - + + - - + + + @@ -30,13 +34,14 @@ - + + @@ -47,6 +52,7 @@ + @@ -71,7 +77,7 @@ - @@ -104,6 +109,7 @@ +
@@ -115,61 +121,58 @@
-

Data taken from FOCUS (2006), Appendix 7, p. 350.

- 
FOCUS_2006_Z
- + +

Format

An gmkinws object with dataset Z taken from FOCUS (2006), together with most of the models used in the corresponding vignette.

-

Source

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://focus.jrc.ec.europa.eu/dk

- + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

Examples

- 
  
# NOT RUN {
-  save(FOCUS_2006_Z, file = "FOCUS_2006_Z.RData")
+    
  if (FALSE) {
+  save(FOCUS_2006_Z, file = "FOCUS_2006_Z.RData")
   # Now you can load the file "FOCUS_2006_Z.RData" from gmkin
-
-# }

+  }
+ + + diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html index d302d27..1e8abd8 100644 --- a/docs/reference/UBA_model_gallery.html +++ b/docs/reference/UBA_model_gallery.html @@ -8,21 +8,25 @@ A collection of some standard kinetic models — UBA_model_gallery • gmkin + + - + + - - + + + @@ -30,8 +34,8 @@ - + @@ -52,6 +57,7 @@ + @@ -76,7 +82,7 @@ - @@ -109,6 +114,7 @@ +
@@ -120,22 +126,20 @@
-

The UBA model gallery contains predefined kinetic models for some common use cases, with metabolites named as in the commonly used PELMO degradation scheme (Jene 1998). Please use the model gallery of the gmkin GUI to see their definitions. The models use the topology of the models defined by Michael Klein (2010) for DegKinManager, with the exception of the kinetic sorption model.

-
- 
data("UBA_model_gallery")
- + 
data("UBA_model_gallery")
+ +

Format

A list containing 9 lists of four mkinmod models.

-

References

Klein M (2010) Calculation of rates constants according to FOCUS degradation @@ -144,38 +148,38 @@

Jene B (1998) PELMO 3.00 Manual extension, Staatliche Lehr- und Forschungsanstalt für Landwirtschaft, Weinbau und Gartenbau, D-67435 Neustadt/Wstr.

-

Examples

- 
data(UBA_model_gallery)
+ 
data(UBA_model_gallery)
+ + + diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html index f3e9729..fa33831 100644 --- a/docs/reference/gmkin.html +++ b/docs/reference/gmkin.html @@ -8,21 +8,25 @@ Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit. — gmkin • gmkin + + - + + - - + + + @@ -30,8 +34,8 @@ - + @@ -39,6 +43,7 @@ for an explanation how this toolkit works." /> + @@ -49,6 +54,7 @@ for an explanation how this toolkit works." /> + @@ -73,7 +79,7 @@ for an explanation how this toolkit works." /> - @@ -106,6 +111,7 @@ for an explanation how this toolkit works." /> +
@@ -117,15 +123,13 @@ for an explanation how this toolkit works." />
-

This function starts a browser based GUI. Please visit the github page of gWidgetsWWW2 for an explanation how this toolkit works.

- 
gmkin(script_name, show.log = FALSE)
- +

Arguments

@@ -141,39 +145,41 @@ script shipped with the package.

Rook apps.

- +

Value

The function is called for its side effect, namely starting the GUI in a browser. For the curious, the desperate or the adventurous, the gmkin app (a GWidgetsApp object) is returned.

- + + + diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html index 4a264e9..7d3b2a0 100644 --- a/docs/reference/gmkinws.html +++ b/docs/reference/gmkinws.html @@ -8,21 +8,25 @@ A workspace class for gmkin — gmkinws • gmkin + + - + + - - + + + @@ -30,13 +34,14 @@ - + + @@ -47,6 +52,7 @@ + @@ -71,7 +77,7 @@ - @@ -104,6 +109,7 @@ +
@@ -115,55 +121,59 @@
-

Datasets, models and fits are stored in lists.

- 
gmkinws
- + +

Format

An R6Class generator object.

-

Fields

-
+ +
observed

Names of the observed variables in the datasets, named by the names used in the models contained in field m

-
ds

A list of datasets compatible with mkinfit (long format)

-
m

A list of mkinmod models

-
f

A list of mkinfit objects

+ +
ds

A list of datasets compatible with mkinfit (long format)

+ +
m

A list of mkinmod models

+ +
f

A list of mkinfit objects

+
- +

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/index.html b/docs/reference/index.html index 96635b9..c96681b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -8,21 +8,25 @@ Function reference • gmkin + + - + + - - + + + @@ -30,10 +34,12 @@ + + @@ -44,6 +50,7 @@ + @@ -68,7 +75,7 @@ - @@ -101,6 +107,7 @@ +
@@ -167,19 +174,23 @@
+ + + -- cgit v1.2.1