snha-gui

This github pages host the GUI application and the R-library for the St. Nicolas House Algorithm which allows to create correlation networks based on association chains. For more background on the theory of this algorithm have a look at the following publications:

• Groth, D., Scheffler, C., & Hermanussen, M. (2019). Body height in stunted Indonesian children depends directly on parental education and not via a nutrition mediated pathway-Evidence from tracing association chains by St. Nicolas House Analysis. Anthr Anz, 76(5), 445-451. DOI: 10.1127/anthranz/2019/1027
• Hermanussen, M., Aßmann, C., & Groth, D. (2021). Chain Reversion for Detecting Associations in Interacting Variables - St. Nicolas House Analysis. Int J Env Res Pub Health, 18(4), 1741. DOI: 10.3390/ijerph18041741

The graphical application and the library needs an installed version of R on your computer. To use this software from this page please install R first either using your package manager or usually for Windows and Mac-OSX using the download facilities of the R-project: https://cran.r-project.org/mirrors.html

St. Nicolas House Algorithm - Graphical User Interface

Windows

For users which are not experienced R users there exists a graphical user interface which can be installed either using the standalone single R-script file or, for Windows systems, using a Windows installer which can be downloaded from here:

snha-install.exe

Experienced users might as well use the Unix script snha-gui.Rz mentioned below from a terminal.

Unix / Linux / Mac-OSX

For Unix systems like Linux or Mac-OSX there is as a single file application: snha-gui.Rz

Download this file and either run the file directly from a terminal with Rscript like this

Rscript /path/to/snha-gui.Rz

or make the file executable like this chmod 755 snha-gui.Rz and move the file thereafter to a folder belonging to your PATH variable, so that you can execute this file from any folder by just typing snha-gui.Rz in the terminal regardless of your current working directory.

Mac-OSX

Please note, that on Mac-OSX you need usually to have a X-Server installation for instance of XQuartz and you have to start the application from a X-terminal. In some cases you might as well change the first line of the file snha-gui.Rz so that it points to the right Rscript interpreter on your hard disk.

Library

For advanced users as well the R-library can be download and installed separately. It offers more features to modify the analysis and the graphical output then the GUI but needs the usual knowledge of the R statisical programming language.

You can install the package directly from Github using the following lines of code from within your R-console:

URL="https://github.com/mittelmark/snha-gui/raw/main/lib/asg_0.9.0.tar.gz"
install.packages(URL,repos=NULL)
library(asg)

You should be then able to start to analyse your data like this:

data(swiss)
data=swiss # fill in your data
as=asg.new(data)
plot(as,layout="sam")

A good place to start is the help page of the asg.new function.

TODO's

• repository asg for the library
• code release for the GUI

Bugs

Please use the Github isses page to report problems and to give suggestions:

https://github.com/mittelmark/snha-gui/issues

ChangeLog

• GUI

  • Version 0.7.0
    • adding data filtering
    • two MDS distances can be used
    • correlation values can be shown on the graph

• Library:

  • Version 0.8.1
    • adding plot option edge.text
  • Version 0.8.2
    • adding asg.impute
    • adding as.list S3 method for writing report with openxlsx
  • Version 0.8.3
    • adding asg.mdsplot
    • adding asg.pcadata
    • adding asg.impute
    • adding asg.nd - network deconvolution
  • Version 0.9.0
    • adding mgraph methods to create different graphs and data for them using Monte Carlo simulations
    • adding mgraph.new
    • adding mgraph.components
    • adding mgraph.degree
    • adding mgraph.d2u
    • adding mgraph.nodeColors
    • adding mgraph.u2d
    • adding plot.mgraph

License

The code is released using the MIT license.

Copyright 2022, Detlef Groth, University of Potsdam, Germany

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.