# Creates a vector of Gabelhouse lengths for each species in an entire data frame. Creates a vector of the Gabelhouse lengths specific to a species for all individuals in an entire data frame. ```r psdAdd(len, ...) ## Default S3 method: psdAdd( len, species, units = c("mm", "cm", "in"), use.names = TRUE, addSpec = NULL, addLens = NULL, verbose = TRUE, ... ) ## S3 method for class 'formula' psdAdd( len, data = NULL, units = c("mm", "cm", "in"), use.names = TRUE, addSpec = NULL, addLens = NULL, verbose = TRUE, ... ) ``` ## Arguments - `len`: A numeric vector that contains lengths measurements or a formula of the form `len~spec` where len generically represents the length variable and spec generically represents the species variable. Note that this formula can only contain two variables and must have the length variable on the left-hand-side and the species variable on the right-hand-side. - ``...``: Not used. - `species`: A character or factor vector that contains the species names. Ignored if `len` is a formula. - `units`: A string that indicates the type of units used for the lengths. Choices are `mm` for millimeters (DEFAULT), `cm` for centimeters, and `in` for inches. - `use.names`: A logical that indicates whether the vector returned is numeric (`=FALSE`) or string (`=TRUE`; default) representations of the Gabelhouse lengths. See details. - `addSpec`: A character vector of species names for which `addLens` will be provided. - `addLens`: A numeric vector of lengths that should be used in addition to the Gabelhouse lengths for the species in `addSpec`. See examples. - `verbose`: A logical that indicates whether detailed messages about species without Gabelhouse lengths or with no recorded values should be printed or not. - `data`: A data.frame that minimally contains the length measurements and species names if `len` is a formula. ## Returns A numeric or factor vector that contains the Gabelhouse length categories. ## Details This computes a vector that contains the Gabelhouse lengths specific to each species for all individuals in an entire data frame. The vector can be appended to an existing data.frame to create a variable that contains the Gabelhouse lengths for each individual. The Gabelhouse length value will be `NA` for each individual for which Gabelhouse length definitions do not exist in `PSDlit`. Species names in the data.frame must be the same as those used in `PSDlit`. See the examples for one method for changing species names to something that this function will recognize. Individuals shorter than stock length will be listed as `substock` if `use.names=TRUE` or `0` if `use.names=FALSE`. Additional lengths to be used for a species may be included by giving a vector of species names in `addSpec` and a corresponding vector of additional lengths in `addLens`. Note, however, that `use.names` will be reset to `FALSE` if `addSpec` and `addLens` are specified, as there is no way to order the names for all species when additional lengths are used. ## IFAR Chapter 6-Size Structure. ## Examples ```r ## Create random data for three species # only for repeatability set.seed(345234534) dbg <- data.frame(species=factor(rep(c("Bluegill"),30)), tl=round(rnorm(30,130,50),0)) dbg$wt <- round(4.23e-06*dbg$tl^3.316+rnorm(30,0,10),1) dlb <- data.frame(species=factor(rep(c("Largemouth Bass"),30)), tl=round(rnorm(30,350,60),0)) dlb$wt <- round(2.96e-06*dlb$tl^3.273+rnorm(30,0,60),1) dbt <- data.frame(species=factor(rep(c("Bluefin Tuna"),30)), tl=round(rnorm(30,1900,300),0)) dbt$wt <- round(4.5e-05*dbt$tl^2.8+rnorm(30,0,6000),1) df <- rbind(dbg,dlb,dbt) str(df) ## Examples (non-dplyr) # Add variable using category names -- formula notation df$PSD <- psdAdd(tl~species,data=df) head(df) # Add variable using category names -- non-formula notation df$PSD1 <- psdAdd(df$tl,df$species) head(df) # Add variable using length values as names df$PSD2 <- psdAdd(tl~species,data=df,use.names=FALSE) head(df) # Add additional length and name for Bluegill df$PSD3 <- psdAdd(tl~species,data=df,addSpec="Bluegill",addLens=175) head(df) # Add add'l lengths and names for Bluegill and Largemouth Bass from a data.frame addls <- data.frame(species=c("Bluegill","Largemouth Bass","Largemouth Bass"), lens=c(175,254,356)) df$psd4 <- psdAdd(tl~species,data=df,addSpec=addls$species,addLens=addls$lens) head(df) ## All of the above but using dplyr if (require(dplyr)) { df <- df %>% mutate(PSD1A=psdAdd(tl,species)) %>% mutate(PSD2A=psdAdd(tl,species,use.names=FALSE)) %>% mutate(psd3a=psdAdd(tl,species,addSpec="Bluegill",addLens=175)) %>% mutate(psd4a=psdAdd(tl,species,addSpec=addls$species,addLens=addls$lens)) } df ``` ## 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. Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS). Fisheries 31:86-87. [Was (is?) from http://pubstorage.sdstate.edu/wfs/415-F.pdf.] Guy, C.S., R.M. Neumann, D.W. Willis, and R.O. Anderson. 2006. Proportional size distribution (PSD): A further refinement of population size structure index terminology. Fisheries 32:348. [Was (is?) from http://pubstorage.sdstate.edu/wfs/450-F.pdf.] Willis, D.W., B.R. Murphy, and C.S. Guy. 1993. Stock density indices: development, use, and limitations. Reviews in Fisheries Science 1:203-222. [Was (is?) from http://web1.cnre.vt.edu/murphybr/web/Readings/Willis%20et%20al.pdf.] ## See Also `psdVal`, `psdCalc`, `psdPlot`, `PSDlit`, and `wrAdd` for related functions. See `mapvalues` for help in changing species names to match those in `PSDlit`. ## Author(s) Derek H. Ogle, DerekOgle51@gmail.com

psdAdd function