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update readme file
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tmesaglio committed Jul 1, 2024
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6 changes: 3 additions & 3 deletions README.Rmd
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Expand Up @@ -20,11 +20,11 @@ knitr::opts_chunk$set(
[![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)
<!-- badges: end -->

This shiny-based application allows users to extract plant 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 museum), a sound file, or a photographic voucher (stored in 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.
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.

## Use the app

The app can be accessed here:https://posit-connect-unsw.intersect.org.au/infinitylists/
The app can be accessed here: https://unsw.shinyapps.io/infinitylists/


## Local Installation
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## Adding new taxa

InfinityList 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 into a directory where infinitylistapp 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}
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17 changes: 7 additions & 10 deletions README.md
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<!-- 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)
[![Codecov test
coverage](https://codecov.io/gh/traitecoevo/infinitylists/branch/master/graph/badge.svg)](https://app.codecov.io/gh/traitecoevo/infinitylists?branch=master)
<!-- badges: end -->

This shiny-based application allows users to extract plant occurrence
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 museum), a sound file, or a
photographic voucher (stored in iNaturalist) are extracted. For each
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.

## Use the app

The app can be accessed
here: https://unsw.shinyapps.io/infinitylists/
The app can be accessed here: <https://unsw.shinyapps.io/infinitylists/>

## Local Installation

Expand All @@ -42,12 +39,12 @@ infinitylistApp()

## Adding new taxa

InfinityList comes with 5 taxa loaded to start with: plants,
butterflies, cicadas, marsupials, and dragonflies+damselflies. If you
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 into a directory where infinitylistapp can find it. The value for
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
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