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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 that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures",
out.width = "100%"
)
```
# otndo
<!-- badges: start -->
[](https://www.repostatus.org/#wip)
[](https://www.tidyverse.org/lifecycle/#experimental)
[](https://github.com/mhpob/otndo/actions/workflows/R-CMD-check.yaml)
[](https://mhpob.r-universe.dev/otndo)
[](https://codecov.io/gh/mhpob/otndo)
<!-- badges: end -->
*entiendo* /ˌenˈtjendo/ [ˌẽn̪ˈt̪jẽn̪.̪o]\
Spanish, 1st person indicative; "*I understand*"
***otndo*** /ˌoʊˈtjendo/ [ˌoʊ̪ˈt̪jẽn̪.d̪o]\
English, bad pun; "*I understand (OTN data)*"
The purpose of `otndo` is to provide a high-level summary of your acoustic telemetry transmitter matches from the Ocean Tracking Network, all while putting the "network" back in "tracking network" by noting the related projects and investigators.
## Installation
You can install the most-up-to-date version from [R-universe](https://mhpob.r-universe.dev/otndo) or [GitHub](https://github.com/mhpob/otndo).
R-universe:
```{r eval=FALSE}
install.packages(
"otndo",
repos = c(
"https://mhpob.r-universe.dev",
"https://cloud.r-project.org"
)
)
```
GitHub:
```{r eval=FALSE}
# install.packages("remotes")
remotes::install_github("mhpob/otndo")
```
## Tag push summary example
This is a basic example of how you might use `otndo` to summarize your transmitter data:
```{r tag_push, eval=FALSE}
# Download some example data
td <- file.path(tempdir(), "otndo_test_files")
dir.create(td)
download.file(
paste0(
"https://members.oceantrack.org/data/repository/pbsm/detection-extracts/",
"pbsm_matched_detections_2018.zip/@@download/file"
),
destfile = file.path(td, "pbsm_matched_detections_2018.zip"),
mode = "wb"
)
unzip(file.path(td, "pbsm_matched_detections_2018.zip"),
exdir = td
)
# Make a tag push summary
library(otndo)
make_tag_push_summary(
matched = file.path(td, "pbsm_matched_detections_2018.csv")
)
```
You will get a report in your working directory with a few goodies!
A summary of the number of matched individuals and detections by researcher and project:
The overall extent of the projects to which your tags have been matched:
When your fish were heard in each project:
The ever-ubiquitous "abacus plot", showing when each tag was heard, colored by project:
An interactive map showing detections by receiver:
A general estimate of the number of transmitters that were active at a given date:
## Receiver push summary example
This is a basic example of how you might use `otndo` to summarize your receiver data:
```{r rec_push, eval=FALSE}
# Download some example data
## Deployment metadata
download.file(
paste0(
"https://members.oceantrack.org/data/repository/pbsm/data-and-metadata/",
"archived-records/2018/pbsm-instrument-deployment-short-form-2018.xls/@@download/file"
),
destfile = file.path(td, "pbsm-instrument-deployment-short-form-2018.xls"),
mode = "wb"
)
## Qualified detections
download.file(
paste0(
"https://members.oceantrack.org/data/repository/pbsm/detection-extracts/",
"pbsm_qualified_detections_2018.zip/@@download/file"
),
destfile = file.path(td, "pbsm_qualified_detections_2018.zip")
)
unzip(file.path(td, "pbsm_qualified_detections_2018.zip"),
exdir = td
)
## Unqualified detections
download.file(
paste0(
"https://members.oceantrack.org/data/repository/pbsm/detection-extracts/",
"pbsm_unqualified_detections_2018.zip/@@download/file"
),
destfile = file.path(td, "pbsm_unqualified_detections_2018.zip")
)
unzip(file.path(td, "pbsm_unqualified_detections_2018.zip"),
exdir = td
)
# Make a receiver push summary
make_receiver_push_summary(
qualified = file.path(td, "pbsm_qualified_detections_2018.csv"),
unqualified = file.path(td, "pbsm_unqualified_detections_2018.csv"),
deployment = file.path(td, "pbsm-instrument-deployment-short-form-2018.xls")
)
```
A summary of the number of matched individuals and detections by researcher and project:
The overall extent of the projects associated with the tags your receivers have heard:
When your receivers heard each project's fish:
A Gantt chart of your receivers' deployments:
The number of detections and individuals per receiver:
An interactive map showing detections by receiver:
A summary of your unmatched detections, including those that are likely false...
...and those that may be real!
A summary of when the unmatched detections occurred, by receiver:
## Getting in contact
If something doesn't work the way it should or if you just need a little help, feel free to [open an issue on GitHub](https://github.com/mhpob/otndo/issues) or [email me (Mike O'Brien: [email protected]) directly](mailto:[email protected]).