# Use an age-length key to assign age to individuals in the unaged sample. Use either the semi- or completely-random methods from Isermann and Knight (2005) to assign ages to individual fish in the unaged sample according to the information in an age-length key supplied by the user. ```r alkIndivAge( key, formula, data, type = c("SR", "CR"), breaks = NULL, seed = NULL ) ``` ## Arguments - `key`: A numeric matrix that contains the age-length key. The format of this matrix is important. See details. - `formula`: A formula of the form `age~length` where `age` generically represents the variable that will contain the estimated ages once the key is applied (i.e., should currently contain no values) and `length` generically represents the variable that contains the known length measurements. If only `~length` is used, then a new variable called age will be created in the resulting data frame. - `data`: A data.frame that minimally contains the length measurements and possibly contains a variable that will receive the age assignments as given in `formula`. - `type`: A string that indicates whether to use the semi-random (`type="SR"`, default) or completely-random (`type="CR"`) methods for assigning ages to individual fish. See the [IFAR chapter](https://fishr-core-team.github.io/fishR/pages/books.html#introductory-fisheries-analyses-with-r) for more details. - `breaks`: A numeric vector of lower values that define the length intervals. See details. - `seed`: A single numeric that is given to `set.seed` to set the random seed. This allows repeatability of results. ## Returns The original data.frame in `data` with assigned ages added to the column supplied in `formula` or in an additional column labeled as `age`. See details. ## Details The age-length key in `key` must have length intervals as rows and ages as columns. The row names of `key` (i.e., `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 `key` (i.e., `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 unaged sample to which the age-length key is to be applied (i.e., sent in the `length` portion of the `formula`). If this constraint is not met, then the function will stop with an error message. If `breaks=NULL`, then the length intervals for the unaged sample will be determined with a starting interval at the minimum value of the row names in `key` and a width of the length intervals as determined by the minimum difference in adjacent row names of `key`. If length intervals of differing widths were used when constructing `key`, then those breaks should be supplied to `breaks=`. Use of `breaks=` may be useful when uneven length interval widths were used because the lengths in the unaged sample are not fully represented in the aged sample. See the examples. Assigned ages will be stored in the column identified on the left-hand-side of `formula` (if the formula has both a left- and right-hand-side). If this variable is missing in `formula`, then the new column will be labeled with `age`. ## Testing The `type="SR"` method worked perfectly on a small example. The `type="SR"` method provides results that reasonably approximate the results from `alkAgeDist` and `alkMeanVar`, which suggests that the age assessments are reasonable. ## IFAR Chapter 5-Age-Length Key. ## Examples ```r ## First Example -- Even breaks for length categories WR1 <- WR79 # add length categories (width=5) WR1$LCat <- lencat(WR1$len,w=5) # isolate aged and unaged samples WR1.age <- subset(WR1, !is.na(age)) WR1.len <- subset(WR1, is.na(age)) # note no ages in unaged sample head(WR1.len) # create age-length key raw <- xtabs(~LCat+age,data=WR1.age) ( WR1.key <- prop.table(raw, margin=1) ) # apply the age-length key WR1.len <- alkIndivAge(WR1.key,age~len,data=WR1.len) # now there are ages head(WR1.len) # combine orig age & new ages WR1.comb <- rbind(WR1.age, WR1.len) # mean length-at-age Summarize(len~age,data=WR1.comb,digits=2) # age frequency distribution ( af <- xtabs(~age,data=WR1.comb) ) # proportional age distribution ( ap <- prop.table(af) ) ## Second Example -- length sample does not have an age variable WR2 <- WR79 # isolate age and unaged samples WR2.age <- subset(WR2, !is.na(age)) WR2.len <- subset(WR2, is.na(age)) # remove age variable (for demo only) WR2.len <- WR2.len[,-3] # add length categories to aged sample WR2.age$LCat <- lencat(WR2.age$len,w=5) # create age-length key raw <- xtabs(~LCat+age,data=WR2.age) ( WR2.key <- prop.table(raw, margin=1) ) # apply the age-length key WR2.len <- alkIndivAge(WR2.key,~len,data=WR2.len) # add length cat to length sample WR2.len$LCat <- lencat(WR2.len$len,w=5) head(WR2.len) # combine orig age & new ages WR2.comb <- rbind(WR2.age, WR2.len) Summarize(len~age,data=WR2.comb,digits=2) ## Third Example -- Uneven breaks for length categories WR3 <- WR79 # set up uneven breaks brks <- c(seq(35,100,5),110,130) WR3$LCat <- lencat(WR3$len,breaks=brks) WR3.age <- subset(WR3, !is.na(age)) WR3.len <- subset(WR3, is.na(age)) head(WR3.len) raw <- xtabs(~LCat+age,data=WR3.age) ( WR3.key <- prop.table(raw, margin=1) ) WR3.len <- alkIndivAge(WR3.key,age~len,data=WR3.len,breaks=brks) head(WR3.len) WR3.comb <- rbind(WR3.age, WR3.len) Summarize(len~age,data=WR3.comb,digits=2) ``` ## References Ogle, D.H. 2016. [Introductory Fisheries Analyses with R](https://fishr-core-team.github.io/fishR/pages/books.html#introductory-fisheries-analyses-with-r). Chapman & Hall/CRC, Boca Raton, FL. Isermann, D.A. and C.T. Knight. 2005. A computer program for age-length keys incorporating age assignment to individual fish. North American Journal of Fisheries Management, 25:1153-1160. [Was (is?) from http://www.tandfonline.com/doi/abs/10.1577/M04-130.1.] ## See Also See `alkAgeDist` and `alkMeanVar` for alternative methods to derived age distributions and mean (and SD) values for each age. See `alkPlot` for methods to visualize age-length keys. ## Author(s) Derek H. Ogle, DerekOgle51@gmail.com . This is largely an R version of the SAS code provided by Isermann and Knight (2005).

alkIndivAge function