Using FishBase with ranemone • ranemone

Setup

Load packages. tidyverse is a collection of useful packages for data science.

# install.packages("pak")
# pak::pak("tidyverse")
library(conflicted) # for safety
library(tidyverse)
library(ranemone)

Set options for your data and cache directories. See the Get started page for details.

options(ranemone.directory_prefix = "~/db")
options(ranemone.cache_dir = "~/.cache/ranemone")

Reading FishBase tables

Read and join FishBase tables: “species”, “ecology”, and “estimate”.

fb_sp_ecol = ranemone::fb_species_ecology_estimate() |>
  dplyr::mutate(species = paste(.data$Genus, .data$Species))

Individual tables can be read as well.

fb_species = ranemone::read_fb_tbl("species")
fb_ecology = ranemone::read_fb_tbl("ecology")
fb_estimate = ranemone::read_fb_tbl("estimate")

Combining FishBase data with ANEMONE data

Read ANEMONE community tables and summarize them into a species-level table.

community_df = ranemone::read_tsv_xz("community_qc3nn_target.tsv.xz")
species_df = community_df |>
  ranemone::summarize_ncopies(.by = species)

Combine it with FishBase ecology data and summarize them for each sample.

species_df |>
  dplyr::left_join(fb_sp_ecol, by = "species") |>
  dplyr::summarize(
    FoodTroph_mean = mean(FoodTroph, na.rm = TRUE),
    FoodTroph_wmean = weighted.mean(FoodTroph, ncopiesperml, na.rm = TRUE),
    FoodTroph_coverage = sum(!is.na(FoodTroph)) / dplyr::n(),
    TempPrefMean_mean = mean(TempPrefMean, na.rm = TRUE),
    TempPrefMean_wmean = weighted.mean(TempPrefMean, ncopiesperml, na.rm = TRUE),
    TempPrefMean_coverage = sum(!is.na(TempPrefMean)) / dplyr::n(),
    .by = "samplename"
  )

See Summarizing data for getting other statistics such as alpha diversity.