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README.Rmd
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---
output: github_document
---
TODO:
- fix folde /data. Is needes? (now in buildignore)
- Remove get_anomalies_season, Nacho_workflow_demo.R, data-raw
and work_flow.R (now in buildignore)
- tests are failing (both get and evenness)
- examples fail, recheck
- Datasets (if any) need documentation.
- generar web con packege down
-
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# Bloomers
<!-- badges: start -->
[](https://github.com/EcologyR/templateRpackage/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/EcologyR/templateRpackage?branch=master)
`r badger::badge_lifecycle("experimental")`
`r badger::badge_repostatus("WIP")`
<!-- `r badger::badge_codefactor("ecologyr/templaterpackage")` -->
<!-- badges: end -->
The main objective of Bloomers package is to detect sharp changes in abundances for individual taxa in microbial communities.
## Installation
``` r
# install.packages("devtools")
devtools::install_github("EcologyR/Bloomers")
```
The code to create this package is available [here](https://github.com/EcologyR/Bloomers).
##The workflow of the bloomers package is summarized in the following graph
## Example
This is a basic example which shows you how to solve a common problem:
```{r example}
# library(templateRpackage)
## basic example code
```
What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
```{r cars}
summary(cars)
```
You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/v1/examples>.
Put here a plot representing blooming species and how we do detect anomalies
```{r plot.bloomers, echo = TRUE, eval = FALSE}
#plot(bloomersdata$pseudoabundance) #improve this example
#load("./data/bloomersdata.rda")
```{r pressure, echo = TRUE, eval = FALSE}
plot(pressure)
```
In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN.
## Citation
If using this package, please cite it:
```{r comment=NA}
#citation("Bloomers")
```
## Funding
The development of this software has been funded by Fondo Europeo de Desarrollo Regional (FEDER) and Consejería de Transformación Económica, Industria, Conocimiento y Universidades of Junta de Andalucía (proyecto US-1381388 led by Francisco Rodríguez Sánchez, Universidad de Sevilla).
