atlantistools (version 0.4.3)

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

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.

Value

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

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.

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
# }