bubble.rs: Plot of abundance indices

In MEDITS: Analysis of MEDITS-Like Survey Data

Description

The function, using TA (table A, hauls data), TB (table B, catches data), and TC (table C, biological data) tables estimates the abundance indices per hauls for recruits and spawners specimens or for all the cougth specimens togheter. Recruits and spawners specimens are selected using the body length cutoff parameter defined by the user. Bathymetrical lines (class: "SpatialLinesDataFrame", "sp") refers respectively to 50m, 200m, and 800m of depth.

Usage

bubble.rs(TA, TB, TC, GSA=NA, sspp =NA, stage ="recruits",
cutoff=NA, buffer =NA, country=NA,wm=wmap,
land=countries, d1=depth_1, d2=depth_2, d3=depth_3)

Arguments

TA	data frame containing the hauls data (TA, table A).
TB	data frame containing the catches data (TB, table B).
TC	data frame containing the aggregated biological data (TC, table C).
GSA	reference Geographical Sub-Area (GSA) for the analysis.
country	string value the country selected for the analysis in case the latter should be performed by country.
sspp	string of the species code (MEDITS format). The default value is NA and, in case in the data there is only one species, the species code is determined by the merge data frame. If there are more than one species, the species code is mandartory.
stage	fraction of the population that is selected for the analysis: "recruits", "spawners" or "all.stages". "all.stages" allows to plot the abundance index by haul, considering all the specimens.
cutoff	numeric value (threshold) of maturity length to be used for selecting the fraction of the population for the analysis.
buffer	numeric value to define the extension (in meters) of the buffer around the study area (haul positions range) in the map.
wm	shapefile of the land's contours of the world map
land	shapefile of the world's land
d1	shapefile of the 50m bathymetrical line
d2	shapefile of the 200m bathymetrical line
d3	shapefile of the 800m bathymetrical line

Details

The function performs the analysis for one stage at time. The abundance indices per haul are estimated selecting either the total number of specimens with Total Length (TL) >= cutoff value for spawners or with TL <= cutoff for recruits.

Value

The function returns the bubble plot of the abundance indices of the selected life stage.

Author(s)

Walter Zupa

Examples

library(MEDITS)
bubble.rs(TA, TB, TC, GSA=10, sspp ="ARISFOL", stage ="recruits",
cutoff=29, buffer =5000, country ="ITA")

MEDITS documentation built on Dec. 23, 2019, 1:06 a.m.