From 062df4d773cd4e57c862054fe9b5232b5a055c34 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Sep 2018 23:46:59 +0200 Subject: Require mkin version that actually works with gmkin Static documentation rebuilt by pkgdown --- docs/articles/gmkin_manual.html | 50 +++++++++++++++++------------------ docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 30 ++++++++++----------- docs/news/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/FOCUS_2006.html | 2 +- docs/reference/FOCUS_2006_Z.html | 2 +- docs/reference/UBA_model_gallery.html | 2 +- docs/reference/gmkin.html | 2 +- docs/reference/gmkinws.html | 2 +- docs/reference/index.html | 2 +- 12 files changed, 50 insertions(+), 50 deletions(-) (limited to 'docs') diff --git a/docs/articles/gmkin_manual.html b/docs/articles/gmkin_manual.html index dc2ef4d..646b534 100644 --- a/docs/articles/gmkin_manual.html +++ b/docs/articles/gmkin_manual.html @@ -29,7 +29,7 @@ gmkin - 0.6.8 + 0.6.9 @@ -75,7 +75,7 @@

Manual for gmkin

Johannes Ranke

-

2018-06-06

+

2018-09-13

@@ -94,11 +94,11 @@

Starting gmkin

As gmkin is an R package, you need to start R and load the gmkin package before you can run gmkin. The latter can be achieved by entering the command

-
library(gmkin)
+
library(gmkin)

into the R console. This will also load the packages that gmkin depends on, most notably gWidgetsWWW2 and mkin. Loading the package only has to be done once after you have started R.

Before you start gmkin, you should make sure that R is using the working directory that you would like to keep your gmkin project file(s) in. If you use the standard R GUI application on windows, you can change the working directory from the File menu (‘File’ -> ‘Change dir…’).

Once you are sure that the working directory is what you want it to be, gmkin can be started by entering the R command

-
gmkin()
+
gmkin()

This will cause the default browser to start up or, if it is already running, to pop up and open a new tab for displaying the gmkin user interface.

In the R console, you should see a message that the httpd help server is started, if it wasn’t already started before.

In the browser, you should see something like the screenshot below.

@@ -160,9 +160,9 @@ Importing data from text files

In case you want to work with a larger dataset that is already available as a computer file e.g. in a spreadsheet application, you can export these data as a tab separated or comma separated text file and import it using the “Browse” and “Upload” buttons in the dataset editor.

As an example, we can create a text file from one of the datasets shipped with the mkin package using the following R command:

-
write.table(schaefer07_complex_case, sep = ",", dec = ".", 
-            row.names = FALSE, quote = FALSE, 
-            file = "schaefer07.csv")
+
write.table(schaefer07_complex_case, sep = ",", dec = ".", 
+            row.names = FALSE, quote = FALSE, 
+            file = "schaefer07.csv")

This produces a text file with comma separated values in the current working directory of R.

Loading this text file into gmkin using the “Browse” and “Upload” buttons

@@ -241,23 +241,23 @@

Fitting the model

In many cases the starting parameters and the fit options do not need to be modified and the model fitting process can simply be started by pressing the “Run fit” button. In the R console, the progressive reduction in the model cost can be monitored and will be displayed in the following way:

-
Model cost at call  1 :  15156.12 
-Model cost at call  3 :  15156.12 
-Model cost at call  7 :  14220.79 
-Model cost at call  8 :  14220.79 
-Model cost at call  11 :  14220.79 
-Model cost at call  12 :  3349.268 
-Model cost at call  15 :  3349.268 
-Model cost at call  17 :  788.6367 
-Model cost at call  18 :  788.6366 
-Model cost at call  22 :  374.0575 
-Model cost at call  23 :  374.0575 
-Model cost at call  27 :  371.2135 
-Model cost at call  28 :  371.2135 
-Model cost at call  32 :  371.2134 
-Model cost at call  36 :  371.2134 
-Model cost at call  37 :  371.2134 
-Optimisation by method Port successfully terminated.
+

If plotting of the fitting progress was selected, a new separate graphics window should either pop up, or a graphics window previously started for this purpose will be reused.

If your screen size allows for it, you can arrange the R plotting window and the R console in a way that you can see everything at the same time:

@@ -321,7 +321,7 @@ Optimisation by method Port successfully terminated.
  • Enter replicates ‘1’
  • Enter observed variable ‘parent, A1’
  • Press ‘Generate grid for entering kinetic data’
    • -
  • In the value column of the dataset editor, enter values ‘100’, ‘30’, ‘10’, ‘5’, ‘3’, ‘’ (nothing), ’3’, ‘8’, ‘7’, ‘5’
    • +
  • In the value column of the dataset editor, enter values ‘100’, ‘30’, ‘10’, ‘5’, ‘3’, ’’ (nothing), ‘3’, ‘8’, ‘7’, ‘5’
  • Press ‘Keep changes’
  • Select the ‘Model gallery’ to the right
  • From the model gallery, press ‘FOMC, one met’ below the corresponding model scheme
    • diff --git a/docs/articles/index.html b/docs/articles/index.html index c7c7845..66f320b 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -58,7 +58,7 @@ gmkin - 0.6.8 + 0.6.9
    diff --git a/docs/authors.html b/docs/authors.html index 3e0114c..bd814b3 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -58,7 +58,7 @@ gmkin - 0.6.8 + 0.6.9 diff --git a/docs/index.html b/docs/index.html index a654b22..0df4c29 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ gmkin - 0.6.8 + 0.6.9 @@ -93,14 +93,14 @@

    Installing gmkin and gWidgetsWWW2

    Windows and Linux users running R 3.1.0 or later can make use of my drat package repository on github. Before installing gmkin, you should update your R packages already installed, e.g. by starting R, and pasting the command

    -
    update.packages()
    +
    update.packages()

    or similar, depending on your R installation.

    For installing gmkin or upgrading to the latest released version, please install the drat package

    -
    install.packages("drat")
    +
    install.packages("drat")

    add my repository

    -
    drat::addRepo("jranke")
    +
    drat::addRepo("jranke")

    and install as usual

    -
    install.packages("gmkin")
    +
    install.packages("gmkin")

    The latest changes to gmkin are recorded in the NEWS file, more details can be found in the commit history.

    gmkin screenshot

    @@ -109,8 +109,8 @@

    Usage

    Without further preparation, you can start the GUI by starting R and pasting the following commands into the R terminal (R console on Windows):

    -
    require(gmkin)
-gmkin()
    +
    require(gmkin)
+gmkin()

    You may also want to adapt the browser that R starts (using e.g. options(browser="/usr/bin/firefox") on linux, or setting the default browser on Windows).

    @@ -137,9 +137,9 @@ gmkin()

    Installation using the devtools package

    Users of the devtools package can also install gWidgetsWWW2 and gmkin directly from the respective github repositories:

    -
    require(devtools)
-install_github("jverzani/gWidgetsWWW2", quick = TRUE)
-install_github("jranke/gmkin", quick = TRUE)
    +
    require(devtools)
+install_github("jverzani/gWidgetsWWW2", quick = TRUE)
+install_github("jranke/gmkin", quick = TRUE)

    Installing gWidgetsWWW2 in this way yields a lot of warnings concerning overly long path names (see Notes on gWidgetsWWW2 above). Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.

    @@ -147,11 +147,11 @@ install_github("jranke/gmkin", quick = TRUE) Simplifying the start of gmkin under Windows

    You can put the commands

    -
    require(gmkin)
-gmkin()
-while (TRUE) {
-  Sys.sleep(10)
-}
    +
    require(gmkin)
+gmkin()
+while (TRUE) {
+  Sys.sleep(10)
+}

    into an R script (e.g. under C:\Users\<your username>\AppData\Roaming\gmkin_start.R), and create a Windows shortcut, e.g. on the Desktop, with the target "C:\Program Files\R\R-3.x.y\bin\R.exe" --slave -f c:\Users\<your username>\AppData\Roaming\gmkin_start.R, where R.x.y is the version of R that you would like to use with gmkin. This will start a non-interactive R console that runs the gmkin GUI. In the properties dialogue of the shortcut, you can also set the working directory in which it starts gmkin. Thanks to Jonas Klein of the Umweltbundesamt for the trick with using Sys.sleep in a while loop and for suggesting the AppData directory for the start script.

    diff --git a/docs/news/index.html b/docs/news/index.html index 24be3d7..d8cce8c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -58,7 +58,7 @@ gmkin - 0.6.8 + 0.6.9
    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 75e5968..d836be5 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 1.19.2.4 +pandoc: 2.2.1 pkgdown: 1.1.0 pkgdown_sha: ~ articles: diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html index 93153ad..4a96697 100644 --- a/docs/reference/FOCUS_2006.html +++ b/docs/reference/FOCUS_2006.html @@ -63,7 +63,7 @@ gmkin - 0.6.8 + 0.6.9 diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html index ee01417..8a1cc24 100644 --- a/docs/reference/FOCUS_2006_Z.html +++ b/docs/reference/FOCUS_2006_Z.html @@ -61,7 +61,7 @@ gmkin - 0.6.8 + 0.6.9 diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html index 00f84ae..a7e6f59 100644 --- a/docs/reference/UBA_model_gallery.html +++ b/docs/reference/UBA_model_gallery.html @@ -66,7 +66,7 @@ gmkin - 0.6.8 + 0.6.9 diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html index 70c2d07..21961bb 100644 --- a/docs/reference/gmkin.html +++ b/docs/reference/gmkin.html @@ -63,7 +63,7 @@ gmkin - 0.6.8 + 0.6.9 diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html index e0fee8b..7355823 100644 --- a/docs/reference/gmkinws.html +++ b/docs/reference/gmkinws.html @@ -61,7 +61,7 @@ gmkin - 0.6.8 + 0.6.9 diff --git a/docs/reference/index.html b/docs/reference/index.html index 1b9bd74..f0a6712 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -58,7 +58,7 @@ gmkin - 0.6.8 + 0.6.9 -- cgit v1.2.1