agePrecision: Compute measures of precision among sets of ages.

Description

Computes overall measures of precision for multiple age assignments made on the same individuals. Ages may be from two or more readers of the same structure, one reader at two or more times, or two or more stuctures (e.g., scales, spines, otoliths). Measures of precision include ACV (Average Coefficient of Variation), APE (Average Percent Error), and various percentage difference values.

Usage

agePrecision(formula, data)
"summary"(object, what = c("precision", "difference", "absolute difference", "details"), percent = TRUE, trunc.diff = NULL, digits = 4, ...)

Arguments

formula

A formula of the form ~var1+var2+var3+... or, alternatively, var1~var2+var3+..., where the varX generically represent the variables that contain the age assignments. The alternative formula allows for similar code as used in ageBias and can have only one variable on the left-hand side.

data

A data.frame that minimally contains the variables in formula.

object

An object of class agePrec, usually from agePrecision.

what

A string (or vector of strings) that indicates what type of summary to print. See details.

percent

A logical that indicates whether the difference table (see details) should be represented as percentages (TRUE; default) or frequency (FALSE) of fish.

trunc.diff

A single integer that identifies the age for which all values that age and greater are combined into one category. See the examples.

digits

A single numeric that indicates the minimum number of digits to print when using summary.

...

Additional arguments for methods.

Value

The main function returns a list with the following items:

detail A data.frame with all data given in data and intermediate calculations for each fish. See details
rawdiff A frequency table of fish by differences for each pair of ages.
absdiff A frequency table of fish by absolute differences for each pair of ages.
APE The mean average percent error.
ACV The mean coefficient of variation.
n Number of fish in data.
validn Number of fish in data that have non-NA data for all R age estimates.
R Number of age estimates for each fish given in formula.

The summary returns the result if what= contains one item, otherwise it returns nothing. See details for what is printed.

Testing

Tested all precision results against published results in Herbst and Marsden (2011) for the WhitefishLC data and the results for the AlewifeLH data set from FSAdata against results from the online resource at http://www.nefsc.noaa.gov/fbp/age-prec/.

IFAR Chapter

4-Age Comparisons.

Details

If what="precision" in summary then a summary table that contains the following items will be printed:

n Number of fish in data.
validn Number of fish in data that have non-NA data for all R age estimates.
R Number of age estimates given in formula.
ACV The mean coefficient of variation. See the IFAR chapter for calculational details.
APE The mean average percent error. See the IFAR chapter for calculational details.
PercAgree The percentage of fish for which all age assignments perfectly agree.

If what="difference" is used in summary, then a table that describes either the percentage (if percent=TRUE, default) or frequency of fish by the difference in paired age assignments. This table has one row for each possible pair of age assignments.

If what="absolute difference" is used in summary, then a table that describes either the percentage (if percent=TRUE, default) or frequency of fish by the absolute value of the difference in paired age assignments. This table has one row for each possible pair of age assignments. The “1” column, for example, represents age assignments that disagree by one year (in either direction).

If what="detail" is used in summary, then a data frame of the original data along with the intermediate caculations of the average age, standard deviation of age, APE, and ACV for each individual will be printed. These details are generally only used to check or to understand calculations.

All percentage calulations above use the validn value in the denominator.

References

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

Beamish, R.J. and D.A. Fournier. 1981. A method for comparing the precision of a set of age determinations. Canadian Journal of Fisheries and Aquatic Sciences 38:982-983. [Was (is?) available from http://www.pac.dfo-mpo.gc.ca/science/people-gens/beamish/PDF_files/compareagecjfas1981.pdf.]

Campana, S.E. 1982. Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods. Journal of Fish Biology 59:197-242. [Was (is?) available from http://www.denix.osd.mil/nr/crid/Coral_Reef_Iniative_Database/References_for_Reef_Assessment_files/Campana,%202001.pdf.]

Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. Graphical and statistical methods for determining the consistency of age determinations. Transactions of the American Fisheries Society 124:131-138. [Was (is?) available from http://www.bio.gc.ca/otoliths/documents/Campana%20et%20al%201995%20TAFS.pdf.]

Chang, W.Y.B. 1982. A statistical method for evaluating the reproducibility of age determination. Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210. [Was (is?) available from http://www.nrcresearchpress.com/doi/abs/10.1139/f82-158.]

McBride, R.S. 2015. Diagnosis of paired age agreement: A simulation approach of accuracy and precision effects. ICES Journal of Marine Science, 72:2149-2167.

Examples

Run this code

## Example with just two age assignments
data(WhitefishLC)
ap1 <- agePrecision(~otolithC+scaleC,data=WhitefishLC)
summary(ap1)
summary(ap1,what="precision")
summary(ap1,what="difference")
summary(ap1,what="difference",percent=FALSE)
summary(ap1,what="absolute")
summary(ap1,what="absolute",percent=FALSE)
summary(ap1,what="absolute",trunc.diff=4)
summary(ap1,what="absolute",percent=FALSE)
summary(ap1,what=c("precision","difference"))

barplot(ap1$rawdiff,ylab="Frequency",xlab="Otolith - Scale Age")
summary(ap1,what="detail")

## Example with three age assignments
ap2 <- agePrecision(~otolithC+finrayC+scaleC,data=WhitefishLC)
summary(ap2)
summary(ap2,what="precision")
summary(ap2,what="difference")
summary(ap2,what="difference",percent=FALSE)
summary(ap2,what="absolute")
summary(ap2,what="absolute",percent=FALSE)
summary(ap2,what="absolute",trunc.diff=4)
summary(ap2,what="absolute",percent=FALSE,trunc.diff=4)
summary(ap2,what="detail")

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