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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit this file -->
<!-- Very likely that you'll need to run rmarkdown::render('readme.rmd') rather than the knit button. -->
<!-- readme.html will be created and is unnecessary, so delete that. -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# matos
<!-- badges: start -->
[![Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![R-CMD-check](https://github.com/mhpob/matos/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mhpob/matos/actions/workflows/R-CMD-check.yaml)
[![matos status badge](https://mhpob.r-universe.dev/badges/matos)](https://mhpob.r-universe.dev/matos)
[![codecov](https://codecov.io/gh/mhpob/matos/graph/badge.svg?token=TFI406AVHP)](https://codecov.io/gh/mhpob/matos)
<!-- badges: end -->
{matos} is an API to the [Mid-Atlantic Acoustic Telemetry Observing System website](https://matos.asascience.com/), powered by a suite of [httr](https://httr.r-lib.org/) and [rvest](https://rvest.tidyverse.org/) functions.
Please note that you will need a MATOS account, [which you can sign up for here](https://matos.asascience.com/account/signup), in order to interface with any project-specific files.
## Installation
You can install the most-up-to-date version from [R-universe](https://mhpob.r-universe.dev/matos) or [GitHub](https://github.com/mhpob/matos).
R-universe:
```{r eval=FALSE}
install.packages(
"matos",
repos = c(
"https://mhpob.r-universe.dev",
"https://cloud.r-project.org"
)
)
```
GitHub:
```{r eval=FALSE}
# install.packages("remotes")
remotes::install_github("mhpob/matos")
```
## Quick start
There are functions to list, download, and upload files to MATOS -- check out the vignettes for some worked examples. If you don't want to read and just want to get your detection files, here are the bare bones to get you up and running:
### `list_my_projects`
Logs you into the MATOS database and pings each project in turn to see if you have read/write access, listing those that you do.
### `list_extract_files`
Once you have a project name or number from `list_my_projects`, use this function to list all of the files containing Ocean Tracking Network matched detections.
### `get_extract_file`
Now that you have the URLs of the detection extract files from `list_extract_files`, put it in here to download the file to your computer.
## Development
As is noted above, this package is undergoing a ton of development. If there's something I missed, please [open an issue on GitHub](https://github.com/mhpob/matos/issues) or [email me (Mike O'Brien: obrien@umces.edu) directly](mailto:obrien@umces.edu).