Computes the mean value-at-age in a larger sample based on an age-length-key created from a subsample of ages through a two-stage random sampling design. The mean values could be mean length-, weight-, or fecundity-at-age, for example. The methods of Bettoli and Miranda (2001) or Quinn and Deriso (1999) are used. A standard deviation is computed for the Bettoli and Miranda (2001) method and standard error for the Quinn and Deriso (1999) method. See the testing section notes.
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A numeric matrix that contains the age-length key. See details.
A formula of the form
A data.frame that minimally contains the length intervals, assessed ages, and the variable to be summarized (i.e., this should be the aged sample) as given in
A vector of sample sizes for each length interval in the complete sample (i.e., all fish regardless of whether they were aged or not).
A string that indicates which method of calculation should be used. See details.
The age-length key
key must have length intervals as rows and ages as columns. The row names of
rownames(key)) must contain the minimum values of each length interval (e.g., if an interval is 100-109, then the corresponding row name must be 100). The column names of
colnames(key)) must contain the age values (e.g., the columns can NOT be named with “age.1”, for example).
The length intervals in the rows of
key must contain all of the length intervals present in the larger sample. Thus, the length of
len.n must, at least, equal the number of rows in
key. If this constraint is not met, then the function will stop with an error message.
Note that the function will stop with an error if the formula in
formula does not meet the specific criteria outlined in the parameter list above.
A data.frame with as many rows as ages (columns) present in
key and the following three variables:
age The ages.
mean The mean value at each age.
sd,se The SD if
method="BettoliMiranda" or SE of the mean if
method="QuinnDeriso" for the value at each age.
The results of these functions have not yet been rigorously tested. The Bettoli and Miranda (2001) results appear, at least, approximately correct when compared to the results from
alkIndivAge. The Quinn and Deriso (1999) results appear at least approximately correct for the mean values, but do not appear to be correct for the SE values. Thus, a note is returned with the Quinn and Deriso (1999) results that the SE should not be trusted.
Derek H. Ogle, email@example.com
Ogle, D.H. 2016. Introductory Fisheries Analyses with R. Chapman & Hall/CRC, Boca Raton, FL.
Bettoli, P. W. and Miranda, L. E. 2001. A cautionary note about estimating mean length at age with subsampled data. North American Journal of Fisheries Management, 21:425-428.
Quinn, T. J. and R. B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York, New York. 542 pages
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## Example -- Even breaks for length categories WR1 <- WR79 # add length intervals (width=5) WR1$LCat <- lencat(WR1$len,w=5) # get number of fish in each length interval in the entire sample len.n <- xtabs(~LCat,data=WR1) # isolate aged sample WR1.age <- subset(WR1, !is.na(age)) # create age-length key raw <- xtabs(~LCat+age,data=WR1.age) ( WR1.key <- prop.table(raw, margin=1) ) ## use age-length key to estimate mean length-at-age of all fish # Bettoli-Miranda method alkMeanVar(WR1.key,len~LCat+age,WR1.age,len.n) # Quinn-Deriso method alkMeanVar(WR1.key,len~LCat+age,WR1.age,len.n,method="QuinnDeriso")
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