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Remove sapply; update README
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@willgearty
willgearty committed Oct 23, 2024
1 parent 809f854 commit caf5f65
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61 changes: 61 additions & 0 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,32 @@ rredlist
========

```{r echo=FALSE}
library("knitr")
library("rredlist")
hook_output <- knitr::knit_hooks$get("output")
knitr::knit_hooks$set(output = function(x, options) {
lines <- options$output.lines
if (is.null(lines)) {
return(hook_output(x, options)) # pass to default hook
}
x <- unlist(strsplit(x, "\n"))
more <- "..."
if (length(lines)==1) { # first n lines
if (length(x) > lines) {
# truncate the output, but add ....
x <- c(head(x, lines), more)
}
} else {
x <- c(if (abs(lines[1])>1) more else NULL,
x[lines],
if (length(x)>lines[abs(length(lines))]) more else NULL
)
}
# paste these lines together
x <- paste(c(x, ""), collapse = "\n")
hook_output(x, options)
})
knitr::opts_chunk$set(
warning = FALSE,
message = FALSE,
Expand All @@ -10,6 +36,7 @@ knitr::opts_chunk$set(
)
```

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/663_status.svg)](https://github.com/ropensci/software-review/issues/663)
[![Project Status: 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)
[![cran version](https://www.r-pkg.org/badges/version/rredlist)](https://cran.r-project.org/package=rredlist)
[![R-check](https://github.com/ropensci/rredlist/actions/workflows/R-check.yml/badge.svg)](https://github.com/ropensci/rredlist/actions/workflows/R-check.yml)
Expand All @@ -34,6 +61,40 @@ remotes::install_github("ropensci/rredlist")
install.packages("rredlist", repos = "https://ropensci.r-universe.dev/")
```

## Authentication

Use of this package requires an IUCN API key which can be acquired at https://api.iucnredlist.org/users/sign_up. There is a helper function to help you get the key and store it properly:

```{r eval=FALSE}
rredlist::rl_use_iucn()
```

**Keep this key private.** You can pass the key in to each function via the key parameter, but it’s better to store the key either as a environment variable (`IUCN_REDLIST_KEY`) or an R option (`iucn_redlist_key`) - we recommend using the former option. Note that there is not a default API key that is used as a fallback, and the package will not function without providing/storing your own API key.

## Example usage

### Loading the package
```{r}
library("rredlist")
```

### Search for assessments for a particular species
```{r output.lines=1:10}
rl_species("Gorilla", "gorilla")$assessments
```

### Search for assessments that recommend particular conservation actions

#### Get a list of all conservation actions
```{r output.lines=1:10}
rl_actions()
```

#### Return assessments with a particular conservation action
```{r output.lines=1:10}
rl_actions("2_2", all = FALSE)$assessments
```

## Meta

* Please [report any issues or bugs](https://github.com/ropensci/rredlist/issues).
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73 changes: 73 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ rredlist
========



[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/663_status.svg)](https://github.com/ropensci/software-review/issues/663)
[![Project Status: 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)
[![cran version](https://www.r-pkg.org/badges/version/rredlist)](https://cran.r-project.org/package=rredlist)
Expand Down Expand Up @@ -29,6 +30,78 @@ remotes::install_github("ropensci/rredlist")
install.packages("rredlist", repos = "https://ropensci.r-universe.dev/")
```

## Authentication

Use of this package requires an IUCN API key which can be acquired at https://api.iucnredlist.org/users/sign_up. There is a helper function to help you get the key and store it properly:


``` r
rredlist::rl_use_iucn()
```

**Keep this key private.** You can pass the key in to each function via the key parameter, but it’s better to store the key either as a environment variable (`IUCN_REDLIST_KEY`) or an R option (`iucn_redlist_key`) - we recommend using the former option. Note that there is not a default API key that is used as a fallback, and the package will not function without providing/storing your own API key.

## Example usage

### Loading the package

``` r
library("rredlist")
```

### Search for assessments for a particular species

``` r
rl_species("Gorilla", "gorilla")$assessments
#> year_published latest sis_taxon_id url assessment_id scopes
#> 1 2016 FALSE 9404 https://www.iucnredlist.org/species/9404/17963949 17963949 Global, 1
#> 2 2016 FALSE 9404 https://www.iucnredlist.org/species/9404/102330408 102330408 Global, 1
#> 3 2018 TRUE 9404 https://www.iucnredlist.org/species/9404/136250858 136250858 Global, 1
#> 4 2008 FALSE 9404 https://www.iucnredlist.org/species/9404/12983787 12983787 Global, 1
#> 5 2007 FALSE 9404 https://www.iucnredlist.org/species/9404/12983966 12983966 Global, 1
#> 6 2000 FALSE 9404 https://www.iucnredlist.org/species/9404/12983737 12983737 Global, 1
#> 7 1996 FALSE 9404 https://www.iucnredlist.org/species/9404/12983764 12983764 Global, 1
#> 8 1994 FALSE 9404 https://www.iucnredlist.org/species/9404/12984167 12984167 Global, 1
#> 9 1990 FALSE 9404 https://www.iucnredlist.org/species/9404/12984186 12984186 Global, 1
...
```

### Search for assessments that recommend particular conservation actions

#### Get a list of all conservation actions

``` r
rl_actions()
#> $conservation_actions
#> en code
#> 1 Land/water protection 1
#> 2 Site/area protection 1_1
#> 3 Resource & habitat protection 1_2
#> 4 Land/water management 2
#> 5 Site/area management 2_1
#> 6 Invasive/problematic species control 2_2
#> 7 Habitat & natural process restoration 2_3
#> 8 Species management 3
...
```

#### Return assessments with a particular conservation action

``` r
rl_actions("2_2", all = FALSE)$assessments
#> year_published latest sis_taxon_id url assessment_id code
#> 1 2019 TRUE 132523146 https://www.iucnredlist.org/species/132523146/497499 497499 2_2
#> 2 2019 TRUE 10767 https://www.iucnredlist.org/species/10767/498370 498370 2_2
#> 3 2013 TRUE 1078 https://www.iucnredlist.org/species/1078/498639 498639 2_2
#> 4 2019 TRUE 132521900 https://www.iucnredlist.org/species/132521900/498826 498826 2_2
#> 5 2020 FALSE 1086 https://www.iucnredlist.org/species/1086/499235 499235 2_2
#> 6 2019 TRUE 1117 https://www.iucnredlist.org/species/1117/500918 500918 2_2
#> 7 2019 TRUE 11797 https://www.iucnredlist.org/species/11797/503908 503908 2_2
#> 8 2021 TRUE 12124 https://www.iucnredlist.org/species/12124/505402 505402 2_2
#> 9 2019 TRUE 12695 https://www.iucnredlist.org/species/12695/507698 507698 2_2
...
```

## Meta

* Please [report any issues or bugs](https://github.com/ropensci/rredlist/issues).
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4 changes: 2 additions & 2 deletions tests/testthat/test-rl_threats.R
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Expand Up @@ -79,8 +79,8 @@ test_that("secret query parameters work", {
})

aa_filt <- subset(aa$assessments, latest & year_published == "2017" &
sapply(aa$assessments$scopes,
function(df) "2" %in% df$code))
unlist(lapply(aa$assessments$scopes,
function(df) "2" %in% df$code)))
expect_equal(nrow(aa_filt), nrow(bb$assessments))
})

Expand Down

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