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Create Community Temperature Index as per Day et al. 2018

create_cti.Rd

This function creates a new dataframe containing Community Temperature Index (CTI) for fish species from abundance data. The function is designed to work with data extracted from GlobalArchive using the 'ga_api_count' function, and processed using provided scripts. The input dataframe must contain columns for 'campaignid', 'sample', 'count', 'family', 'genus' and 'species'. CTI is calculated

Usage

create_cti(data, life_history = CheckEM::australia_life_history)

Arguments

data

A dataframe with columns for 'campaignid', 'sample', 'count', 'family', 'genus' and 'species'

life_history

A dataframe containing thermal niche data for fish species. For an example dataframe see CheckEM::australia_life_history.

Value

A data frame containing campaignid, sample and cti (the value for Community Temperature Index). Note that this dataframe may have less rows than your number of samples, as you may have samples that have no fish with valid thermal niche data.

Examples

if (FALSE) { # \dontrun{
# Fetch metadata for a specific synthesis
count <- readRDS(paste0("data/geographe/raw/", name, "_complete_count.RDS")) %>%
  dplyr::select(campaignid, sample, family, genus, species, count) %>%
  dplyr::mutate(scientific_name = paste(family, genus, species, sep = " ")) %>%
  glimpse()
  
cti <- create_cti(data = count) %>%
  dplyr::rename(number = cti) %>% # Rename the column to number to match with other dataframes for FSSgam modelling
  dplyr::mutate(response = "cti") %>%
  glimpse()
  
} # }