catchsurvey {fishmethods} | R Documentation |
Catch-Survey Analysis
Description
This function applies the catch-survey analysis method of Collie and Kruse (1998) for estimating abundance from catch and survey indices of relative abundance
Usage
catchsurvey(year = NULL, catch = NULL, recr = NULL, post = NULL, M = NULL,
T = NULL, phi = NULL, w = 1, initial = c(NA,NA,NA),uprn = NA, graph = TRUE)
Arguments
year |
vector containing the time series of numeric year labels. |
catch |
vector containing the time series of catch (landings) data. |
recr |
vector containing the time series of survey indices for recruit individuals. |
post |
vector containing the time series of survey indices for post-recruit individuals. |
M |
instantaneous natural mortality rate. Assumed constant throughout time series |
T |
proportion of year between survey and fishery. |
phi |
relative recruit catchability. |
w |
recruit sum of squares weight. |
initial |
initial recruit estimate,initial postrecruit estimate in year 1, and initial catchability estimate. |
uprn |
the upper bound for the recruit and postrecruit estimates. |
graph |
logical indicating whether observed versus predicted recruit and post-recruit indices, total abundance and fishing mortality should be plotted. Default=TRUE. |
Details
Details of the model are given in Collie and Kruse (1998).
Value
List containing the estimate of catchability, predicted recruit index by year (rest), estimate of recruit abundance (R), predicted post-recruit index by year (nest), post-recruit abundance (N), total abundance (TA: R+N), total instantaneous mortality (Z), and fishing mortality (Fmort)
Author(s)
Gary A. Nelson, Massachusetts Division of Marine Fisheries gary.nelson@mass.gov
References
Collie JS and GH Kruse 1998. Estimating king crab (Paralithodes camtschaticus) abundance from commercial catch and research survey data. In: Jamieson GS, Campbell A, eds. Proceedings of the North Pacific Symposium on Invertebrate Stock Assessment and Management. Can Spec Publ Fish Aquat Sci. 125; p 73-83.
See also Collie JS and MP Sissenwine. 1983. Estimating population size from relative abundance data measured with error. Can J Fish Aquat Sci. 40:1871-1879.
Examples
## Example takes a bit of time to run
## Not run:
data(nshrimp)
catchsurvey(year=nshrimp$year,catch=nshrimp$C,recr=nshrimp$r,post=nshrimp$n,M=0.25,
T=0.5,phi=0.9,w=1,initial=c(500,500,0.7),uprn=10000)
## End(Not run)