README.md

In justinpriest/cwtr: CWT Helper Functions

cwtr

This R package allows for simple calculation of CWT estimates and bootstrap intervals for tag recovery and sampling in fisheries.

Installation

You can install the development version of cwtr from GitHub with:

# install.packages("remotes")
remotes::install_github("justinpriest/cwtr", build_vignettes = TRUE)

Example Usage

cwtr allows you to quickly calculate point estimates using the function cwtEst().

 library(cwtr) 
 x <- cwtEst(N=c(33666,NA), n=7618, 
             lambda=c(138,140,116,116), m=1, theta=c(0.01886,102.15))
 summary(x) 
#> Point Estimates Summary:
#>       Estimate  Variance      SE    CV   CI_lwr  CI_upp
#> r.est  237.716 56279.662 237.233 0.998 -152.498 627.930
#> t.est    4.483    15.617   3.952 0.881   -2.017  10.983
#> q.est    0.007     0.000   0.007 0.998   -0.005   0.019
#> 
#> NOTE:
#> r is the # of fish caught
#> t is the # of tagged fish caught
#> q is the % of fish caught

The function cwtBoot() calculates bootstrapped intervals for the cwt estimates and can be specified for different methods.

library(cwtr)
x <- cwtEst(N=c(33666,NA), n=7618, 
            lambda=c(138,140,116,116), m=1, theta=c(0.01886,102.15))
xBoot <- cwtBoot(x, method="parametric", nreps=10000)
summary(xBoot)
#> Point Estimates Summary:
#>       Estimate  Variance      SE    CV   CI_lwr  CI_upp
#> r.est  237.716 56279.662 237.233 0.998 -152.498 627.930
#> t.est    4.483    15.617   3.952 0.881   -2.017  10.983
#> q.est    0.007     0.000   0.007 0.998   -0.005   0.019
#> 
#> Bootstrap Estimates Summary:
#>        Mean     Variance SE       CV        Bias      CI_lwr CI_uppr 
#> r.boot 242.4064 58018.03 240.8693 0.9936592 4.690692  0      698.9541
#> t.boot 4.6845   5.514911 2.348385 0.5013096 0.2011825 1      9       
#> m.boot 1.0577   1.111082 1.054079 0.9965762 1.050639  0      3       
#> 
#> NOTE:
#> r is the # of fish caught
#> t is the # of tagged fish caught
#> q is the % of fish caught

These data are of class cwt which allows for simple use of the plot method to generate plots of the bootstrap simulation:

library(cwtr)
x <- cwtEst(N=c(33666,NA), n=7618, 
            lambda=c(138,140,116,116), m=1, theta=c(0.01886,102.15)) 
xBoot <- cwtBoot(x, method="parametric", nreps=10000)
plot(xBoot) 

justinpriest/cwtr documentation built on April 22, 2022, 12:51 a.m.