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Last data update: 2014.03.03

R: Computes Chapman-Robson estimates of S and Z.

chapmanRobson

R Documentation

Computes Chapman-Robson estimates of S and Z.

Description

Computes the Chapman-Robson estimates of annual survival rate (S) and instantaneous mortality rate (Z) from catch-at-age data on the descending limb of a catch-curve. Method functions extract estimates with associated standard errors and confidence intervals. A plot method highlights the descending-limb, shows the linear model on the descending limb, and, optionally, prints the estimated Z and A.

Usage

chapmanRobson(x, ...)

## Default S3 method:
chapmanRobson(x, catch, ages2use = age,
  zmethod = c("Smithetal", "Hoenigetal", "original"), ...)

## S3 method for class 'formula'
chapmanRobson(x, data, ages2use = age,
  zmethod = c("Smithetal", "Hoenigetal", "original"), ...)

## S3 method for class 'chapmanRobson'
summary(object, verbose = FALSE, ...)

## S3 method for class 'chapmanRobson'
confint(object, parm = c("all", "both", "S", "Z"),
  level = conf.level, conf.level = 0.95, ...)

## S3 method for class 'chapmanRobson'
plot(x, pos.est = "topright", cex.est = 0.95,
  ylab = "Catch", xlab = "Age", col.pt = "gray30", ...)

Arguments

`x`	A numerical vector of the assigned ages in the catch curve or a formula of the form `catch~age` when used in `chapmanRobson`. An object saved from `chapmanRobson` (i.e., of class `chapmanRobson`) when used in the methods.
`catch`	A numerical vector of the catches or CPUEs for the ages in the catch curve. Not used if `x` is a formula.
`ages2use`	A numerical vector of the ages that define the descending limb of the catch curve.
`zmethod`	A string that indicates the method to use for estimating Z. See details.
`data`	A data frame from which the variables in the `x` formula can be found. Not used if `x` is not a formula.
`object`	An object saved from the `chapmanRobson` call (i.e., of class `chapmanRobson`).
`verbose`	A logical that indicates whether the method should return just the estimate (`FALSE`; default) or a more verbose statement.
`parm`	A numeric or string (of parameter names) vector that specifies which parameters are to be given confidence intervals If missing, all parameters are considered.
`level`	Same as `conf.level`. Used for compatability with the generic `confint` function.
`conf.level`	A number representing the level of confidence to use for constructing confidence intervals.
`pos.est`	A string to identify where to place the estimated mortality rates on the plot. Can be set to one of `"bottomright"`, `"bottom"`, `"bottomleft"`, `"left"`, `"topleft"`, `"top"`, `"topright"`, `"right"` or `"center"` for positioning the estimated mortality rates on the plot. Typically `"bottomleft"` (DEFAULT) and `"topright"` will be “out-of-the-way” placements. Set `pos.est` to `NULL` to remove the estimated mortality rates from the plot.
`cex.est`	A single numeric characther expansion value for the estimated mortaliry rates on the plot.
`ylab`	A label for the y-axis (`"Catch"` is the default).
`xlab`	A label for the x-axis (`"Age"` is the default).
`col.pt`	a string that indicates the color of the plotted points.
`...`	Additional arguments for methods.

Details

The default is to use all ages in the age vector. This is only appropriate if the age and catch vectors contain only the ages and catches on the descending limb of the catch curve. Use ages2use to isolate only the catch and ages on the descending limb.

The Chapman-Robson method provides an estimate of the annual survival rate, with the annual mortality rate (A) determined by 1-S. The instantaneous mortality rate is often computed as -log(S). However, Hoenig et al. (1983) showed that this produced a biased (over)estimate of Z and provided a correction. The correction is applied by setting zmethod="Hoenigetal". Smith et al. (2012) showed that the Hoenig et al. method should be corrected for a variance inflation factor. This correction is applied by setting zmethod="Smithetal" (which is the default behavior). Choose zmethod="original" to use the original estimates for Z and it's SE as provided by Chapman and Robson.

Value

A list with the following items:

age the original vector of assigned ages.
catch the original vector of observed catches or CPUEs.
age.e a vector of assigned ages used to estimate mortalities.
catch.e a vector of catches or CPUEs used to estimate mortalities.
age.r a vector of recoded ages used to estimate mortalities. See references.
n a numeric holding the intermediate calcualtion of n. See references.
T a numeric holding the intermediate calcualtion of T. See references.
est A 2x2 matrix that contains the estimates and standard errors for S and Z.

Testing

Tested the results of chapmanRobson against the results in Miranda and Bettoli (2007). The point estimates of S matched perfectly but the SE of S did not because Miranda and Bettoli used a rounded estimate of S in the calculation of the SE of S but chapmanRobson does not.

Tested the results against the results from agesurv in fishmethods using the rockbass data.frame in fishmethods. Results for Z and the SE of Z matched perfectly for non-bias-corrected results. The estimate of Z, but not the SE of Z, matched for the bias-corrected (following Smith et al. (2012)) results. FSA uses equation 2 from Smith et al. (2012) whereas fishmethods appears to use equation 5 from the same source to estimate the SE of Z.

IFAR Chapter

11-Mortality.

Author(s)

Derek H. Ogle, derek@derekogle.com

References

Ogle, D.H. 2016. Introductory Fisheries Analyses with R. Chapman & Hall/CRC, Boca Raton, FL.

Chapman, D.G. and D.S. Robson. 1960. The analysis of a catch curve. Biometrics. 16:354-368.

Hoenig, J.M. and W.D. Lawing, and N.A. Hoenig. 1983. Using mean age, mean length and median length data to estimate the total mortality rate. International Council for the Exploration of the Sea, CM 1983/D:23, Copenhagen.

Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.]

Robson, D.S. and D.G. Chapman. 1961. Catch curves and mortality rates. Transactions of the American Fisheries Society. 90:181-189.

Smith, M.W., A.Y. Then, C. Wor, G. Ralph, K.H. Pollock, and J.M. Hoenig. 2012. Recommendations for catch-curve analysis. North American Journal of Fisheries Management. 32:956-967.

Examples

data(BrookTroutTH)
plot(catch~age,data=BrookTroutTH,pch=19)

## demonstration of formula notation
cr1 <- chapmanRobson(catch~age,data=BrookTroutTH,ages2use=2:6)
summary(cr1)
summary(cr1,verbose=TRUE)
confint(cr1)
plot(cr1)

## demonstration of excluding ages2use
cr2 <- chapmanRobson(catch~age,data=BrookTroutTH,ages2use=-c(0,1))
summary(cr2)
plot(cr2)

## demonstration of ability to work with missing age classes
age <- c(  2, 3, 4, 5, 7, 9,12)
ct  <- c(100,92,83,71,56,35, 1)
cr3 <- chapmanRobson(age,ct,4:12)
summary(cr3)
plot(cr3)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(FSA)


 ############################################
 ##      FSA package, version 0.8.7        ##
 ##    Derek H. Ogle, Northland College    ##
 ##                                        ##
 ## Run ?FSA for documentation.            ##
 ## Run citation('FSA') for citation ...   ##
 ##   please cite if used in publication.  ##
 ##                                        ##
 ## See derekogle.com/fishR/ for more      ##
 ##   thorough analytical vignettes.       ##
 ############################################


> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/FSA/chapmanRobson.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chapmanRobson
> ### Title: Computes Chapman-Robson estimates of S and Z.
> ### Aliases: chapmanRobson chapmanRobson.default chapmanRobson.formula
> ###   confint.chapmanRobson plot.chapmanRobson summary.chapmanRobson
> ### Keywords: htest manip
> 
> ### ** Examples
> 
> data(BrookTroutTH)
> plot(catch~age,data=BrookTroutTH,pch=19)
> 
> ## demonstration of formula notation
> cr1 <- chapmanRobson(catch~age,data=BrookTroutTH,ages2use=2:6)
> summary(cr1)
    Estimate Std. Error
S 49.4600432  2.3260749
Z  0.7018264  0.1153428
> summary(cr1,verbose=TRUE)
Intermediate statistics: n=235; T=229
    Estimate Std. Error
S 49.4600432  2.3260749
Z  0.7018264  0.1153428
> confint(cr1)
     95% LCI    95% UCI
S 44.9010202 54.0190662
Z  0.4757586  0.9278941
> plot(cr1)
> 
> ## demonstration of excluding ages2use
> cr2 <- chapmanRobson(catch~age,data=BrookTroutTH,ages2use=-c(0,1))
> summary(cr2)
    Estimate Std. Error
S 49.4600432  2.3260749
Z  0.7018264  0.1153428
> plot(cr2)
> 
> ## demonstration of ability to work with missing age classes
> age <- c(  2, 3, 4, 5, 7, 9,12)
> ct  <- c(100,92,83,71,56,35, 1)
> cr3 <- chapmanRobson(age,ct,4:12)
Warning message:
Some 'ages2use' not in observed ages. 
> summary(cr3)
    Estimate Std. Error
S 63.2683658  1.8679976
Z  0.4569234  0.1465991
> plot(cr3)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>