get_growth_fishbase: Extract growth parameters from http:://www.fishbase.se.

In atlantistools: Process and Visualise Output from Atlantis Models

Description

This function extracts values for Linf, k and t0 from http:://www.fishbase.se

Usage

get_growth_fishbase(fish, mirror = "se")

Arguments

fish	Vector of fish species with genus and species information.
mirror	Character string defining the url mirror to use. Defaults to se. In case data extraction is slow use a different mirror. Try to avoid frequently used mirrors like uk or com.

Details

Before the actual extraction takes place fishbase IDs for every species are extracted using get_ids_fishbase. The IDs are needed to generate the urls later on.

Value

Dataframe with species, country, locality, linf and k.

Examples

## Not run: 
# For some reason the examples break with appveyor.
fish <- c("Gadus morhua", "Merlangius merlangus")
df <- get_growth_fishbase(fish)
head(df)

df <- get_growth_fishbase(fish, mirror = "de")
head(df)

fish <- c("Sprattus sprattus")
df <- get_growth_fishbase(fish)
head(df)
# Only use for debugging purposes.
fish <- read.csv("Z:/my_data_alex/fish_species_names_from_ibts.csv", stringsAsFactors = FALSE)[, 1]
url <- get_growth_fishbase(fish)
url <- urls$ref_url

## End(Not run)

atlantistools documentation built on Aug. 16, 2017, 9:05 a.m.