Merge pull request #18 from tenderle/master

Update Readme.md

README.md

@@ -13,6 +13,66 @@ This package is developed within the SGA `Open source tools for perturbative con
 
 We have a first rough version with which interested users may play around. Feedback (via issues) with regards to bugs or features requests are very welcome as well as pull-requests.
 
+### Installation
+
+The package can directly be installed from `github` using the `devtools` package which must be installed on your system
+
+``` r
+if (!require("devtools")) install.packages("devtools")
+library(devtools)
+
+# update all packages
+update.packages(ask=FALSE)
+
+# finally install the ptable package directly from github
+devtools::install_github("sdcTools/ptable", dependencies=c("Depends","Imports"), force=TRUE, build_opts="--build-vignettes")
+```
+
+If you experience a timeout due to a proxy server while downloading, one can work around this issue by specifying the proxy-server using the `hhtr` package:
+
+``` r
+httr::set_config(use_proxy(url="xxx.xxx.xxx.xxx, port=yy))
+```
+
+### Usage
+
+#### Load the package
+
+To load the package `ptable` you have to call
+
+``` r
+## load the package
+library(ptable)
+```
+
+#### Help
+
+``` r
+## help for specifying the perturbation parameters
+?pt_create_pParams
+
+## help for producing the perturbation table
+?pt_create_pTable
+```
+
+#### Documentation
+
+Once finished, the package will also contain a package **vignette**. The unfinished introduction vignette can be looked at using the following command:
+
+``` r
+pt_vignette()
+```
+
+#### Graphical User Interface (GUI)
+
+For first time users and visual learners there is a GUI. The unfinished dashboard can be started using the following command:
+
+``` r
+ptable()
+```
+
+The download buttons (for downloading the ptable and the graphics) only works within a browser.
+
 ### News
 
 #### ToDo's
@@ -80,96 +140,3 @@ We have a first rough version with which interested users may play around. Feedb
 #### Version 0.1.0
 
 -   first uploaded version
-
-### Installation
-
-The package can directly be installed from `github`
-
-``` r
-devtools::install_github("sdcTools/ptable", build_vignette=TRUE)
-```
-
-### Usage
-
-#### Load the package
-
-To load the package `ptable` you have to call
-
-``` r
-## load the package
-library(ptable)
-```
-
-#### Help
-
-``` r
-## help for specifying the perturbation parameters
-?pt_create_pParams
-
-## help for producing the perturbation table
-?pt_create_pTable
-```
-
-#### Basic Example
-
-This is a basic example which shows you how to solve a common problem with `D=3` (maximum deviation) and `V=0.7` (perturbation variance):
-
-``` r
-## basic example code
-params <- pt_create_pParams(D=3, V=0.7)
-ptable_destatis <- pt_create_pTable(params = params, type="destatis")
-ptable_abs <- pt_create_pTable(params = params, type="abs")
-```
-
-#### Extended Example (prevent small frequencies)
-
-To prevent small frequencies (e.g. 1s and 2s) in perurbed frequency tables, you can set the treshold parameter `js=...` when specifying the perturbation table (i.e. all positive integers less equal `js` are no target frequencies for the perturbation and, hence, blocked):
-
-``` r
-## extended example code
-params <- pt_create_pParams(D=5, V=3, js=2)
-ptable_destatis <- pt_create_pTable(params = params, type="destatis")
-```
-
-#### Extended Example (prevent small frequencies and pre-setting of probabilities)
-
-Additionally, you can pre-set the probability that original frequencies won't be perturbed using the parameter `pstay=...`. In the following example the probability that values shouldn't be perturbed is pre-set to 50%:
-
-``` r
-## extended example code
-params <- pt_create_pParams(D=5, V=3, js=2, pstay=0.5)
-ptable_destatis <- pt_create_pTable(params = params, type="destatis")
-```
-
-However, a pre-set probability does neither hold for blocked frequencies (small frequencies such as 1s and 2s) nor for original zeroes. The probabilites for blocked frequencies are always `0` (i.e. they must be perturbed) and for original zeroes the probability is always `1` (i.e. zeroes won't be perturbed).
-
-#### Plot the perturbation table and save the plot
-
-``` r
-## plot the ptable
-fifi_plot(ptable_destatis)
-## ... and save the plot as pdf
-fifi_plot(ptable_destatis, file="graph.pdf")
-
-## Perturbation Panel
-fifi_plot(ptable_destatis, type="p")
-## Transition Matrix
-fifi_plot(ptable_destatis, type="t")
-```
-
-#### Export the perturbation table (e.g. for importing the file in tauargus)
-
-``` r
-pt_export(ptable_destatis,file="Test")
-```
-
-### Dashboard (experimental status)
-
-To try the dashboard just call
-
-``` r
-## start the dashbaord
-ptable()
-```
-
-The download buttons (for downloading the ptable and the graphics) only works within a browser.