Documentation Project

https://docs.ropensci.org/rredlist/
Admin
This repository contains general documentation, articles, news, and reference materials.
Tokens:51,340
Snippets:375
Trust Score:9.8
Update:4 months ago
Show doc for...
Tokens:
Raw
### Example: Get all comprehensive groups

Source: https://docs.ropensci.org/rredlist/reference/rl_comp_groups.html

This example demonstrates how to call `rl_comp_groups` without any arguments to retrieve a list of all available comprehensive groups.

```R
# Get list of all comprehensive groups
rl_comp_groups()
```

--------------------------------

### Example: Get assessment summary for a specific group

Source: https://docs.ropensci.org/rredlist/reference/rl_comp_groups.html

This example shows how to fetch the assessment summary for a specific comprehensive group by providing its name, such as 'seasnakes'.

```R
# Get assessment summary for sea snakes
rl_comp_groups('seasnakes')
```

--------------------------------

### Example: Get Fungi Kingdom Assessment Summary

Source: https://docs.ropensci.org/rredlist/reference/rl_kingdom.html

Demonstrates how to call `rl_kingdom` to get assessment data for the 'Fungi' kingdom and check the number of assessments returned.

```R
if (FALSE) { # \dontrun{
# Get assessment summary for kingdom
ex1 <- rl_kingdom(kingdom = "Fungi")
nrow(ex1$assessments)
} # }
```

--------------------------------

### Get All Conservation Actions

Source: https://docs.ropensci.org/rredlist/reference/rl_actions.html

This example demonstrates how to retrieve a list of all available conservation actions by calling `rl_actions()` without any arguments. This is useful for understanding the available codes.

```R
# Get list of all conservation actions
rl_actions()
```

--------------------------------

### Get list of all systems

Source: https://docs.ropensci.org/rredlist/reference/rl_systems.html

Retrieves a list of all available ecological systems from the IUCN Red List API. This is a basic usage example.

```r
rl_systems()
```

--------------------------------

### Get Assessment Details Example

Source: https://docs.ropensci.org/rredlist/reference/rl_assessment.html

Demonstrates how to retrieve and access specific details (red list category code and systems) for a given assessment ID.

```R
if (FALSE) { # \dontrun{
# Get assessment details for Fratercula arctica
ex1 <- rl_assessment(id = 166290968)
ex1$red_list_category$code
ex1$systems
} # }
```

--------------------------------

### Example: Sign up for an IUCN API Key

Source: https://docs.ropensci.org/rredlist/reference/rl_use_iucn.html

Demonstrates how to initiate the process of signing up for an IUCN Red List API key. This example is typically run interactively and requires user input on the IUCN website.

```r
if (FALSE) { # \dontrun{
# Sign up for an API key
rl_use_iucn()
} # }
```

--------------------------------

### Clone Repository Example

Source: https://docs.ropensci.org/rredlist/CONTRIBUTING.html

Clone your forked version of the rredlist repository to your local machine.

```bash
git clone https://github.com/<yourgithubusername>/rredlist.git
```

--------------------------------

### Get count of species with assessments

Source: https://docs.ropensci.org/rredlist/reference/rl_sp_count.html

This example shows how to get the count of species that have assessments in the IUCN Red List. It requires an active internet connection and potentially an IUCN API token if not already configured.

```r
if (FALSE) { # \dontrun{
# Get count of species with assessments
rl_sp_count()
} # }
```

--------------------------------

### Load rredlist and microbenchmark Libraries

Source: https://docs.ropensci.org/rredlist/articles/benchmarks.html

Load the necessary libraries for benchmarking. Ensure these libraries are installed before running.

```r
library(rredlist)
library(microbenchmark)
```

--------------------------------

### Get Assessments with Specific Conservation Action

Source: https://docs.ropensci.org/rredlist/reference/rl_actions.html

This example shows how to query for species assessments that require a specific conservation action, using the code '3_2' for 'Species recovery'. This helps in identifying species that need targeted conservation efforts.

```R
# Get assessments with Species recovery conservation action needed
rl_actions("3_2")
```

--------------------------------

### Install rredlist from CRAN

Source: https://docs.ropensci.org/rredlist/index.html

Install the stable version of the rredlist package from CRAN.

```r
install.packages("rredlist")
```

--------------------------------

### Install rredlist Development Version

Source: https://docs.ropensci.org/rredlist/index.html

Install the latest development version of the rredlist package from GitHub or an R-universe repository.

```r
remotes::install_github("ropensci/rredlist")
```

```r
install.packages("rredlist", repos = "https://ropensci.r-universe.dev/")
```

--------------------------------

### Get Stable Population Trend Assessments

Source: https://docs.ropensci.org/rredlist/reference/rl_pop_trends.html

This example demonstrates how to filter and retrieve only the population trend assessments that are marked as 'stable'. The code '2' is used as the filter.

```r
rl_pop_trends("2")
```

--------------------------------

### Add Upstream Remote Example

Source: https://docs.ropensci.org/rredlist/CONTRIBUTING.html

Add the official rredlist repository as an upstream remote to track changes.

```bash
git remote add upstream https://github.com/ropensci/rredlist.git
```

--------------------------------

### Set up IUCN API Key

Source: https://docs.ropensci.org/rredlist/index.html

Use the helper function to get and store your IUCN API key for package authentication. Ensure your key is kept private.

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

--------------------------------

### Get List of All Habitats

Source: https://docs.ropensci.org/rredlist/reference/rl_habitats.html

Call `rl_habitats()` without any arguments to retrieve a list of all available habitats.

```r
rl_habitats()
```

--------------------------------

### Get all growth forms

Source: https://docs.ropensci.org/rredlist/reference/rl_growth_forms.html

Retrieves a list of all available growth forms. This is useful for understanding the available categories.

```r
if (FALSE) { # \dontrun{
# Get list of all growth forms
rl_growth_forms()
# Get assessment summary for lichens
rl_growth_forms("LC")
} # }
```

--------------------------------

### Get assessment summary for a specific scope

Source: https://docs.ropensci.org/rredlist/reference/rl_scopes.html

Use the 'code' argument to specify a particular scope and retrieve its assessment summary. This example uses the code for the Gulf of Mexico.

```r
rl_scopes(code = "45433062")
```

--------------------------------

### Get Assessments for a Specific Habitat

Source: https://docs.ropensci.org/rredlist/reference/rl_habitats.html

Use the `code` argument to specify a habitat code (e.g., "12" for Marine Intertidal) to get its assessments.

```r
rl_habitats("12")
```

--------------------------------

### Get assessment summary for an order

Source: https://docs.ropensci.org/rredlist/reference/rl_order.html

Retrieves the assessment summary for the specified order. Use this to get a list of all assessments for a given taxonomic order.

```r
if (FALSE) { # \dontrun{
# Get assessment summary for order
ex1 <- rl_order(order = "Apiales")
nrow(ex1$assessments)
} # }
```

--------------------------------

### Get SIS Assessment Summary

Source: https://docs.ropensci.org/rredlist/reference/rl_sis.html

Fetches the assessment summary for a given species ID from the IUCN SIS. The output is parsed into a list by default. This example demonstrates how to retrieve the data and check the number of assessments.

```r
if (FALSE) { # \dontrun{
# Get assessment summary for species
ex1 <- rl_sis(id = 9404)
nrow(ex1$assessments)
} # }
```

--------------------------------

### Helper to get and save IUCN API key

Source: https://docs.ropensci.org/rredlist/reference/index.html

Use `rl_use_iucn()` as a helper function to get and save your IUCN API key.

```r
rl_use_iucn()
```

--------------------------------

### Get the Red List version

Source: https://docs.ropensci.org/rredlist/reference/index.html

Use `rl_version()` to retrieve the current version of the Red List data.

```r
rl_version()
```

--------------------------------

### Benchmark: Get Species Count

Source: https://docs.ropensci.org/rredlist/articles/benchmarks.html

Compares the performance of rl_sp_count() and rl_sp_count_() for retrieving species counts. Both functions are tested 10 times.

```r
microbenchmark(
  rl_sp_count(),
  rl_sp_count_(),
  times = 10
)
```

--------------------------------

### Install Older rredlist Version for API v3

Source: https://docs.ropensci.org/rredlist/articles/rredlist.html

Install a specific older version (<= 0.7.1) of the rredlist package to use the now-defunct version 3 of the IUCN Red List API. This can be done from the CRAN archive or an r-universe repository.

```r
# From CRAN archive
remotes::install_version("rredlist", version = "0.7.1")

# From r-universe
remotes::install_version("rredlist", version = "0.7.1",
                         repos = "https://ropensci.r-universe.dev/")
```

--------------------------------

### Get all threats

Source: https://docs.ropensci.org/rredlist/reference/rl_threats.html

Call `rl_threats()` without any arguments to retrieve a list of all available threat codes.

```r
rl_threats()
```

--------------------------------

### Load Required R Packages

Source: https://docs.ropensci.org/rredlist/articles/research_workflows.html

Loads the rredlist, dplyr, ggplot2, and patchwork packages. Ensure these packages are installed before running.

```r
library(rredlist)
library(dplyr)
library(ggplot2)
library(patchwork)
```

--------------------------------

### Get List of All Countries

Source: https://docs.ropensci.org/rredlist/reference/rl_countries.html

This snippet demonstrates how to retrieve a list of all countries for which Red List assessments are available. Ensure you have an internet connection.

```R
if (FALSE) { # \dontrun{
# Get list of all countries
rl_countries()
}

```

--------------------------------

### Get all stresses

Source: https://docs.ropensci.org/rredlist/reference/rl_stresses.html

To retrieve a list of all available stresses, call the `rl_stresses()` function without any arguments.

```r
rl_stresses()
```

--------------------------------

### Get assessment summary for a class

Source: https://docs.ropensci.org/rredlist/reference/rl_class.html

Retrieves the assessment summary for the 'Mammalia' class. The number of assessments is then printed.

```r
if (FALSE) { # \dontrun{
# Get assessment summary for class
ex1 <- rl_class(class = "Mammalia")
nrow(ex1$assessments)
} # }
```

--------------------------------

### Get all use and trade assessments

Source: https://docs.ropensci.org/rredlist/reference/rl_use_and_trade.html

Fetches all available use and trade assessments. This function requires no arguments to retrieve the complete list.

```r
rl_use_and_trade()
```

--------------------------------

### Get a list of all FAO regions

Source: https://docs.ropensci.org/rredlist/reference/rl_faos.html

Demonstrates how to call `rl_faos()` without any arguments to retrieve a list of all available FAO regions. This is useful for identifying region codes.

```r
# Get a list of all scopes
rl_faos()
```

--------------------------------

### Get IUCN Red List API Version

Source: https://docs.ropensci.org/rredlist/reference/rl_api_version.html

Fetches the current version of the IUCN Red List API. Requires an API key if not already set.

```r
rl_api_version()
```

--------------------------------

### Get All Red List Categories

Source: https://docs.ropensci.org/rredlist/reference/rl_categories.html

Fetches all available Red List categories when no specific code is provided. This is useful for exploring the available categories.

```R
rl_categories()
```

--------------------------------

### Retrieve all stress assessments with pagination handled internally

Source: https://docs.ropensci.org/rredlist/reference/rl_stresses.html

This example demonstrates how to fetch all stress assessments. The `all = TRUE` argument ensures that all pages of results are retrieved and combined. The `quiet = FALSE` argument (default) will show progress for multi-page downloads.

```r
rl_stresses(all = TRUE, quiet = FALSE)
```

--------------------------------

### Get assessment summary for a specific stress

Source: https://docs.ropensci.org/rredlist/reference/rl_stresses.html

To get the assessment summary for a particular stress, provide its corresponding code to the `rl_stresses()` function. For example, to retrieve information on 'Ecosystem degradation', use the code '1_2'.

```r
rl_stresses("1_2")
```

--------------------------------

### Get assessment summary for a specific threat

Source: https://docs.ropensci.org/rredlist/reference/rl_threats.html

To get assessment summaries for a particular threat, provide its corresponding code. For example, to find assessments related to intentional hunting and trapping, use the code "5_1_1". Note that sub-threats require separate requests.

```r
rl_threats("5_1_1")
```

--------------------------------

### Get assessment summary for phylum

Source: https://docs.ropensci.org/rredlist/reference/rl_phylum.html

Retrieves conservation assessment summaries for a specified phylum. Ensure you have the 'rredlist' package installed and potentially an IUCN API key configured if required by the API.

```R
if (FALSE) { # \dontrun{
# Get assessment summary for phylum
ex1 <- rl_phylum(phylum = "Annelida`")
nrow(ex1$assessments)
} # }
```

--------------------------------

### Benchmark: Taxonomic Lookup with Query (~40 Pages)

Source: https://docs.ropensci.org/rredlist/articles/benchmarks.html

Compares the performance of rl_family() and rl_family_() when querying for a family with approximately 40 pages of results ('Tyrannidae'). The 'quiet = TRUE' argument is used, and functions are tested 10 times.

```r
microbenchmark(
  rl_family("Tyrannidae", quiet = TRUE),
  rl_family_("Tyrannidae", quiet = TRUE),
  times = 10
)
```

--------------------------------

### Benchmark: Taxonomic Lookup with Query (~10 Pages)

Source: https://docs.ropensci.org/rredlist/articles/benchmarks.html

Compares the performance of rl_family() and rl_family_() when querying for a family with approximately 10 pages of results ('Corvidae'). The 'quiet = TRUE' argument is used, and functions are tested 10 times.

```r
microbenchmark(
  rl_family("Corvidae", quiet = TRUE),
  rl_family_("Corvidae", quiet = TRUE),
  times = 10
)
```

--------------------------------

### Get assessment details for multiple assessments

Source: https://docs.ropensci.org/rredlist/reference/rl_assessment_list.html

Use `rl_assessment_list` to retrieve details for multiple assessments by providing a vector of their unique identifiers. This example demonstrates fetching data for two specific assessment IDs.

```r
if (FALSE) { # \dontrun{
# Get assessment details for multiple assessments
ex1 <- rl_assessment_list(ids = c(166290968, 136250858))
} # }
```

--------------------------------

### Benchmark: Taxonomic Lookup with Defaults

Source: https://docs.ropensci.org/rredlist/articles/benchmarks.html

Compares the performance of rl_family() and rl_family_() for a default taxonomic lookup. Both functions are tested 10 times.

```r
microbenchmark(
  rl_family(),
  rl_family_(),
  times = 10
)
```

--------------------------------

### Get assessment summary for medicinal use and trade

Source: https://docs.ropensci.org/rredlist/reference/rl_use_and_trade.html

Retrieves the assessment summary for a specific use and trade, identified by its code. In this example, code '3' is used to fetch details related to medicinal use and trade.

```r
rl_use_and_trade("3")
```

--------------------------------

### Benchmark: Taxonomic Lookup with Query (~900 Pages)

Source: https://docs.ropensci.org/rredlist/articles/benchmarks.html

Compares the performance of rl_class() and rl_class_() when querying for a class with approximately 900 pages of results ('Aves'). The 'quiet = TRUE' argument is used, and functions are tested 10 times.

```r
microbenchmark(
  rl_class("Aves", quiet = TRUE),
  rl_class_("Aves", quiet = TRUE),
  times = 10
)
```

--------------------------------

### Benchmark: Taxonomic Lookup with Query (One Page)

Source: https://docs.ropensci.org/rredlist/articles/benchmarks.html

Compares the performance of rl_family() and rl_family_() when querying for a specific family ('Rheidae'). Both functions are tested 10 times.

```r
microbenchmark(
  rl_family("Rheidae"),
  rl_family_("Rheidae"),
  times = 10
)
```

--------------------------------

### Summarize and Calculate Habitat Proportions

Source: https://docs.ropensci.org/rredlist/articles/research_workflows.html

Summarizes habitat data by removing duplicates, counting species per habitat for each clade, and calculating the proportion of species in each habitat. This allows for direct comparison between clades.

```r
gymno_counts <- gymno_habitats %>%
  select(sis_id, clade, code_major, habitat_major) %>%
  unique() %>%
  group_by(clade) %>%
  count(code_major, habitat_major, name = "cnt") %>%
  mutate(prop = cnt/length(
    unique(subset(gymno_habitats, clade == cur_group()$clade)$sis_id)
  ))
```

--------------------------------

### Get Extinct Taxa Assessment Summary

Source: https://docs.ropensci.org/rredlist/reference/rl_extinct.html

Fetches an assessment summary for extinct taxa. The `rl_extinct` function returns a parsed list by default. Use `rl_extinct_` to get raw JSON.

```r
if (FALSE) { # \dontrun{
ex1 <- rl_extinct()
nrow(ex1$assessments)
} # }
```

--------------------------------

### Download Assessments with Helper Function

Source: https://docs.ropensci.org/rredlist/articles/research_workflows.html

Utilizes the `rl_assessment_list()` helper function to download multiple assessment records, which automatically includes recommended delays between queries to avoid timeouts.

```r
assessment_list <- rl_assessment_list(assessment_ids)
```

--------------------------------

### Get species latest assessment

Source: https://docs.ropensci.org/rredlist/reference/index.html

Use `rl_species_latest()` to retrieve the latest assessment for a species.

```r
rl_species_latest()
```

--------------------------------

### Example: Plotting with IUCN Fill Scale

Source: https://docs.ropensci.org/rredlist/reference/scale_iucn.html

Demonstrates how to use `scale_fill_iucn` to color points in a ggplot2 scatter plot based on IUCN Red List categories. Ensure the `ggplot2` library is loaded.

```r
library(ggplot2)
categories <- c("NE", "DD", "LC", "NT", "VU", "EN", "CR", "RE", "EW", "EX")
df <- data.frame(
  x = runif(1000, 0, 10), y = runif(1000, 0, 10),
  color = sample(categories, 1000, TRUE), shape = 21
)
ggplot(df) +
  geom_point(aes(x = x, y = y, fill = color), shape = 21) +
  scale_fill_iucn(name = "IUCN Category") +
  theme_classic()
```

--------------------------------

### Query assessments by habitats and systems

Source: https://docs.ropensci.org/rredlist/reference/index.html

Use `rl_habitats()` and `rl_systems()` to query assessments based on habitats and ecological systems. Variants with an underscore (e.g., `rl_habitats_()`) are also available.

```r
rl_habitats()
rl_habitats_()
rl_systems()
rl_systems_()
```

--------------------------------

### Fetch and Merge Upstream Changes

Source: https://docs.ropensci.org/rredlist/CONTRIBUTING.html

Fetch and merge the latest changes from the upstream repository before making your own modifications.

```bash
git fetch upstream
# or
git pull upstream
```

--------------------------------

### Get details for one or more assessments

Source: https://docs.ropensci.org/rredlist/reference/index.html

Retrieve specific assessment details or a list of assessments from the Red List.

```APIDOC
## rl_assessment() / rl_assessment_()

### Description
Retrieve details for one or more assessments.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)

## rl_assessment_list()

### Description
Retrieve a list of assessments.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)

## rl_species_latest()

### Description
Retrieve the latest assessment for a species.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)

## rl_sis_latest()

### Description
Retrieve the latest assessment using SIS ID.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)

## rl_assessment_extract()

### Description
Extract a specific element from an assessment.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)
```

--------------------------------

### Visualization tools

Source: https://docs.ropensci.org/rredlist/reference/index.html

Color scales for visualizing IUCN Red List data.

```APIDOC
## scale_color_iucn() / scale_fill_iucn() / scale_discrete_iucn()

### Description
IUCN Red List color scales for visualizations.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)
```

--------------------------------

### Get Family Assessment Summary

Source: https://docs.ropensci.org/rredlist/reference/rl_family.html

Retrieves the assessment summary for the 'Hominidae' family. The number of assessments is then printed.

```R
if (FALSE) { # \dontrun{
# Get assessment summary for family
ex1 <- rl_family(family = "Hominidae")
nrow(ex1$assessments)
} # }
```

--------------------------------

### Get a list of all scopes

Source: https://docs.ropensci.org/rredlist/reference/rl_scopes.html

Call rl_scopes without any arguments to retrieve a list of all available geographical assessment scopes.

```r
rl_scopes()
```

--------------------------------

### Red List information and statistics

Source: https://docs.ropensci.org/rredlist/reference/index.html

Functions to get Red List information, statistics, and manage API keys.

```APIDOC
## rl_sp_count() / rl_sp_count_()

### Description
Get the count of species in the Red List.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)

## rl_version()

### Description
Get the Red List version.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)

## rl_api_version()

### Description
Get the Red List API version.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)

## rl_citation()

### Description
Get the citation for the Red List API.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)

## rl_use_iucn()

### Description
Helper function to get and save the IUCN API key.

### Method
Not applicable (R function)

### Endpoint
Not applicable (R function)

### Parameters
(Specific parameters not detailed in source)

### Request Example
(Not provided in source)

### Response
(Specific response details not detailed in source)
```
Tokens:
Raw