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updating readme
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@wcornwell
wcornwell committed Jul 7, 2024
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12 changes: 8 additions & 4 deletions README.Rmd
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Expand Up @@ -18,9 +18,11 @@ knitr::opts_chunk$set(

<!-- badges: start -->
[![R-CMD-check](https://github.com/traitecoevo/infinitylists/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/traitecoevo/infinitylists/actions/workflows/R-CMD-check.yaml)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12677594.svg)](https://doi.org/10.5281/zenodo.12677594)
[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
<!-- badges: end -->

This shiny-based application allows users to extract species occurrence data from the Atlas of Living Australia (ALA) and generate a species list for any defined area. All records associated with either a physical voucher (stored in Australian herbaria or museums), or a photographic voucher or audio file uploaded to iNaturalist are extracted. For each species within the defined area, the application will return voucher type, number of vouchers, date of the most recent voucher, spatial coordinates, voucher location, and the voucher collector. Records are displayed both in a table and on a map, and are downloadable as a CSV. The app is currently using data downloaded from the ALA on 1st July 2024.
This shiny-based application allows users to extract species occurrence data from the Atlas of Living Australia (ALA) and generate a species list for any defined area. All records associated with either a physical voucher (stored in Australian herbaria or museums), or a photographic voucher or audio file uploaded to iNaturalist are extracted. For each species within the defined area, the application will return voucher type, number of vouchers, date of the most recent voucher, spatial coordinates, voucher location, and the voucher collector. Records are displayed both in a table and on a map, and are downloadable as a CSV. The app is currently using data downloaded from the ALA on 5 July 2024.

## Which records are returned?

Expand All @@ -33,7 +35,7 @@ The app can be accessed here: https://unsw.shinyapps.io/infinitylists/

## Local installation

You can install the development version of 'infinitylists' from [GitHub](https://github.com/traitecoevo/infinitylists) with:
You can install and run a local version of `infinitylists` from [GitHub](https://github.com/traitecoevo/infinitylists). This allows more flexibility for loading taxa that are not automatically loaded in the web app. The code to do this is:

```{r}
# install.packages("remotes")
Expand All @@ -48,7 +50,7 @@ infinitylistApp()

## Adding new taxa

infinitylists comes with 5 taxa loaded to start with: plants, butterflies, cicadas, marsupials, and dragonflies + damselflies. If you want to add another taxon, you'll need to download the data first via the [galah interface](https://github.com/AtlasOfLivingAustralia/galah-R) to the ALA. The function `download_ala_obs` will download the data and put it into a directory where infinitylists can find it. The value for `taxon` needs to be a [valid taxonomic group as recognized by the ALA](https://support.ala.org.au/support/solutions/articles/6000261677-taxonomy-a-species-filing-system). The download step is fast for taxa with small number of observations in ALA and slower for taxa with millions of observations.
`infinitylists` comes with 5 taxa loaded to start with: plants, butterflies, cicadas, marsupials, and dragonflies + damselflies. If you want to add another taxon, you'll need to download the data first via the [galah interface](https://github.com/AtlasOfLivingAustralia/galah-R) to the ALA. The function `download_ala_obs` will download the data and put it into a directory where infinitylists can find it. The value for `taxon` needs to be a [valid taxonomic group as recognized by the ALA](https://support.ala.org.au/support/solutions/articles/6000261677-taxonomy-a-species-filing-system). The download step is fast for taxa with small number of observations in ALA and slower for taxa with millions of observations.

```{r}
Expand All @@ -69,4 +71,6 @@ infinitylistApp()

## Why did I get disconnected from the server?

If infinitylists is left open but idle in your browser for too long, you will be disconnected from the server. Applying the *Use my location* filter without having given your browser access to your current location will also disconnect you from the server. If this occurs, please amend your settings.
If `infinitylists` is left open but idle in your browser for too long, you will be disconnected from the server.

Applying the *Use my location* filter without first having given your browser access to your current location will also disconnect you from the server. If this occurs, please amend your settings and try again.
24 changes: 14 additions & 10 deletions README.md
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Expand Up @@ -6,6 +6,8 @@
<!-- badges: start -->

[![R-CMD-check](https://github.com/traitecoevo/infinitylists/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/traitecoevo/infinitylists/actions/workflows/R-CMD-check.yaml)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12677594.svg)](https://doi.org/10.5281/zenodo.12677594)
[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
<!-- badges: end -->

This shiny-based application allows users to extract species occurrence
Expand All @@ -17,8 +19,7 @@ species within the defined area, the application will return voucher
type, number of vouchers, date of the most recent voucher, spatial
coordinates, voucher location, and the voucher collector. Records are
displayed both in a table and on a map, and are downloadable as a CSV.
The app is currently using data downloaded from the ALA on 1st July
2024.
The app is currently using data downloaded from the ALA on 5 July 2024.

## Which records are returned?

Expand All @@ -36,8 +37,10 @@ The app can be accessed here: <https://unsw.shinyapps.io/infinitylists/>

## Local installation

You can install the development version of ‘infinitylists’ from
[GitHub](https://github.com/traitecoevo/infinitylists) with:
You can install and run a local version of `infinitylists` from
[GitHub](https://github.com/traitecoevo/infinitylists). This allows more
flexibility for loading taxa that are not automatically loaded in the
web app. The code to do this is:

``` r
# install.packages("remotes")
Expand All @@ -51,7 +54,7 @@ infinitylistApp()

## Adding new taxa

infinitylists comes with 5 taxa loaded to start with: plants,
`infinitylists` comes with 5 taxa loaded to start with: plants,
butterflies, cicadas, marsupials, and dragonflies + damselflies. If you
want to add another taxon, you’ll need to download the data first via
the [galah interface](https://github.com/AtlasOfLivingAustralia/galah-R)
Expand All @@ -78,8 +81,9 @@ infinitylistApp()

## Why did I get disconnected from the server?

If infinitylists is left open but idle in your browser for too long, you
will be disconnected from the server. Applying the *Use my location*
filter without having given your browser access to your current location
will also disconnect you from the server. If this occurs, please amend
your settings.
If `infinitylists` is left open but idle in your browser for too long,
you will be disconnected from the server.

Applying the *Use my location* filter without first having given your
browser access to your current location will also disconnect you from
the server. If this occurs, please amend your settings and try again.

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