Added aStandard and StdIntLit

.Rbuildignore

@@ -9,3 +9,4 @@
 ^README\.md
 ^\.travis\.yml$
 ^appveyor\.yml$
+^data-raw$

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(RFBCoptions)
+export(aStandard)
 export(addRadCap)
 export(backCalc)
 export(bcFuns)

NEWS.md

@@ -5,6 +5,7 @@
 * Added tests.
 * Updated "Collect Data" vignette for changes to `combineData()`.
 * Changed "Back-calculating Lengths" vignette for new `backCalc()`.
+* `aStandard()`: Added. Addresses [#10](https://github.com/droglenc/RFishBC/issues/10).
 * `backCalc()`: Added.
 * `bcFuns()`: Modified. Changed to using `STOP()`. Changed all `Lc` to `Lcap`, `Rc` to `Rcap`, `agec` to `Acap`, and `agei` to `Ai`. Changed all BPH-related models to use `a`, `b`, and `c` and all SPH-related odels to use `A`, `B`, and `C`. Started using `iGetBCMethod()`. Removed `verbose=` (moved to within the returned function).
 * `bcUtilChecker()`: Modified. Changed to using `STOP()` and `WARN()`.
@@ -13,6 +14,7 @@
 * `iGetBCMethod()`: Added. Used in `backCalc()` and `bcFuns()`.
 * `SMBassWB1`: Added.
 * `SMBassWB2`: Added.
+* `StdIntLit`: Added.
 
 # RFishBC 0.0.8 13-May-18
 * Added tests.

R/StdIntLit.R

@@ -0,0 +1,17 @@
+#' @title Standard intercepts for Fraser-Lee model by species.
+#'
+#' @description Standard intercepts (in mm) for Fraser-Lee model for all species for which the standard has been defined.
+#'
+#' @format A data frame with 1 rows and 3 variables:
+#' \describe{
+#'   \item{species}{Fish species.}
+#'   \item{a}{Standard intercept value (in mm).}
+#'   \item{source}{Source of the standard.}
+#' }
+#' 
+#' @references Beck, H.D., D.W. Willis, and J.M. Francis. 1997. A proposed standard intercept for the White Bass body length-scale relationship. North American Journal of Fisheries Management 32:239-248.
+#' 
+#' Carlander, K.D. 1982. Standard intercepts for calculating lengths from scale measurements for some centrarchid and percid fishes. Transactions of the American Fisheries Society 111:333-336.
+#' 
+#' @seealso \code{\link{aStandard}}
+"StdIntLit"

R/aStandard.R

@@ -0,0 +1,32 @@
+#' @title Finds standard intercept (a) for Fraser-Lee back-calculation model for a particular species.
+#'
+#' @description Finds standard intercept (a; mm) for Fraser-Lee back-calculation model for a particular species for all species for which a value of a has been defined.
+#'
+#' @param species A string that contains the species name for which to find teh standard intercept value.
+#' @return A single value from \code{\link{StdIntLit}} that is the standard intercept value (a; mm) for the species provided in \code{species}.
+#' 
+#' @author Derek H. Ogle, \email{derek@@derekogle.com}
+#'
+#' @seealso \code{\link{StdIntLit}}
+#' 
+#' @keywords manip
+#'
+#' @examples
+#' aStandard("Bluegill")
+#' aStandard("Walleye")
+#'
+#' @export
+aStandard <- function(species) {
+  # Load StdIntLit data frame into this function's environment. The data/get
+  #   combination are used to avoide the "no global binding" note at CHECK
+  StdIntLit <- get(utils::data("StdIntLit",envir=environment()),envir=environment())
+  # Check species
+  if (missing(species)) STOP("'species' must be one of: ",
+                             paste(StdIntLit$species,collapse=", "))
+  species <- FSA::capFirst(species)
+  if (length(species)>1) STOP("Can have only one name in 'species'.")
+  if (!species %in% StdIntLit$species) STOP("'species' must be one of: ",
+                                            paste(StdIntLit$species,collapse=", "))
+  # Return a for that species
+  StdIntLit$a[StdIntLit==species]
+}

_pkgdown.yml

@@ -1,5 +1,7 @@
 title: RFishBC
 
+url: http://derekogle.com/RFishBC
+
 authors:
   Derek H. Ogle:
     href: http://derekogle.com
@@ -25,6 +27,7 @@ reference:
     contents:
       - backCalc
       - bcFuns
+      - aStandard
   - title: Utilities
     desc: Functions to perform miscellaneous utilities.
     contents:
@@ -36,6 +39,7 @@ reference:
     contents:
       - SMBassWB1
       - SMBassWB2
+      - StdIntLit
 
 navbar:
   type: inverse

data-raw/StdIntLit.R

@@ -0,0 +1,3 @@
+StdIntLit <- read.csv("data-raw/StdIntLit.csv",stringsAsFactors=FALSE)
+str(StdIntLit)
+save(StdIntLit,file="data/StdIntLit.RData")

data-raw/StdIntLit.csv

@@ -0,0 +1,13 @@
+species,a,source
+Black Crappie,35,Carlander (1982)
+Bluegill,20,Carlander (1982)
+Green Sunfish,10,Carlander (1982)
+Largemouth Bass,20,Carlander (1982)
+Pumpkinseed,25,Carlander (1982)
+Rock Bass,25,Carlander (1982)
+Smallmouth Bass,35,Carlander (1982)
+Walleye,55,Carlander (1982)
+Warmouth,20,Carlander (1982)
+White Bass,40,Beck et al. (1997)
+White Crappie,35,Carlander (1982)
+Yellow Perch,30,Carlander (1982)

docs/pkgdown.yml

@@ -7,4 +7,7 @@ articles:
   BCIntro: BCIntro/BCIntro.html
   collectRadiiData: MeasureRadii/collectRadiiData.html
   seeRadiiData: MeasureRadii/seeRadiiData.html
+urls:
+  reference: http://derekogle.com/RFishBC/reference
+  article: http://derekogle.com/RFishBC/articles