search

hzi-braunschweig / SORMAS-Stats-next-gen

SORMAS-Stats contain functions to analyze and visualize surveillance data collected by SORMAS.
GNU General Public License v3.0
4 stars 6 forks source link

Startup error: postgresqlNewConnection(drv, ...): RS-DBI driver: ( #156

Open jielab opened 2 years ago

jielab commented 2 years ago

Hi, there:

I am trying to run SORMAS-Stats-next-gen locally.

I first downloaded the code from https://github.com/hzi-braunschweig/SORMAS-Stats-next-gen and unzipped it.

Then, I set the R PATH to where the example-app.Rproj is saved on my PC. However, after I run shiny::runApp(), I got the following error message.

image

Your Github instruction also mentioned something about Docker and "The container uses these environment parameters for configuration". Do I need these, even if I just want to run locally from R? If so, how should I get sormas-postgres running?

I simply need a step-by-step instruction that works....

Thanks!

Jie

bernardsilenou commented 2 years ago

@jielab The error message is because R cannot connect to the sormas DB because there is none. If you want to run sormas-stats locally, then you must not have a docker instance. However, you first need to have sormas app installed and running on your machine. The easiest way to have sormas running on your PC is to set up the docker instance, you can get more information here https://github.com/hzi-braunschweig/SORMAS-Docker . Linux OS is better.

After having sormas running and testing that you can connect to the DB from R, then you can launch the sormas-stats app.

bernardsilenou commented 2 years ago

sormas app repo https://github.com/hzi-braunschweig/SORMAS-Project

jielab commented 2 years ago

Thanks, Bernard!

The SORMAS software is very powerful and comprehensive. But it is also quite complicated.

Is there a way to tease apart a couple of simple R script or package that could be used to draw the two plots shown in your paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9159465/)? I have a text file with detailed information for ~1,000 COVID-19 cases. I know who transmitted to whom at what date. I am looking for an easy-to-use R package to draw the transmission chain and estimate basic transmission dynamics parameters.

Thank you very much & best regards, Jie

image

image