-
Notifications
You must be signed in to change notification settings - Fork 1
/
README.Rmd
49 lines (34 loc) · 1.92 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
```{r, include=FALSE}
devtools::load_all(".")
```
# Automated workflow for incorporation and evaluation of data uncertainty in ecological networks with __autoLIMR__
<!-- badges: start -->
[![R-CMD-check](https://github.com/gemmagerber/autoLIMR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/gemmagerber/autoLIMR/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/gemmagerber/autoLIMR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/gemmagerber/autoLIMR?branch=main)
[![test-coverage](https://github.com/gemmagerber/autoLIMR/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/gemmagerber/autoLIMR/actions/workflows/test-coverage.yaml)
[![Style](https://github.com/gemmagerber/autoLIMR/actions/workflows/style.yaml/badge.svg)](https://github.com/gemmagerber/autoLIMR/actions/workflows/style.yaml)
<!-- badges: end -->
![autoLIMR](vignettes/images/autoLIMR_logo.png)
The goal of __autoLIMR__ is to facilitate the inclusion of data uncertainty in ecological models. __autoLIMR__ does this by:
1. Automated construction of input files from network data, directly compatible with R packages [LIM](https://CRAN.R-project.org/package=LIM) and
[limSolve](https://CRAN.R-project.org/package=limSolve)
2. Calculation of multiple plausible network configuration using linear inverse modelling and Markov Chain Monte Carlo (LIM-MCMC), and
3. Evaluation of model quality using several visual and statistical MCMC convergence diagnostics.
## Installation
You can install the latest version of __autoLIMR__ from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("gemmagerber/autoLIMR")
```