Closing v0_3_8

Author: droglenc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: FSAdata
 Title: Data to Support Fish Stock Assessment ('FSA') Package
-Version: 0.3.7
-Date: 2019-03-24
+Version: 0.3.8
+Date: 2019-05-17
 Description: The datasets to support the Fish Stock Assessment ('FSA') package.
 Authors@R: person("Derek","Ogle",
     email="[email protected]",

NEWS.md

@@ -1,3 +1,6 @@
+# 0.3.8 17-May-19
+* Corrected misues of `\concept` in Rd files per CRAN request.
+
 # 0.3.7 24-Mar-19
 * Added `Encoding: UTF-8` to DESCRIPTION.
 * `PygmyWFBC`: Modified. Added the 2000 data (thought they were there but they were not).

R/AHerringChile.R

@@ -20,7 +20,9 @@
 #'    \item Somers model
 #'  }
 #'  
-#' @concept 'Seasonal Growth' 'von Bertalanffy' Somers
+#' @concept Seasonal Growth
+#' @concept von Bertalanffy
+#' @concept Somers
 #' 
 #' @source From figure 9 of Cubillos, L.A., D.F. Arcosa, D.A. Bucareya, M.T. Canalesa.  2001.  Seasonal growth of small pelagic fish off Talcahuano, Chile (37S, 73W): a consequence of their reproductive strategy to seasonal upwelling?  Aquatic Living Resources, 14:115-124.
 #' 

R/AlewifeLH.R

@@ -20,7 +20,9 @@
 #'    \item Ageing Error
 #'  }
 #' 
-#' @concept Age Precision Bias 'Age Comparison'
+#' @concept Age Precision
+#' @concept Age Bias
+#' @concept Age Comparison
 #' 
 #' @source From Table 1A of Hoenig, J.M., M.J. Morgan, and C.A. Brown. 1995.  Analysing differences between two age determination methods by tests of symmetry.  Canadian Journal of Fisheries And Aquatic Systems, 52:364-368.  Originally from O'Gorman, R., D.H. Barwick, and C.A. Bowen.  1987.  Discrepancies between ages determined from scales and otoliths for alewives from the Great Lakes.  pp. 203-210 In.  Summerfelt, R.C. and G.E. Hall (Eds.)  Age and Growth of Fish.  Iowa State University Press, Ames, IA.
 #' 

R/AnchovetaChile.R

@@ -21,7 +21,9 @@
 #'    \item Somers model 
 #'  }
 #'  
-#' @concept 'Seasonal Growth' 'von Bertalanffy' Somers
+#' @concept Seasonal Growth
+#' @concept von Bertalanffy
+#' @concept Somers
 #' 
 #' @source Directly from the authors of Cubillos, L.A., D.F. Arcosa, D.A. Bucareya, M.T. Canalesa.  2001.  Seasonal growth of small pelagic fish off Talcahuano, Chile (37S, 73W): a consequence of their reproductive strategy to seasonal upwelling?  Aquatic Living Resources, 14:115-124.  Data were in Figure 9.
 #' 

R/BGHRfish.R

@@ -21,7 +21,7 @@
 #'    \item Data Manipulation
 #'  }
 #'  
-#' @concept 'Data Manipulation'
+#' @concept Data Manipulation
 #' 
 #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book.
 #' 

R/BGHRsample.R

@@ -19,7 +19,7 @@
 #'    \item Data Manipulation
 #'  }
 #'  
-#' @concept 'Data Manipulation'
+#' @concept Data Manipulation
 #' 
 #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book.
 #' 

R/BSkateGB.R

@@ -22,9 +22,10 @@
 #'    \item Recruitment
 #'  }
 #' 
-#' @concept 'Stock-Recruit' Recruitment
+#' @concept Stock-Recruit
+#' @concept Recruitment
 #' 
-#' @source estimated (using digitize) from figures 4-6 in Gedamke, T., J.M. Hoenig, W.D. DuPaul, and J.A. Musick.  2009.  Stock-recruitment dynamics and the maximum population growth rate of the barndoor skate on Georges Bank.  North American Journal of Fisheries Management 29:512-526.
+#' @source Estimated (using digitize) from figures 4-6 in Gedamke, T., J.M. Hoenig, W.D. DuPaul, and J.A. Musick. 2009. Stock-recruitment dynamics and the maximum population growth rate of the barndoor skate on Georges Bank. North American Journal of Fisheries Management 29:512-526.
 #' 
 #' @keywords datasets
 #' 

R/BassFL.R

@@ -21,9 +21,10 @@
 #'    \item Catch curve 
 #'  }
 #'  
-#' @concept Mortality 'Catch Curve'
+#' @concept Mortality
+#' @concept Catch Curve
 #' 
-#' @source From Figure 2 of Bonvechio, T.F., M.S. Allen, and R.L. Cailteux.  2005.  Relative Abundance, Growth, and Mortality of Suwannee Bass  in Four Florida Rivers.  North American Journal of Fisheries Management 25:275-283.  [Was (is?) from http://sfrc.ufl.edu/allenlab/publications/2005bonvechio_allen_cailteux.pdf.]
+#' @source From Figure 2 of Bonvechio, T.F., M.S. Allen, and R.L. Cailteux. 2005. Relative Abundance, Growth, and Mortality of Suwannee Bass in Four Florida Rivers. North American Journal of Fisheries Management 25:275-283. [Was (is?) from http://sfrc.ufl.edu/allenlab/publications/2005bonvechio_allen_cailteux.pdf.]
 #' 
 #' @keywords datasets
 #' 

R/BlackDrum2001.R

@@ -26,7 +26,9 @@
 #'    \item Weight-Length
 #'  }
 #'  
-#' @concept Growth 'von Bertalanffy' 'Weight-Length'
+#' @concept Growth
+#' @concept von Bertalanffy
+#' @concept Weight-Length
 #' 
 #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book.
 #' 

R/BloaterLH.R

@@ -19,9 +19,10 @@
 #'    \item Recruitment
 #'  }
 #' 
-#' @concept 'Stock-Recruit' Recruitment
+#' @concept Stock-Recruit
+#' @concept Recruitment
 #' 
-#' @source From (approximately) Figure 7 of Schaeffer, J.S. 2004.  Population dynamics of bloaters \emph{Coregonus hoyi} in Lake Huron, 1980-1998.  Ann Zool Fennici. 41:271-279.
+#' @source From (approximately) Figure 7 of Schaeffer, J.S. 2004. Population dynamics of bloaters \emph{Coregonus hoyi} in Lake Huron, 1980-1998. Ann Zool Fennici. 41:271-279.
 #' 
 #' @keywords datasets
 #' 

R/BlueCatfish.R

@@ -18,9 +18,10 @@
 #'    \item von Bertalanffy
 #'  }
 #'  
-#' @concept Growth 'von Bertalanffy'
+#' @concept Growth
+#' @concept von Bertalanffy
 #' 
-#' @source From (approximately) Figure 2 of Maceina, M.J.  2007.  Use of piecewise nonlinear models to estimate variable size-related mortality rates.  North American Journal of Fisheries Management, 27:971-977.
+#' @source From (approximately) Figure 2 of Maceina, M.J. 2007. Use of piecewise nonlinear models to estimate variable size-related mortality rates. North American Journal of Fisheries Management, 27:971-977.
 #' 
 #' @keywords datasets
 #' 

R/BlueCrab.R

@@ -22,9 +22,14 @@
 #'    \item Catchability
 #'  }
 #'  
-#' @concept Abundance 'Population Size' Leslie DeLury Depletion Catchability
-#' 
-#' @source From Fischler, K.J.  1965.  The use of catch-effort, catch-sampling, and tagging data to estimate a population of blue crabs.  Transactions of the American Fisheries Society, 94:287-310.
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Leslie
+#' @concept DeLury
+#' @concept Depletion
+#' @concept Catchability
+#' 
+#' @source From Fischler, K.J. 1965. The use of catch-effort, catch-sampling, and tagging data to estimate a population of blue crabs. Transactions of the American Fisheries Society, 94:287-310.
 #' 
 #' @keywords datasets
 #' 

R/BluefishAge.R

@@ -18,7 +18,9 @@
 #'   \item Ageing Error
 #'  }
 #' 
-#' @concept Age Precision Bias 'Age Comparison'
+#' @concept Age Precision
+#' @concept Age Bias
+#' @concept Age Comparison
 #' 
 #' @source From Figure 2 in Chapter 3 (Bluefish) of the VMRC Final Report on Finfish Ageing, 2003 by the Center for Quantitative Fisheries Ecology at Old Dominion University.
 #' 

R/BluegillIL.R

@@ -22,9 +22,11 @@
 #'    \item Fabens method 
 #'  }
 #'  
-#' @concept Growth 'von Bertalanffy' Fabens
+#' @concept Growth
+#' @concept von Bertalanffy
+#' @concept Fabens
 #' 
-#' @source These unpublished data are from Derek H. Ogle, Northland College.  \bold{Do not use for other than educational purposes without permission from the source.}
+#' @source These unpublished data are from Derek H. Ogle, Northland College. \bold{Do not use for other than educational purposes without permission from the source.}
 #' 
 #' @keywords datasets
 #' 

R/BluegillLM.R

@@ -22,7 +22,9 @@
 #'    \item Length Frequency
 #'  }
 #' 
-#' @concept 'Weight-Length' 'Length Conversion' 'Length Frequency'
+#' @concept Weight-Length
+#' @concept Length Conversion
+#' @concept Length Frequency
 #' 
 #' @keywords datasets
 #' 

R/BluntnoseIL1.R

@@ -21,7 +21,10 @@
 #'     \item PSD
 #'   }
 #'   
-#' @concept 'Length Frequency' 'Size Structure' PSD 'Length Expansion'
+#' @concept Length Frequency
+#' @concept Size Structure
+#' @concept PSD
+#' @concept Length Expansion
 #' 
 #' @seealso \code{\link{InchLake1}}, \code{\link{InchLake2}}.
 #' 

R/Bonito.R

@@ -21,7 +21,9 @@
 #'    \item Somers model
 #'  }
 #'  
-#' @concept 'Seasonal Growth' 'von Bertalanffy' Somers
+#' @concept Seasonal Growth
+#' @concept von Bertalanffy
+#' @concept Somers
 #' 
 #' @source From figure 3 of Stewart, J., W. Robbins, K. Rowling, A. Hegarty, and A. Gould. 2013. A multifaceted approach to modelling growth of the Australian bonito, \emph{Sarda australis} (Family Scombridae), with some observations on its reproductive biology. Marine and Freshwater Research 64:671-678.
 #' 

R/BrookTroutNC.R

@@ -20,9 +20,10 @@
 #'    \item Recruitment
 #'  }
 #' 
-#' @concept 'Stock-Recruit' Recruitment
+#' @concept Stock-Recruit
+#' @concept Recruitment
 #' 
-#' @source From (approximately) Figure 5 in Grossman, G.D., R.E. Ratajczak, C.M. Wagner, and J.T. Petty.  2010. Dynamics and regulation of the southern brook trout (\emph{Salvelinus fontinalis}) population in an Appalachian stream.  Freshwater Biology 55:1494-1508.
+#' @source From (approximately) Figure 5 in Grossman, G.D., R.E. Ratajczak, C.M. Wagner, and J.T. Petty. 2010. Dynamics and regulation of the southern brook trout (\emph{Salvelinus fontinalis}) population in an Appalachian stream. Freshwater Biology 55:1494-1508.
 #' 
 #' @keywords datasets
 #' 

R/BrookTroutNEWP.R

@@ -24,9 +24,11 @@
 #'    \item Removal
 #'  }
 #' 
-#' @concept Abundance 'Population Size' Removal
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Removal
 #' 
-#' @source From Table 1 in Schnute, J.  1983.  A new approach to estimating populations by the removal method.  Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169.
+#' @source From Table 1 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169.
 #' 
 #' @seealso See \code{\link{BrookTroutNEWP1}} for these data AND the results from Schnute (1983).
 #' 

R/BrookTroutNEWP1.R

@@ -37,9 +37,11 @@
 #'    \item Removal
 #'  }
 #' 
-#' @concept Abundance 'Population Size' Removal
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Removal
 #' 
-#' @source From Tables 1-3 in Schnute, J.  1983.  A new approach to estimating populations by the removal method.  Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169.
+#' @source From Tables 1-3 in Schnute, J. 1983. A new approach to estimating populations by the removal method. Canadian Journal of Fisheries and Aquatic Sciences, 40:2153-2169.
 #' 
 #' @seealso See \code{\link{BrookTroutNEWP}} for only the data (note the results from Schnute (1983)).
 #' 

R/BrookTroutOnt.R

@@ -24,9 +24,13 @@
 #'    \item Petersen
 #'  }
 #'  
-#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen'
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Mark-Recapture
+#' @concept Capture-Recapture
+#' @concept Petersen
 #' 
-#' @source From Table 1 of Curry, R.A., C. Brady, and G.E. Morgan.  2003.  Effects of Recreational Fishing on the Population Dynamics of Lake-Dwelling Brook Trout.  North American Journal of Fisheries Management 23:35-47.
+#' @source From Table 1 of Curry, R.A., C. Brady, and G.E. Morgan. 2003. Effects of Recreational Fishing on the Population Dynamics of Lake-Dwelling Brook Trout. North American Journal of Fisheries Management 23:35-47.
 #' 
 #' @keywords datasets
 #' 

R/BrownTroutVC1.R

@@ -22,9 +22,13 @@
 #'    \item Petersen
 #'  }
 #' 
-#' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Petersen'
+#' @concept Abundance
+#' @concept Population Size
+#' @concept Mark-Recapture
+#' @concept Capture-Recapture
+#' @concept Petersen
 #' 
-#' @source Obtained directly from Tom Kwak, North Carolina Cooperate Unit at North Carolina State University and part of the data published in Kwak, T.J. and T.F. Waters.  1997.  Trout production dynamics and water quality in Minnesota streams.  Transactions of the American Fisheries Society, 126:35-48.
+#' @source Obtained directly from Tom Kwak, North Carolina Cooperate Unit at North Carolina State University and part of the data published in Kwak, T.J. and T.F. Waters. 1997. Trout production dynamics and water quality in Minnesota streams. Transactions of the American Fisheries Society, 126:35-48.
 #' 
 #' @keywords datasets
 #' 

R/BullTroutRML1.R

@@ -21,9 +21,10 @@
 #'    \item Length Frequency
 #'  }
 #' 
-#' @concept 'Weight-Length' 'Length Frequency'
+#' @concept Weight-Length
+#' @concept Length Frequency
 #' 
-#' @source From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald.  2007.  Bull trout population responses to reductions in angler effort and retention limits.  North American Journal of Fisheries Management, 27:848-859.  [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.]
+#' @source From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.]
 #' 
 #' @keywords datasets
 #' 

R/BullTroutRML2.R

@@ -22,9 +22,10 @@
 #'    \item Von Bertalanffy growth model 
 #'  }
 #' 
-#' @concept Growth 'Von Bertalanffy'
+#' @concept Growth
+#' @concept Von Bertalanffy
 #' 
-#' @source From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald.  2007.  Bull trout population responses to reductions in angler effort and retention limits.  North American Journal of Fisheries Management, 27:848-859.  [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.]
+#' @source From (approximately) Figure 2 of Parker, B.R., D.W. Schindler, F.M. Wilhelm, and D.B. Donald. 2007. Bull trout population responses to reductions in angler effort and retention limits. North American Journal of Fisheries Management, 27:848-859. [Was (is?) from https://www.researchgate.net/publication/233144141_Bull_Trout_Population_Responses_to_Reductions_in_Angler_Effort_and_Retention_Limits.]
 #' 
 #' @keywords datasets
 #' 

R/BullTroutTC.R

@@ -18,9 +18,10 @@
 #'    \item Catch curve
 #'  }
 #'  
-#' @concept Mortality 'Catch Curve'
+#' @concept Mortality
+#' @concept Catch Curve
 #' 
-#' @source From (approximately) Figure 4a in Downs, C.C., D. Horan, E. Morgan-Harris, and R. Jakubowski.  2006.  Spawning demographics and juvenile dispersal of an adfluvial bull trout population in Trestle Creek, Idaho.  North American Journal of Fisheries Management 26:190-200.
+#' @source From (approximately) Figure 4a in Downs, C.C., D. Horan, E. Morgan-Harris, and R. Jakubowski. 2006. Spawning demographics and juvenile dispersal of an adfluvial bull trout population in Trestle Creek, Idaho. North American Journal of Fisheries Management 26:190-200.
 #' 
 #' @keywords datasets
 #' 

R/CCatfishNB.R

@@ -19,11 +19,12 @@
 #'    \item Catch curve 
 #'  }
 #'  
-#' @concept Mortality 'Catch Curve'
+#' @concept Mortality
+#' @concept Catch Curve
 #' 
 #' @note Used in the \href{http://derekogle.com/IFAR/}{Introductory Fisheries Analyses with R} book.
 #' 
-#' @source From (approximately) Figure 3-14 in Barada, T.J. 2009. Catfish population dynamics in the Platte River, Nebraska.  Master's thesis, University of Nebraska, Lincoln, NE.  [Was (is?) from http://nlc1.nlc.state.ne.us/epubs/U1500/B013-2009.pdf.]  
+#' @source From (approximately) Figure 3-14 in Barada, T.J. 2009. Catfish population dynamics in the Platte River, Nebraska. Master's thesis, University of Nebraska, Lincoln, NE. [Was (is?) from http://nlc1.nlc.state.ne.us/epubs/U1500/B013-2009.pdf.]  
 #' 
 #' @keywords datasets
 #' 

R/Cabezon.R

@@ -22,9 +22,11 @@
 #'    \item von Bertalanffy 
 #'  }
 #' 
-#' @concept Growth 'von Bertalanffy' Maturity
+#' @concept Growth
+#' @concept von Bertalanffy
+#' @concept Maturity
 #' 
-#' @source Actual data obtained directly (from Bob Hanna) from Hannah, R.W, M.T.O. Blume, and J.E. Thompson.  2009.  Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity.  Oregon Department of Fish and Wildlife, Information Reports 2009-04.  [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf.]
+#' @source Actual data obtained directly (from Bob Hanna) from Hannah, R.W, M.T.O. Blume, and J.E. Thompson. 2009. Length and age at maturity of female yelloweye rockfish (\emph{Sebastes rubberimus}) and cabezon (\emph{Scorpaenichthys marmoratus}) from Oregon waters based on histological evaluation of maturity. Oregon Department of Fish and Wildlife, Information Reports 2009-04. [Was (is?) from http://www.dfw.state.or.us/mrp/publications/docs/Info200904_YlwEyeRF_Maturity.pdf.]
 #' 
 #' @keywords datasets
 #' 

R/Casselman1990.R

@@ -21,7 +21,7 @@
 #'
 #' @concept Other
 #'   
-#' @source From Figure 8 of Casselman, J.M.  1990.  Growth and relative size of calcified structures of fish.  Transactions of the American Fisheries Society.  119:673-688.
+#' @source From Figure 8 of Casselman, J.M. 1990. Growth and relative size of calcified structures of fish. Transactions of the American Fisheries Society. 119:673-688.
 #'
 #' @keywords datasets
 #'

R/ChinookKR.R

@@ -19,7 +19,8 @@
 #'    \item Recruitment
 #'  }
 #' 
-#' @concept 'Stock-Recruit' Recruitment
+#' @concept Stock-Recruit
+#' @concept Recruitment
 #' 
 #' @source Was (is?) from http://www.pcouncil.org/bb/2006/0406/age2a_supp_att3.pdf.
 #' 

R/CiscoTL.R

@@ -24,7 +24,8 @@
 #'    \item Length Frequency
 #'  }
 #'  
-#' @concept 'Weight-Length' 'Length Frequency'
+#' @concept Weight-Length
+#' @concept Length Frequency
 #'
 #' @source Was (is?) available for download from http://www.limnology.wisc.edu/.
 #'

R/CrappieARMS.R

@@ -18,9 +18,10 @@
 #'    \item Recruitment
 #'  }
 #' 
-#' @concept 'Stock-Recruit' Recruitment
+#' @concept Stock-Recruit
+#' @concept Recruitment
 #'
-#' @source From (approximately) Figure 2 of Allen, M.S. and L.E. Miranda.  1998.  An age-structured model for erratic crappie fisheries.  Ecological Modeling 107:289-303.
+#' @source From (approximately) Figure 2 of Allen, M.S. and L.E. Miranda. 1998. An age-structured model for erratic crappie fisheries. Ecological Modeling 107:289-303.
 #'
 #' @keywords datasets
 #'