Added sources to PSDlit and related modifications (fixes #76 )

NEWS.md

@@ -17,8 +17,8 @@
 * `paletteChoices()`: Removed. See `chooseColors()` above. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65).
 * `psdAdd()`: Modified. Changed a `levels()` in `iPSDlitCheck()` to `unique()` because `species` is no longer a factor due to updating `PSDlit` (i.e., rdata file changed with new `read.csv()`).
 * `psdCalc()`: Modified. Added a catch for when "tibble"s are sent in `data=` (addresses [#75](https://github.com/droglenc/FSA/issues/75)).
-* `PSDlit`: Modified. Added length categories for Shoal Bass. Added Striped Bass (Hybrid) and Striped Bass x White Bass; though these are the same as the existing Palmetto Bass.
-* `psdVal()`: Modified. Changed a `levels()` in `iPSDlitCheck()` and `iListSpecies()` to `unique()` because `species` is no longer a factor due to updating `PSDlit` (i.e., rdata file changed with new `read.csv()`).
+* `PSDlit`: Modified. Added length categories for Shoal Bass and Pallid Sturgeon. Added Striped Bass (Hybrid) and Striped Bass x White Bass; though these are the same as the existing Palmetto Bass. Added "source"s for each entry.
+* `psdVal()`: Modified. Changed a `levels()` in `iPSDlitCheck()` and `iListSpecies()` to `unique()` because `species` is no longer a factor due to updating `PSDlit` (i.e., rdata file changed with new `read.csv()`). Added a `showJustSource=` argument that will show the source info (if `TRUE`) or not (if `FALSE`; default), which partially addresses [#76](https://github.com/droglenc/FSA/issues/76).
 * `removal()`: Modified. Added check and then warning if non-whole numbers are in `catch=` (addresses [#60](https://github.com/droglenc/FSA/issues/60)). Also modified checks of data integrity to be more robust (e.g., if a character vector is sent).
 * `residPlot()`: Modified. Removed use of `chooseColors()` (see above).
 * `Subset()`: Removed. Added to `FSA-defunct`. Partially addresses [#65](https://github.com/droglenc/FSA/issues/65).

R/PSDlit.R

@@ -19,6 +19,7 @@
 #'    \item{preferred.cm}{Preferred length in cm.}
 #'    \item{memorable.cm}{Memorable length in cm.}
 #'    \item{trophy.cm}{Trophy length in cm.}
+#'    \item{source}{Literature source for the length entries.}
 #'  }
 #'
 #' @section Topic(s):

R/psdVal.R

@@ -7,6 +7,7 @@
 #' @param incl.zero A logical that indicates if a zero is included in the first position of the returned vector (DEFAULT) or not. This position will be named \dQuote{substock}. See details.
 #' @param addLens A numeric vector that contains minimum length definitions for additional categories. See details.
 #' @param addNames A string vector that contains names for the additional length categories added with \code{addLens}. See details.
+#' @param showJustSource A logical that indicates whether just the literature source information should be returned (\code{TRUE}) or not. If \code{TRUE} this will NOT return any of the Gabelhouse length information.
 #'
 #' @details Finds the Gabelhouse lengths from \code{data(PSDlit)} for the species given in \code{species}. The species name must be spelled exactly (within capitalization differences) as it appears in \code{data(PSDlit)}. Type \code{psdVal()} to see the list of species and how they are spelled.
 #'
@@ -50,45 +51,50 @@
 #' psdVal("Bluegill",units="in",addLens=c(7,9),addNames=c("MinSlot","MaxSlot"))
 #' psdVal("Bluegill",units="in",addLens=c("MinLen"=7))
 #' psdVal("Bluegill",units="in",addLens=c("MinSlot"=7,"MaxSlot"=9))
+#' psdVal("Bluegill",showJustSource=TRUE)
 #'
 #' @export psdVal
 psdVal <- function(species="List",units=c("mm","cm","in"),incl.zero=TRUE,
-                   addLens=NULL,addNames=NULL) {
+                   addLens=NULL,addNames=NULL,showJustSource=FALSE) {
   units <- match.arg(units)
   # load RSDlit data frame into this function's environment
   # data/get combination are used to avoid the "no global binding" note at CHECK
   PSDlit <- get(utils::data("PSDlit",envir=environment()),envir=environment())
   # continue if species name is correct
   if (iPSDLitCheck(PSDlit,species <- capFirst(species))) {
-    # identify columns based on units
-    ifelse(units=="in",cols <- 2:6,cols <- 7:11)
-    # get the length categories
-    PSDvec <- as.matrix(PSDlit[PSDlit$species==species,cols])[1,]
-    # convert to mm if necessary
-    if (units=="mm") PSDvec <- PSDvec*10
-    names(PSDvec) <- c("stock","quality","preferred","memorable","trophy")
-    # add a zero category if asked to
-    if (incl.zero) {
-      PSDvec <- c(0,PSDvec)
-      names(PSDvec)[1] <- "substock"
-    }
-    # add additional lengths if asked to
-    if (!is.null(addLens)) {
-      # add names to the addLens vector
-      addLens <- iHndlAddNames(addLens,addNames)
-      # handle duplicated values
-      tmp <- which(PSDvec %in% addLens)
-      if (length(tmp>0)) {
-        WARN("At least one Gabelhouse length that was in 'addLens' has been removed.")
-        PSDvec <- PSDvec[-tmp]
+    if (showJustSource) {
+      PSDlit[PSDlit$species==species,c(1,12)]
+    } else {
+      # identify columns based on units
+      ifelse(units=="in",cols <- 2:6,cols <- 7:11)
+      # get the length categories
+      PSDvec <- as.matrix(PSDlit[PSDlit$species==species,cols])[1,]
+      # convert to mm if necessary
+      if (units=="mm") PSDvec <- PSDvec*10
+      names(PSDvec) <- c("stock","quality","preferred","memorable","trophy")
+      # add a zero category if asked to
+      if (incl.zero) {
+        PSDvec <- c(0,PSDvec)
+        names(PSDvec)[1] <- "substock"
       }
-      # append the new lens to the Gabelhouse lengths
-      PSDvec <- c(PSDvec,addLens)
-      # re-order so the new values are within the Gabelhouse lengths
-      PSDvec <- PSDvec[order(PSDvec)]
-    }        
-    PSDvec
-  }    
+      # add additional lengths if asked to
+      if (!is.null(addLens)) {
+        # add names to the addLens vector
+        addLens <- iHndlAddNames(addLens,addNames)
+        # handle duplicated values
+        tmp <- which(PSDvec %in% addLens)
+        if (length(tmp>0)) {
+          WARN("At least one Gabelhouse length that was in 'addLens' has been removed.")
+          PSDvec <- PSDvec[-tmp]
+        }
+        # append the new lens to the Gabelhouse lengths
+        PSDvec <- c(PSDvec,addLens)
+        # re-order so the new values are within the Gabelhouse lengths
+        PSDvec <- PSDvec[order(PSDvec)]
+      }        
+      PSDvec
+    }
+  }
 }
 
 

data-raw/PSDlit.csv

@@ -1,67 +1,68 @@
-species,stock.in,quality.in,preferred.in,memorable.in,trophy.in,stock.cm,quality.cm,preferred.cm,memorable.cm,trophy.cm
-Arctic Grayling,8,12,16,20,22,20,30,40,50,55
-Bighead Carp,11.75,21.25,26.75,35,43.75,30,54,68,89,111
-Bigmouth Buffalo,11,18,24,30,37,28,46,61,76,94
-Black Bullhead,6,9,12,15,18,15,23,30,39,46
-Black Carp,15.75,28.25,35.5,46.5,58.25,40,72,90,118,148
-Black Crappie,5,8,10,12,15,13,20,25,30,38
-Blue Catfish,12,20,30,35,45,30,51,76,89,114
-Bluegill,3,6,8,10,12,8,15,20,25,30
-Brook Trout (lentic),8,13,NA,NA,NA,20,33,NA,NA,NA
-Brook Trout (lotic),5,8,NA,NA,NA,13,20,NA,NA,NA
-Brook Trout,8,12,16,20,24,20,30,40,50,60
-Brown Bullhead,5,8,11,14,17,13,20,28,36,43
-Brown Trout (lentic),8,12,16,20,24,20,30,40,50,60
-Brown Trout (lotic),6,9,12,15,18,15,23,30,38,46
-Bull Trout,8,16,20,26,31,20,40,50,65,80
-Burbot,8,15,21,26,32,20,38,53,67,82
-Chain Pickerel,10,15,20,25,30,25,38,51,63,76
-Channel Catfish,11,16,24,28,36,28,41,61,71,91
-Chinook Salmon (landlocked),11,18,24,30,37,28,46,61,76,94
-Common Carp,11,16,21,26,33,28,41,53,66,84
-Cutthroat Trout,8,14,18,24,30,20,35,45,60,75
-Flathead Catfish,14,20,28,34,40,35,51,71,86,102
-Freshwater Drum,8,12,15,20,25,20,30,38,51,63
-Gizzard Shad,7,11,NA,NA,NA,18,28,NA,NA,NA
-Golden Trout,8,10,14,18,22,20,25,35,45,55
-Grass Carp,11.75,21.25,26.75,35,43.75,30,54,68,89,111
-Green Sunfish,3,6,8,10,12,8,15,20,25,30
-Kokanee,8,10,12,16,20,12,25,30,40,50
-Lake Trout,12,20,26,31,39,30,50,65,80,100
-Largemouth Bass,8,12,15,20,25,20,30,38,51,63
-Longnose Gar,16,27,36,45,55,41,69,91,114,140
-Muskellunge,20,30,38,42,50,51,76,97,107,127
-Northern Pike,14,21,28,34,44,35,53,71,86,112
-Paddlefish,16,26,33,41,51,41,66,84,104,130
-Pumpkinseed,3,6,8,10,12,8,15,20,25,30
-Rainbow Trout,10,16,20,26,31,25,40,50,65,80
-Redear Sunfish,4,7,9,11,13,10,18,23,28,33
-River Carpsucker,7,11,14,18,22,18,28,36,46,56
-Rock Bass,4,7,9,11,13,10,18,23,28,33
-Ruffe,2.2,3.5,4.7,5.5,6.9,5.5,9,12,14,17.5
-Sauger,8,12,15,20,25,20,30,38,51,63
-Saugeye,9,14,15,22,27,23,35,46,56,69
-Shoal Bass,7.1,11,13.8,16.9,20.1,18,28,35,43,51
-Shorthead Redhorse,6,10,13,16,20,15,25,33,41,51
-Silver Carp,10,17.75,22,29,36.5,25,45,56,74,93
-Smallmouth Bass,7,11,14,17,20,18,28,35,43,51
-Smallmouth Buffalo ,11,18,24,30,37,28,46,61,76,94
-Splake,8,10,14,16,22,20,25,35,40,55
-Spotted Bass,7,11,14,17,20,18,28,35,43,51
-Spotted Gar,12,19,25,31,39,30,48,64,79,99
-Striped Bass (landlocked),12,20,30,35,45,30,51,76,89,114
-Suwannee Bass,6,9.75,11.75,13.75,15.75,15,25,30,35,40
-Walleye,10,15,20,25,30,25,38,51,63,76
-Warmouth,3,6,8,10,12,8,15,20,25,30
-White Bass,6,9,12,15,18,15,23,30,38,46
-Palmetto Bass,10,16,20,24,28,25,41,51,61,71
-Palmetto Bass (original),8,12,15,20,25,20,30,38,51,63
-White Catfish,8,13,17,21,26,20,33,43,53,66
-White Crappie,5,8,10,12,15,13,20,25,30,38
-White Perch,5,8,10,12,35,13,20,25,30,38
-White Sucker,6,10,13,16,20,15,25,33,41,51
-Yellow Perch,5,8,10,12,15,13,20,25,30,38
-Yellow Bass,4,7,9,11,13,10,18,23,28,33
-Yellow Bullhead,4,7,9,11,14,10,18,23,28,36
-Striped Bass (hybrid),10,16,20,24,28,25,41,51,61,71
-Striped Bass X White Bass,10,16,20,24,28,25,41,51,61,71
+species,stock.in,quality.in,preferred.in,memorable.in,trophy.in,stock.cm,quality.cm,preferred.cm,memorable.cm,trophy.cm,source
+Arctic Grayling,8,12,16,20,22,20,30,40,50,55,Hyatt (2000)
+Bighead Carp,11.75,21.25,26.75,35,43.75,30,54,68,89,111,Phelps and Willis (2013)
+Bigmouth Buffalo,11,18,24,30,37,28,46,61,76,94,Bister et al. (2000)
+Black Bullhead,6,9,12,15,18,15,23,30,39,46,Gabelhouse (1984a)
+Black Carp,15.75,28.25,35.5,46.5,58.25,40,72,90,118,148,Phelps and Willis (2013)
+Black Crappie,5,8,10,12,15,13,20,25,30,38,Gabelhouse (1984a)
+Blue Catfish,12,20,30,35,45,30,51,76,89,114,Gabelhouse (1984a)
+Bluegill,3,6,8,10,12,8,15,20,25,30,Gabelhouse (1984a)
+Brook Trout (lentic),8,13,NA,NA,NA,20,33,NA,NA,NA,Anderson (1980)
+Brook Trout (lotic),5,8,NA,NA,NA,13,20,NA,NA,NA,Anderson (1980)
+Brook Trout,8,12,16,20,24,20,30,40,50,60,Hyatt (2000)
+Brown Bullhead,5,8,11,14,17,13,20,28,36,43,Bister et al. (2000)
+Brown Trout (lentic),8,12,16,20,24,20,30,40,50,60,Hyatt and Hubert (2001)
+Brown Trout (lotic),6,9,12,15,18,15,23,30,38,46,Milewski and Brown (1994)
+Bull Trout,8,16,20,26,31,20,40,50,65,80,Hyatt (2000)
+Burbot,8,15,21,26,32,20,38,53,67,82,Fisher et al. (1996)
+Chain Pickerel,10,15,20,25,30,25,38,51,63,76,Gabelhouse (1984a)
+Channel Catfish,11,16,24,28,36,28,41,61,71,91,Gabelhouse (1984a)
+Chinook Salmon (landlocked),11,18,24,30,37,28,46,61,76,94,Hill and Duffy (1993)
+Common Carp,11,16,21,26,33,28,41,53,66,84,Gabelhouse (1984a)
+Cutthroat Trout,8,14,18,24,30,20,35,45,60,75,Kruse and Hubert (1997)
+Flathead Catfish,14,20,28,34,40,35,51,71,86,102,Quinn (1991)
+Freshwater Drum,8,12,15,20,25,20,30,38,51,63,Gabelhouse (1984a)
+Gizzard Shad,7,11,NA,NA,NA,18,28,NA,NA,NA,Anderson and Gutreuter (1983)
+Golden Trout,8,10,14,18,22,20,25,35,45,55,Hyatt (2000)
+Grass Carp,11.75,21.25,26.75,35,43.75,30,54,68,89,111,Phelps and Willis (2013)
+Green Sunfish,3,6,8,10,12,8,15,20,25,30,Gabelhouse (1984a)
+Kokanee,8,10,12,16,20,12,25,30,40,50,Hyatt (2000)
+Lake Trout,12,20,26,31,39,30,50,65,80,100,Hubert et al. (1994)
+Largemouth Bass,8,12,15,20,25,20,30,38,51,63,Gabelhouse (1984a)
+Longnose Gar,16,27,36,45,55,41,69,91,114,140,Bister et al. (2000)
+Muskellunge,20,30,38,42,50,51,76,97,107,127,Gabelhouse (1984a)
+Northern Pike,14,21,28,34,44,35,53,71,86,112,Gabelhouse (1984a)
+Paddlefish,16,26,33,41,51,41,66,84,104,130,Brown and Murphy (1993)
+Pallid Sturgeon,13,25,33,41,50,33,63,84,104,147,Shuman et al. (2006)
+Palmetto Bass,10,16,20,24,28,25,41,51,61,71,Dumont and Neely (2011)
+Palmetto Bass (original),8,12,15,20,25,20,30,38,51,63,Gabelhouse (1984a)
+Pumpkinseed,3,6,8,10,12,8,15,20,25,30,Gabelhouse (1984a)
+Rainbow Trout,10,16,20,26,31,25,40,50,65,80,Simpkins and Hubert (1996)
+Redear Sunfish,4,7,9,11,13,10,18,23,28,33,Gabelhouse (1984a)
+River Carpsucker,7,11,14,18,22,18,28,36,46,56,Bister et al. (2000)
+Rock Bass,4,7,9,11,13,10,18,23,28,33,Gabelhouse (1984a)
+Ruffe,2.2,3.5,4.7,5.5,6.9,5.5,9,12,14,17.5,Ogle and Winfield (2009)
+Sauger,8,12,15,20,25,20,30,38,51,63,Gabelhouse (1984a)
+Saugeye,9,14,15,22,27,23,35,46,56,69,Gabelhouse (1984a)
+Shoal Bass,7.1,11,13.8,16.9,20.1,18,28,35,43,51,Bonvechio et al. (2019)
+Shorthead Redhorse,6,10,13,16,20,15,25,33,41,51,Bister et al. (2000)
+Silver Carp,10,17.75,22,29,36.5,25,45,56,74,93,Phelps and Willis (2013)
+Smallmouth Bass,7,11,14,17,20,18,28,35,43,51,Gabelhouse (1984a)
+Smallmouth Buffalo ,11,18,24,30,37,28,46,61,76,94,Bister et al. (2000)
+Splake,8,10,14,16,22,20,25,35,40,55,Hyatt (2000)
+Spotted Bass,7,11,14,17,20,18,28,35,43,51,Gabelhouse (1984a)
+Spotted Gar,12,19,25,31,39,30,48,64,79,99,Bister et al. (2000)
+Striped Bass (landlocked),12,20,30,35,45,30,51,76,89,114,Gabelhouse (1984a)
+Striped Bass (hybrid),10,16,20,24,28,25,41,51,61,71,Dumont and Neely (2011)
+Striped Bass X White Bass,10,16,20,24,28,25,41,51,61,71,Dumont and Neely (2011)
+Suwannee Bass,6,9.75,11.75,13.75,15.75,15,25,30,35,40,Bonvechio et al. (2010)
+Walleye,10,15,20,25,30,25,38,51,63,76,Gabelhouse (1984a)
+Warmouth,3,6,8,10,12,8,15,20,25,30,Gabelhouse (1984a)
+White Bass,6,9,12,15,18,15,23,30,38,46,Gabelhouse (1984a)
+White Catfish,8,13,17,21,26,20,33,43,53,66,Bister et al. (2000)
+White Crappie,5,8,10,12,15,13,20,25,30,38,Gabelhouse (1984a)
+White Perch,5,8,10,12,35,13,20,25,30,38,Gabelhouse (1984a)
+White Sucker,6,10,13,16,20,15,25,33,41,51,Bister et al. (2000)
+Yellow Perch,5,8,10,12,15,13,20,25,30,38,Gabelhouse (1984a)
+Yellow Bass,4,7,9,11,13,10,18,23,28,33,Anderson and Gutreuter (1983)
+Yellow Bullhead,4,7,9,11,14,10,18,23,28,36,Anderson (1980)

tests/testthat/testthat_PSD.R

@@ -252,6 +252,10 @@ test_that("psdVal() returns",{
   expect_equivalent(tmp,c(0,130,200,250,300,380))
   expect_equal(names(tmp),c("substock","stock","quality","preferred",
                             "memorable","trophy"))
+  tmp <- psdVal("yellow Perch",showJustSource=TRUE)
+  expect_is(tmp,"data.frame")
+  expect_equivalent(ncol(tmp),2)
+  expect_equivalent(nrow(tmp),1)
 })
 
 test_that("psdCI() returns",{