-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.Rmd
57 lines (36 loc) · 2.94 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
48
49
50
51
52
53
54
55
56
57
---
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/",
out.width="100%"
)
```
# qraLm <a href='https://github.com/WorldHealthOrganization/qraLm/docs/'><img src='man/figures/hex-qraLm.png' align="right" height="80" /></a>
The qraLm R package is designed to conduct quantitative risk assessments (QRA) specifically for *Listeria monocytogenes* in various food products, including frozen vegetables, ready-to-eat (RTE) diced cantaloupe, and cold-smoked fish. The package was developed as part of the work under the [Joint FAO/WHO Expert Meetings on Microbiological Risk Assessment (JEMRA)](https://www.who.int/publications/m/item/jemra-of-listeria-monocytogenes-in-foods).
## Key Features:
- Dose-Response Models: The package includes models to assess the risk based on different strain virulence and population susceptibility (age, health conditions).
- Monte Carlo Simulations: It supports simulations to estimate risks at various stages of the food production chain, from processing to consumer handling practices.
- Specific Food Pathways: Different modules represent distinct pathways for contamination and risk for each food type, such as blanching, packaging, and defrosting in frozen vegetables, or cross-contamination and processing stages in cold-smoked fish and cantaloupe.
- Shiny Application: A built-in Shiny app allows users to interactively simulate risk assessments for different food types and contamination scenarios.
## Installation
- You can install `qraLm` from [GitHub: https://github.com/WorldHealthOrganization/qraLm](https://github.com/WorldHealthOrganization/qraLm)
using the `devtools` package, with the R code below.
- You must first install the `doseresponsemodels` package from [github: https://github.com/WorldHealthOrganization/DRLm/](https://github.com/WorldHealthOrganization/DRLm/), which implements the dose-response models for Listeria monocytogenes.
- For Windows users it is recommended to install
[Rtools: https://cran.r-project.org/bin/windows/Rtools/](https://cran.r-project.org/bin/windows/Rtools/) before.
- The packages on which `qraLm` depends are: `Hmisc`, `extraDistr`, `mc2d`, `matrixStats`, `DT`, `dplyr`,
`ggplot2`, `plotly`, `doseresponsemodels` and `BH`; you should install them before installing `qraLm`.
```{r, eval=FALSE}
if (!require("devtools")) install.packages("devtools")
devtools::install_github("https://github.com/WorldHealthOrganization/DRLm/")
devtools::install_github("https://github.com/WorldHealthOrganization/qraLm")
```
## Using qraLm
You can find the vignettes at the `qraLm` website: [https://github.com/WorldHealthOrganization/qraLm/](https://github.com/WorldHealthOrganization/qraLm/).
## Reporting bugs
You can report bugs at: [https://github.com/WorldHealthOrganization/qraLm/issues](https://github.com/WorldHealthOrganization/qraLm/issues).