rfishbase

https://docs.ropensci.org/rfishbase/
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### R Example: Get Introductions for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/introductions.html

Demonstrates how to call the introductions function to retrieve introduction data for 'Oreochromis niloticus'. This example is intended for interactive use.

```R
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
introductions("Oreochromis niloticus")
} # }
}
```

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

### Example: Get Swimming Data for Oreochromis niloticus

Source: https://docs.ropensci.org/rfishbase/reference/swimming.html

This example demonstrates how to call the swimming function for a specific species, 'Oreochromis niloticus'. This code is part of a non-interactive example and requires interactive mode to run.

```R
swimming("Oreochromis niloticus")
```

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

### Example: Get Reproduction Data for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/reproduction.html

Demonstrates how to retrieve reproduction data for a single species, 'Oreochromis niloticus', using the reproduction function. This example is intended for interactive use.

```R
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
reproduction("Oreochromis niloticus")
} # }
}
```

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

### Example: Get Maturity for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/maturity.html

Demonstrates how to call the maturity function to retrieve maturity data for 'Oreochromis niloticus'. This example is conditional and runs only in interactive sessions.

```R
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
matureity("Oreochromis niloticus")
} # }
}
```

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

### Example Usage of countrysubref

Source: https://docs.ropensci.org/rfishbase/reference/countrysubref.html

Provides an example of how to call the countrysubref function. This example is intended for interactive use and is wrapped in conditional checks.

```R
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
countrysubref()
} # }
}
```

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

### Example usage of stocks function

Source: https://docs.ropensci.org/rfishbase/reference/stocks.html

Demonstrates how to call the stocks function to retrieve data for a specific species. This example is typically run interactively.

```R
stocks("Oreochromis niloticus")
```

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

### Install rfishbase Package

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

Install the rfishbase package from GitHub using the remotes package. This is the primary method for obtaining the latest version.

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

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

### Example: Accessing the 'species' Table

Source: https://docs.ropensci.org/rfishbase/reference/fb_tbl.html

This example demonstrates how to call fb_tbl to retrieve all records from the 'species' table. It is wrapped in an if (FALSE) block to prevent execution during standard package checks.

```R
if (FALSE) { # interactive()
fb_tbl("species")
}
```

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

### Example of using countrysub with species_list

Source: https://docs.ropensci.org/rfishbase/reference/countrysub.html

Demonstrates how to call the countrysub function with a species list obtained from the species_list function. This example is intended for interactive use.

```r
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
countrysub(species_list(Genus='Labroides'))
} # }
}
```

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

### Example of using spawning function

Source: https://docs.ropensci.org/rfishbase/reference/spawning.html

Demonstrates how to call the spawning function with a specific species name to retrieve its spawning information.

```R
spawning("Oreochromis niloticus")
```

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

### Call diet_items function

Source: https://docs.ropensci.org/rfishbase/reference/diet_items.html

This example shows how to call the diet_items function. It is typically used within an interactive session.

```R
if (FALSE) { # interactive() 
if (FALSE) { # \dontrun{ 
diet_items() 
} # } 
}
```

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

### Get all references

Source: https://docs.ropensci.org/rfishbase/reference/references.html

Retrieve all available reference data by calling the function without any arguments.

```R
references()
```

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

### Example Usage of length_freq

Source: https://docs.ropensci.org/rfishbase/reference/length_freq.html

Demonstrates how to call the length_freq function to retrieve length-frequency data for a specific species, 'Oreochromis niloticus'. This example is intended for interactive use and is wrapped in \dontrun{} to prevent execution during package checks.

```R
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
length_freq("Oreochromis niloticus")
}
}

```

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

### List Available Tables - R

Source: https://docs.ropensci.org/rfishbase/reference/fb_tables.html

Call fb_tables() to get a list of all available tables from the default server (FishBase).

```r
if (FALSE) { # interactive()
fb_tables()
}
```

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

### Example of using the brains function

Source: https://docs.ropensci.org/rfishbase/reference/brains.html

Demonstrates how to call the brains function to retrieve data for a specific species, 'Oreochromis niloticus'. This example is intended for interactive use.

```R
if (FALSE) { # interactive() 
 if (FALSE) { # \dontrun{ 
brains("Oreochromis niloticus")
} # }
}
```

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

### Retrieve Oxygen Data for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/oxygen.html

Example of how to call the oxygen function to get oxygen data for 'Oreochromis niloticus'. This is typically run within an interactive session.

```R
oxygen("Oreochromis niloticus")
```

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

### Get Ecology Data for Multiple Species with Specific Fields

Source: https://docs.ropensci.org/rfishbase/reference/ecology.html

Fetch trophic levels and standard errors for a list of species. Specify the desired fields to narrow down the returned columns. This example demonstrates querying multiple species and selecting specific data points.

```r
ecology(c("Oreochromis niloticus", "Salmo trutta"),
        fields=c("SpecCode", "FoodTroph", "FoodSeTroph", "DietTroph", "DietSeTroph"))
```

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

### List Available Releases - rfishbase

Source: https://docs.ropensci.org/rfishbase/reference/available_releases.html

Call the available_releases function to get a list of releases from either the fishbase or sealifebase server. The default is fishbase.

```R
available_releases(server = c("fishbase", "sealifebase"))
```

```R
if (FALSE) { # interactive()
available_releases()
}
```

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

### Get references by code

Source: https://docs.ropensci.org/rfishbase/reference/references.html

Retrieve reference data for a single reference code. Use a range for multiple codes.

```R
references(codes = 1)
```

```R
references(codes = 1:6)
```

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

### Get all FAO areas

Source: https://docs.ropensci.org/rfishbase/reference/faoareas.html

Call faoareas() without arguments to retrieve a table of all fish FAO locations. This example is intended for interactive use.

```r
if (FALSE) { # interactive()
  faoareas()
}
```

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

### Get Ecology Data for a Single Species

Source: https://docs.ropensci.org/rfishbase/reference/ecology.html

Retrieve ecology data for a specific species by providing its scientific name. This is a basic usage example.

```r
ecology("Oreochromis niloticus")
```

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

### Retrieve food items for a specific species

Source: https://docs.ropensci.org/rfishbase/reference/fooditems.html

Example of how to call the fooditems function to get food item data for a single species, 'Oreochromis niloticus'.

```R
fooditems("Oreochromis niloticus")
```

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

### Retrieve Length-Weight Data for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/length_weight.html

Fetches length-weight relationship data for 'Oreochromis niloticus'. This example is typically run interactively and is not executed by default.

```R
if (FALSE) { # interactive() 
if (FALSE) { # \dontrun{ 
length_weight("Oreochromis niloticus") 
} # } 
}
```

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

### Join Spawning and Spawn Aggregation Tables

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

Combine the 'spawning' and 'spawnagg' tables using a left join to get comprehensive spawning data. This is useful for analyzing species spawning behaviors and locations.

```r
library(rfishbase)
library(dplyr)

## Get the whole spawning and spawn agg table, joined together:
spawn <- left_join(fb_tbl("spawning"),  
                   fb_tbl("spawnagg"), 
                   relationship = "many-to-many")
```

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

### Get species by ecosystem

Source: https://docs.ropensci.org/rfishbase/reference/species_by_ecosystem.html

Retrieves a table of species within a given ecosystem from Sealifebase. Ensure the `sealifebase` server is specified.

```R
species_by_ecosystem(ecosystem = "Arctic", server = "sealifebase")
```

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

### Get specific reference fields

Source: https://docs.ropensci.org/rfishbase/reference/references.html

Retrieve specific fields (Author, Year, Title) for a range of reference codes. It is recommended to omit the 'fields' argument and handle subsetting manually.

```R
references(codes = 1:6, fields = c('Author', 'Year', 'Title'))
```

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

### Get Country Information by C_Code

Source: https://docs.ropensci.org/rfishbase/reference/c_code.html

Retrieves a table of country information for a given C_Code from FishBase.org. Ensure interactive() is TRUE for execution.

```R
if (FALSE) { # interactive()
c_code(440)
}
```

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

### Get Country Data for a Species

Source: https://docs.ropensci.org/rfishbase/reference/country.html

Fetches country information for a single species. Ensure the species name is in the "genus species" format.

```R
country("Bolbometopon muricatum")
```

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

### Get All Fish Diet Data

Source: https://docs.ropensci.org/rfishbase/reference/diet.html

Call the diet function without arguments to retrieve a table of diet information for all fish species. This requires an active internet connection to the FishBase or SeaLifeBase database.

```r
diet()
```

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

### Get Country Data

Source: https://docs.ropensci.org/rfishbase/reference/country.html

Retrieves a table of countries for the requested species as reported in FishBase.org. You can specify species, fields, server, and version.

```APIDOC
## country

### Description
Returns a table of country for the requested species, as reported in FishBase.org.

### Usage
```R
country(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments

*   **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **fields** (vector of strings) - Subset to these columns. (recommend to omit this and handle manually)
*   **server** (string) - Either "fishbase" or "sealifebase".
*   **version** (string) - A version string for the database. See `available_releases()` for details.
*   **db** (object) - Database connection, now deprecated.
*   **...** - Additional arguments, currently ignored.

### Examples
```R
# Get country data for a specific species
country("Bolbometopon muricatum")

# Get country data for all species (if species_list is NULL)
# country()
```
```

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

### Get Ration Data for a Species

Source: https://docs.ropensci.org/rfishbase/reference/ration.html

Retrieves ration data for a specific species from FishBase or Sealifebase. Ensure the species name is in the format 'genus species'.

```R
ration("Oreochromis niloticus")
```

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

### Get Genetics Data for Another Species

Source: https://docs.ropensci.org/rfishbase/reference/genetics.html

Retrieve genetics data for a different species by providing its scientific name. This demonstrates fetching data for multiple distinct species.

```R
genetics("Labroides dimidiatus")
```

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

### introductions()

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

Retrieves information about species introductions.

```APIDOC
## introductions()

### Description
Retrieves information about species introductions.

### Method
`introductions()`

### Parameters
None

### Returns
Information about species introductions.
```

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

### Get Larval Data

Source: https://docs.ropensci.org/rfishbase/reference/larvae.html

Retrieves larval data for specified fish species. If no species are provided, it returns data for all fish. You can also specify which fields to retrieve and which server (FishBase or Sealifebase) to query.

```APIDOC
## larvae

### Description
Retrieves larval data for specified fish species from FishBase or Sealifebase.

### Usage
```R
larvae(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments

*   **species_list** (vector of strings) - A vector of scientific names (e.g., "genus species"). If empty, data for all fish will be returned.
*   **fields** (vector of strings, optional) - A subset of columns to retrieve. It is recommended to omit this and handle column selection manually after retrieval.
*   **server** (string) - Specifies the database server to query. Accepts either "fishbase" or "sealifebase".
*   **version** (string) - A version string for the database. Use `available_releases()` to see available versions.
*   **db** (database connection, deprecated) - Database connection object. This argument is deprecated.
*   **...** - Additional arguments, currently ignored.

### Value
A data table containing larval information.

### Examples
```R
# Get larval data for a specific species
larvae("Oreochromis niloticus")

# Get larval data for all species (if species_list is NULL)
# larvae()

# Specify fields to retrieve (example, actual fields may vary)
# larvae(fields = c("Species", "LarvalDuration", "MaxLarvalSize"))

# Query Sealifebase instead of FishBase
# larvae(server = "sealifebase")
```
```

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

### Get Larval Data for a Specific Species - rfishbase

Source: https://docs.ropensci.org/rfishbase/reference/larvae.html

Use the larvae function to retrieve larval data for a given species. Ensure interactive mode is enabled for this example to run.

```r
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
larvae("Oreochromis niloticus")
}
}

```

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

### Get Length-Length Relationships for a Species

Source: https://docs.ropensci.org/rfishbase/reference/length_length.html

Call the length_length function with a specific species scientific name to retrieve its length-length conversion data. This example is intended for interactive use and is wrapped in a conditional to prevent execution during automated checks.

```R
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
length_length("Oreochromis niloticus")
}
}

```

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

### introductions Function

Source: https://docs.ropensci.org/rfishbase/reference/introductions.html

Retrieves a table of species introductions data. It can filter by species list, specific fields, and database server. The 'db' argument is deprecated.

```APIDOC
## introductions

### Usage
```R
introductions(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments

*   **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **fields** (vector of strings, optional) - Subset to these columns. (recommend to omit this and handle manually)
*   **server** (string) - Either "fishbase" or "sealifebase".
*   **version** (string) - A version string for the database. See `available_releases()` for details.
*   **db** (object, deprecated) - Database connection, now deprecated.
*   **...** - Additional arguments, currently ignored.

### Value

A table of species introductions data.

### Examples

```R
# Load the library
# library(rfishbase)

# Get introductions for a specific species
introductions("Oreochromis niloticus")

# Get introductions for all species (if species_list is NULL)
# introductions()
```
```

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

### spawning()

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

Retrieves spawning information for species.

```APIDOC
## spawning()

### Description
Retrieves spawning information for species.

### Method
`spawning()`

### Parameters
None

### Returns
Spawning information for species.
```

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

### R Function Signature: introductions

Source: https://docs.ropensci.org/rfishbase/reference/introductions.html

Defines the usage and arguments for the introductions function. It accepts species lists, fields, server choice, and version.

```R
introductions(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

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

### popqb()

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

Retrieves population-at-age data.

```APIDOC
## popqb()

### Description
Retrieves population-at-age data.

### Method
`popqb()`

### Parameters
None

### Returns
Population-at-age data.
```

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

### ration()

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

Retrieves ration data for species.

```APIDOC
## ration()

### Description
Retrieves ration data for species.

### Method
`ration()`

### Parameters
None

### Returns
Ration data for species.
```

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

### Load rfishbase and dplyr Libraries

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

Load the rfishbase package for accessing FishBase data and the dplyr package for data manipulation. dplyr is convenient but not strictly required.

```r
library("rfishbase")
library("dplyr") # convenient but not required
```

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

### popchar

Source: https://docs.ropensci.org/rfishbase/reference/popchar.html

Fetches population dynamics data (Lmax, Wmax, tmax) for specified species from FishBase or Sealifebase.

```APIDOC
## popchar

### Description
Retrieves population dynamics information including maximum length, weight, and age from FishBase.

### Usage
```R
popchar(species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ...)
```

### Arguments

*   **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **fields** (vector of strings) - Subset to these columns. (recommend to omit this and handle manually)
*   **server** (string) - Either "fishbase" or "sealifebase".
*   **version** (string) - A version string for the database. See `available_releases()` for details.
*   **db** (object) - Database connection, now deprecated.
*   **...** - Additional arguments, currently ignored.

### Details
This table presents information on maximum length (Lmax), weight (Wmax) and age (tmax) from various localities where a species occurs. The largest values from this table are also entered in the SPECIES table. The POPCHAR table also indicates whether the Lmax, Wmax and tmax values or various combinations thereof refer to the same individual fish.

### References
http://www.fishbase.org/manual/english/fishbasethe_popchar_table.htm

### Examples
```R
# Get population dynamics for Oreochromis niloticus
popchar("Oreochromis niloticus")
```
```

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

### available_releases()

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

Lists the available releases of the rfishbase dataset.

```APIDOC
## available_releases()

### Description
Lists available releases of the rfishbase dataset.

### Method
`available_releases()`

### Parameters
None

### Returns
List of available releases.
```

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

### Fecundity Function Usage

Source: https://docs.ropensci.org/rfishbase/reference/fecundity.html

Call the fecundity function with a species name to retrieve its fecundity data. This example is conditional and will only run interactively.

```R
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
fecundity("Oreochromis niloticus")
} # }
}
```

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

### larvae()

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

Retrieves information about larval stages of species.

```APIDOC
## larvae()

### Description
Retrieves information about larval stages of species.

### Method
`larvae()`

### Parameters
None

### Returns
Information about larval stages of species.
```

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

### Get Morphology Data for a Species

Source: https://docs.ropensci.org/rfishbase/reference/morphology.html

Retrieves morphology data for a specific species. Ensure the species name is in 'genus species' format.

```r
morphology("Oreochromis niloticus")
```

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

### stocks()

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

Retrieves stock information for species.

```APIDOC
## stocks()

### Description
Retrieves stock information for species.

### Method
`stocks()`

### Parameters
None

### Returns
Stock information for species.
```

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

### diet()

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

Retrieves diet information for species.

```APIDOC
## diet()

### Description
Retrieves diet information for species.

### Method
`diet()`

### Parameters
None

### Returns
Diet information for species.
```

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

### ecosystem()

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

Retrieves ecosystem information.

```APIDOC
## ecosystem()

### Description
Retrieves ecosystem information.

### Method
`ecosystem()`

### Parameters
None

### Returns
Ecosystem information.
```

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

### Get Morphometrics for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/morphometrics.html

Retrieves morphometric data for 'Oreochromis niloticus'. This function is useful for obtaining detailed measurements of fish species.

```r
morphometrics("Oreochromis niloticus")
```

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

### popqb

Source: https://docs.ropensci.org/rfishbase/reference/popqb.html

Retrieves population and biomass data for fish species.

```APIDOC
## popqb

### Description
Retrieves population and biomass data for fish species.

### Usage
```R
popqb(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments

*   **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **fields** (vector of strings) - Subset to these columns. (recommend to omit this and handle manually)
*   **server** (string) - Either "fishbase" or "sealifebase".
*   **version** (string) - A version string for the database. See `available_releases()` for details.
*   **db** (object) - Database connection, now deprecated.
*   **...** - Additional arguments, currently ignored.

### Value
A table of species popqb.

### References
http://www.fishbase.org/manual/english/fishbasethe_popqb_table.htm

### Examples

```R
# Example 1: Get data for a specific species
popqb("Oreochromis niloticus")
```
```

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

### Fetch and Merge Upstream Changes

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

Before making changes, fetch and merge the latest updates from the upstream repository. You can either fetch and merge separately or in one step.

```bash
git fetch upstream
```

```bash
git pull upstream
```

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

### Clone rfishbase Repository

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

Clone your forked version of the rfishbase repository to your local machine. Replace `<yourgithubusername>` with your actual GitHub username.

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

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

### Get Predators for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/predators.html

Retrieve predator information for a given species by its scientific name. Ensure the species name is in the format 'genus species'.

```R
predators("Oreochromis niloticus")
```

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

### Estimate Trophic Levels for a Species

Source: https://docs.ropensci.org/rfishbase/reference/estimate.html

Use this function to get trophic level estimates for a specific species. Ensure the species name is in the format 'genus species'.

```R
estimate("Oreochromis niloticus")
```

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

### reproduction()

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

Retrieves reproduction data for species.

```APIDOC
## reproduction()

### Description
Retrieves reproduction data for species.

### Method
`reproduction()`

### Parameters
None

### Returns
Reproduction data for species.
```

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

### popgrowth()

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

Retrieves population growth data.

```APIDOC
## popgrowth()

### Description
Retrieves population growth data.

### Method
`popgrowth()`

### Parameters
None

### Returns
Population growth data.
```

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

### ecology

Source: https://docs.ropensci.org/rfishbase/reference/ecology.html

Retrieves species ecology data. By default, it returns one entry per species, but can be increased to get multiple entries for different stocks of the same species.

```APIDOC
## ecology

### Description
Retrieves species ecology data from FishBase or SeaLifeBase. By default, will only return one entry (row) per species. Increase limit to get multiple returns for different stocks of the same species, though often data is either identical to the first or simply missing in the additional stocks.

### Usage
```R
ecology(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments 

* **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
* **fields** (vector of strings) - Subset to these columns. (recommend to omit this and handle manually)
* **server** (string) - Either "fishbase" or "sealifebase".
* **version** (string) - A version string for the database. See `available_releases()` for details.
* **db** (database connection) - Database connection, now deprecated.
* **...** - Additional arguments, currently ignored.

### Value
A table of species ecology data.

### References
http://www.fishbase.org/manual/english/fishbasethe_ecology_table.htm

### Examples
```R
# Get ecology data for a single species
ecology("Oreochromis niloticus")

# Get trophic levels and standard errors for a list of species
ecology(c("Oreochromis niloticus", "Salmo trutta"),
        fields=c("SpecCode", "FoodTroph", "FoodSeTroph", "DietTroph", "DietSeTroph"))
```
```

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

### List available releases

Source: https://docs.ropensci.org/rfishbase/reference/available_releases.html

The available_releases function retrieves a list of available releases from either FishBase or SeaLifeBase.

```APIDOC
## available_releases

### Description
List available releases

### Usage
```R
available_releases(server = c("fishbase", "sealifebase"))
```

### Arguments
#### server
- **server** (character) - Specifies the server to query, either "fishbase" or "sealifebase".

### Examples
```R
if (FALSE) { # interactive()
available_releases()
}
```
```

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

### Get synonyms for a list of species

Source: https://docs.ropensci.org/rfishbase/reference/synonyms.html

Use the synonyms function with a vector of scientific names to find alternative versions. If no species list is provided, it returns all fish synonyms.

```R
synonyms(
  species_list = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

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

### maturity()

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

Retrieves maturity data for species.

```APIDOC
## maturity()

### Description
Retrieves maturity data for species.

### Method
`maturity()`

### Parameters
None

### Returns
Maturity data for species.
```

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

### Get popqb data for a specific species

Source: https://docs.ropensci.org/rfishbase/reference/popqb.html

Use popqb to retrieve population and biological data for 'Oreochromis niloticus'. This function queries FishBase or SeaLifeBase for the requested species.

```R
popqb("Oreochromis niloticus")
```

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

### Get Morphometrics Data

Source: https://docs.ropensci.org/rfishbase/reference/morphometrics.html

Fetches morphometric and physiological data for fish species. Users can specify a list of species, desired fields, and the data source (FishBase or Sealifebase).

```APIDOC
## morphometrics

### Description
Retrieves morphometric and physiological data for fish species from FishBase or Sealifebase.

### Usage
```R
morphometrics(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments

*   **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **fields** (vector of strings) - Subset to these columns. (recommend to omit this and handle manually)
*   **server** (string) - Either "fishbase" or "sealifebase".
*   **version** (string) - A version string for the database. See `available_releases()` for details.
*   **db** (connection) - Database connection, now deprecated.
*   **...** - Additional arguments, currently ignored.

### Value
A table of species morphometrics data.

### Examples
```R
# Get morphometrics for Oreochromis niloticus
morphometrics("Oreochromis niloticus")
```
```

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

### fb_tables

Source: https://docs.ropensci.org/rfishbase/reference/fb_tables.html

Lists available tables from FishBase or SeaLifeBase.

```APIDOC
## fb_tables

### Description
Lists available tables from FishBase or SeaLifeBase.

### Usage
```R
fb_tables(server = c("fishbase", "sealifebase"), version = "latest")
```

### Arguments

* `server` (character) - Access data from fishbase or sealifebase?
* `version` (character) - Version, see `available_releases()`

### Examples
```R
if (FALSE) { # interactive()
  fb_tables()
}
```
```

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

### Get Speed Data for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/speed.html

Retrieves speed data for 'Oreochromis niloticus' from the default server. This function is useful for obtaining specific physiological data for a given species.

```R
speed("Oreochromis niloticus")
```

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

### diet_items()

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

Retrieves information about diet items.

```APIDOC
## diet_items()

### Description
Retrieves information about diet items.

### Method
`diet_items()`

### Parameters
None

### Returns
Information about diet items.
```

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

### speed()

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

Retrieves swimming speed data for species.

```APIDOC
## speed()

### Description
Retrieves swimming speed data for species.

### Method
`speed()`

### Parameters
None

### Returns
Swimming speed data for species.
```

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

### Get Genetics Data for a Species

Source: https://docs.ropensci.org/rfishbase/reference/genetics.html

Call the genetics function with a single species scientific name to retrieve its genetics data. Ensure the species name is in the format 'genus species'.

```R
genetics("Oreochromis niloticus")
```

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

### Get Ecosystem Data for a Species

Source: https://docs.ropensci.org/rfishbase/reference/ecosystem.html

Use the ecosystem function to retrieve ecosystem data for a specific species by providing its scientific name. This function queries the FishBase or SeaLifeBase API.

```R
ecosystem("Oreochromis niloticus")
```

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

### diet()

Source: https://docs.ropensci.org/rfishbase/reference/diet.html

Retrieves diet information for fish species. It can fetch data for a specified list of species or for all fish if no list is provided. Users can also specify the server (FishBase or SealifeBase) and a specific database version.

```APIDOC
## diet

### Description
Retrieves a table of species diet information.

### Usage
```R
diet(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments

*   **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **fields** (vector of strings, optional) - Subset to these columns. (recommend to omit this and handle manually)
*   **server** (string) - Either "fishbase" or "sealifebase".
*   **version** (string) - A version string for the database. See `available_releases()` for details.
*   **db** (database connection, deprecated) - Database connection, now deprecated.
*   **...** - Additional arguments, currently ignored.

### Value
A table of species diet.

### References
http://www.fishbase.org/manual/english/fishbasethe_diet_table.htm

### Examples
```R
# Example of calling the diet function
# diet()
```
```

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

### Get POPCHAR data for a specific species

Source: https://docs.ropensci.org/rfishbase/reference/popchar.html

Call popchar with a single scientific name to retrieve its maximum length, weight, and age information. This is useful for species-specific ecological or fisheries research.

```r
popchar("Oreochromis niloticus")
```

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

### length_weight()

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

Retrieves length-weight relationships for species.

```APIDOC
## length_weight()

### Description
Retrieves length-weight relationships for species.

### Method
`length_weight()`

### Parameters
None

### Returns
Length-weight relationships for species.
```

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

### Retrieve Population Growth Data for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/popgrowth.html

Call the popgrowth function with a scientific name to get population dynamics information for that species. Ensure the species name is in the format 'genus species'.

```R
popgrowth("Oreochromis niloticus")
```

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

### predators()

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

Retrieves predator-prey relationships.

```APIDOC
## predators()

### Description
Retrieves predator-prey relationships.

### Method
`predators()`

### Parameters
None

### Returns
Predator-prey relationships.
```

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

### oxygen()

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

Retrieves oxygen-related data.

```APIDOC
## oxygen()

### Description
Retrieves oxygen-related data.

### Method
`oxygen()`

### Parameters
None

### Returns
Oxygen-related data.
```

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

### Get Common Names for a Specific Species

Source: https://docs.ropensci.org/rfishbase/reference/common_names.html

Use this function to retrieve common names for a single scientific species name. The query is performed against the default server and version unless specified otherwise.

```R
if (FALSE) { # interactive()
common_names("Bolbometopon muricatum")
}
```

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

### morphology()

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

Retrieves morphological data for species.

```APIDOC
## morphology()

### Description
Retrieves morphological data for species.

### Method
`morphology()`

### Parameters
None

### Returns
Morphological data for species.
```

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

### Filter Species by Scientific Name

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

Retrieve species information by filtering tables using scientific names. This example selects species by name and displays their scientific name, common name (FBname), and length.

```r
fish <- c("Oreochromis niloticus", "Salmo trutta")

fb_tbl("species") %>%
  mutate(sci_name = paste(Genus, Species)) %>%
  filter(sci_name %in% fish) %>%
  select(sci_name, FBname, Length)
```

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

### swimming()

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

Retrieves swimming behavior data for species.

```APIDOC
## swimming()

### Description
Retrieves swimming behavior data for species.

### Method
`swimming()`

### Parameters
None

### Returns
Swimming behavior data for species.
```

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

### Validate Scientific Names

Source: https://docs.ropensci.org/rfishbase/reference/validate_names.html

Use this function to check for alternate versions of a scientific name and retrieve the valid name recognized by FishBase. Provide a vector of scientific names or leave empty to get all fish.

```R
validate_names(
  species_list,
  server = getOption("FISHBASE_API", "fishbase"),
  version = get_latest_release(),
  db = default_db(),
  ...
)
```

```R
validate_names("Abramites ternetzi")
```

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

### references()

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

Retrieves reference information.

```APIDOC
## references()

### Description
Retrieves reference information.

### Method
`references()`

### Parameters
None

### Returns
Reference information.
```

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

### Get Scientific Names from Common Names

Source: https://docs.ropensci.org/rfishbase/reference/common_to_sci.html

Use this function to convert common fish names to their scientific equivalents. Specify the language and the database (FishBase or SeaLifeBase) to use. Handles multiple common names and returns all matching scientific names if ambiguities exist.

```R
common_to_sci(c("Bicolor cleaner wrasse", "humphead parrotfish"), Language="English")
common_to_sci(c("Coho Salmon", "trout"))
```

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

### synonyms()

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

Retrieves synonym information for species.

```APIDOC
## synonyms()

### Description
Retrieves synonym information for species.

### Method
`synonyms()`

### Parameters
None

### Returns
Synonym information for species.
```

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

### c_code()

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

Retrieves c_code information.

```APIDOC
## c_code()

### Description
Retrieves c_code information.

### Method
`c_code()`

### Parameters
None

### Returns
c_code information.
```

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

### load_taxa()

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

Loads taxonomic information.

```APIDOC
## load_taxa()

### Description
Loads taxonomic information.

### Method
`load_taxa()`

### Parameters
None

### Returns
Taxonomic information.
```

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

### fooditems()

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

Retrieves information about food items.

```APIDOC
## fooditems()

### Description
Retrieves information about food items.

### Method
`fooditems()`

### Parameters
None

### Returns
Information about food items.
```

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

### length_freq

Source: https://docs.ropensci.org/rfishbase/reference/length_freq.html

Returns a table of species food items.

```APIDOC
## length_freq

### Description
Returns a table of species food items.

### Usage
```R
length_freq(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments

*   **species_list** (vector) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **fields** (vector) - Subset to these columns. (recommend to omit this and handle manually)
*   **server** (character) - Either "fishbase" or "sealifebase".
*   **version** (character) - A version string for the database. See `available_releases()` for details.
*   **db** (connection) - Database connection, now deprecated.
*   **...** - Additional arguments, currently ignored.

### Value
A table of length_freq information by species.

### References
http://www.fishbase.org/manual/english/lengthfrequency.htm

### Examples
```R
if (FALSE) { # interactive()
if (FALSE) { # \dontrun{
length_freq("Oreochromis niloticus")
}
}
```
```

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

### genetics()

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

Retrieves genetic information for species.

```APIDOC
## genetics()

### Description
Retrieves genetic information for species.

### Method
`genetics()`

### Parameters
None

### Returns
Genetic information for species.
```

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

### fishbase

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

Provides a table of all species found in FishBase, including taxonomic classification and Species Code.

```APIDOC
## fishbase

### Description
A table of all the species found in FishBase, including taxonomic classification and the Species Code (SpecCode) by which the species is identified in FishBase.

### Method
`fishbase`

### Parameters
None

### Returns
Table containing FishBase species data.
```

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

### species()

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

Retrieves species information.

```APIDOC
## species()

### Description
Retrieves species information.

### Method
`species()`

### Parameters
None

### Returns
Species information.
```

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

### estimate()

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

Retrieves estimation data.

```APIDOC
## estimate()

### Description
Retrieves estimation data.

### Method
`estimate()`

### Parameters
None

### Returns
Estimation data.
```

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

### ration

Source: https://docs.ropensci.org/rfishbase/reference/ration.html

Retrieves a table of species ration data from FishBase or SeaLifeBase.

```APIDOC
## ration

### Description
Retrieves a table of species ration data from FishBase or SeaLifeBase.

### Usage
```R
ration(
  species_list = NULL,
  fields = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  ...
)
```

### Arguments 

*   **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **fields** (vector of strings, optional) - Subset to these columns. (recommend to omit this and handle manually)
*   **server** (string) - Either "fishbase" or "sealifebase".
*   **version** (string) - A version string for the database. See `available_releases()` for details.
*   **db** (connection, deprecated) - Database connection, now deprecated.
*   **...** - Additional arguments, currently ignored.

### Value
A table of species ration.

### References
http://www.fishbase.org/manual/english/fishbasethe_ration_table.htm

### Examples
```R
# Get ration for a specific species
ration("Oreochromis niloticus")
```
```

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

### Access a FishBase or SealifeBase Table

Source: https://docs.ropensci.org/rfishbase/reference/fb_tbl.html

This function allows you to access specific tables from the FishBase or SealifeBase databases. It retrieves static snapshots of the raw database tables, which may differ slightly from the live website data but ensure stable results. You can specify the table name, server, and data version.

```APIDOC
## Function: fb_tbl

### Description
Accesses a specified table from the FishBase or SealifeBase static database snapshots.

### Usage
```R
fb_tbl(tbl, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, collect = TRUE)
```

### Arguments
* **tbl** (string) - The name of the table to access. Use `fb_tables()` to see available tables.
* **server** (string) - The database server to access. Options are "fishbase" or "sealifebase". Defaults to "fishbase".
* **version** (string) - The version of the database to access. See `available_releases()` for options. Defaults to "latest".
* **db** (connection) - Deprecated. A database connection object.
* **collect** (boolean) - If TRUE, returns an in-memory table. If FALSE, returns a remote table that can be used with dplyr functions. Defaults to TRUE.

### Details
This function accesses static snapshots of the raw database tables used by FishBase and SealifeBase websites. These snapshots may lag behind the live web interface but provide stable results. Data from a single page on the website might be spread across multiple tables, so joining tables may be necessary for comprehensive analysis.

### Examples
```R
# Access the 'species' table from FishBase
if (interactive()) {
  species_data <- fb_tbl("species")
}
```
```

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

### species_names() function signature

Source: https://docs.ropensci.org/rfishbase/reference/species_names.html

This is the usage signature for the species_names function. It accepts server, version, and other arguments for compatibility.

```r
species_names(server = c("fishbase", "sealifebase"), version = "latest", ...)
```

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

### common_names Function

Source: https://docs.ropensci.org/rfishbase/reference/common_names.html

Fetches a table of common names for fish species. You can specify a list of scientific names, the server (FishBase or Sealifebase), the database version, and the desired language for the common names. The `db` argument is deprecated. You can also subset the returned columns using the `fields` argument, though it's recommended to handle this manually.

```APIDOC
## common_names

### Description
Return a table of common names.

### Usage
```R
common_names(
  species_list = NULL,
  server = c("fishbase", "sealifebase"),
  version = "latest",
  db = NULL,
  Language = "English",
  fields = NULL
)
```

### Arguments

*   **species_list** (vector of strings) - A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned.
*   **server** (character) - Either "fishbase" or "sealifebase".
*   **version** (character) - A version string for the database. See `available_releases()` for details.
*   **db** (connection) - Database connection, now deprecated.
*   **Language** (character) - A string specifying the language for the common name, e.g. "English".
*   **fields** (vector of strings) - Subset to these columns. (recommend to omit this and handle manually)

### Value
A data.frame of common names by species queried. If multiple species are queried, the resulting data.frames are concatenated.

### Details
Note that there are many common names for a given sci name.

### Examples
```R
if (FALSE) { # interactive()
common_names("Bolbometopon muricatum")
}
```
```

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

### Filter Spawning Data by Family

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

Load taxonomic data and filter it to a specific family (e.g., Epinephelidae). Then, perform an inner join with the 'spawn' table to retrieve spawning data only for species within that family.

```r
# Filter taxa down to the desired species
groupers <- load_taxa() |> filter(Family == "Epinephelidae")

## A "filtering join" (inner join) 
spawn |> inner_join(groupers)
```

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

### ecology()

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

Retrieves ecological information for species.

```APIDOC
## ecology()

### Description
Retrieves ecological information for species.

### Method
`ecology()`

### Parameters
None

### Returns
Ecological information for species.
```

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

### List Available Data Releases

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

Retrieves a list of all available data release versions for rfishbase. This helps in understanding the recency of the data snapshots.

```r
available_releases()
```
Tokens:
Raw