explore_species_composition: Explores species composition based on landings

In andybeet/indexPPR: Utilities to create ecosystem overfishing indices for the NEFSC State of the Ecosystem report

Description

Species that comprise the top x

Usage

explore_species_composition(
  channel,
  landings,
  threshold,
  filename = NULL,
  speciesCodeCN = "NESPP3",
  catchCN = "CATCH",
  ...
)

Arguments

channel	DBI object. Connection object to database
landings	Data frame (n x r). r >= 3. Must have at least three columns (one named YEAR) The other two necessary columns numst contain Species codes and Catch (units)
threshold	Numeric scalar. Determining the fraction of landings to be represented. Eg. threshold = 0.8 would find the fewest number of species (ordered by landings) that comprise 80% of landings.
filename	Character string. Filename of exported figure
speciesCodeCN	Character string. The name of the column in datafraem that contains the Species codes. Default = "NESPP3"
catchCN	Character string. The name of the column that contains the catch. Default = "CATCH"
...	Other arguments passed to ggplot::ggsave

Value

List:

p	ggplot object
data	Tibble (n x 5). Columns: YEAR,NESPP3,LANDINGS,COMNAME,PresenceAbsence

Attention

For this to work, you need an oracle client installed. Tested with Oracle instantClient_12_2 installed Note: if you use 64 bit Rstudio then you need a 64 bit client Note: if you use 32 bit Rstudio then you need a 32 bit client

You'll also need an account set up on the local server

andybeet/indexPPR documentation built on March 18, 2021, 12:33 p.m.