From d8e00e36f8ebe0513e937a2d2b20d0535101c53d Mon Sep 17 00:00:00 2001 From: Will Cornwell Date: Sun, 7 Jul 2024 16:11:45 +1000 Subject: [PATCH] updating readme --- README.Rmd | 12 ++++++++---- README.md | 24 ++++++++++++++---------- 2 files changed, 22 insertions(+), 14 deletions(-) diff --git a/README.Rmd b/README.Rmd index ed184a6..21e7e72 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,9 +18,11 @@ 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) +[![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) -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? @@ -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") @@ -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} @@ -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. diff --git a/README.md b/README.md index 8d296fc..25825d8 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,8 @@ [![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) This shiny-based application allows users to extract species occurrence @@ -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? @@ -36,8 +37,10 @@ The app can be accessed here: ## 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") @@ -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) @@ -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.