From fabf8073e72d1137937a9587065593e62c78ac89 Mon Sep 17 00:00:00 2001 From: droglenc Date: Thu, 22 Oct 2015 09:25:06 -0500 Subject: [PATCH] Removed all \url and \hrefs --- NEWS.md | 3 ++- R/BluegillJL.R | 2 +- R/BrookTroutTH.R | 2 +- R/ChinookArg.R | 2 +- R/CutthroatAL.R | 4 +++- R/SpotVA1.R | 2 +- R/WhitefishLC.R | 2 +- R/ageComparisons.R | 16 ++++++++-------- R/alkIndivAge.R | 2 +- R/bcFuns.R | 5 ++--- R/capHistConvert.R | 2 +- R/catchCurve.R | 2 +- R/chapmanRobson.R | 2 +- R/depletion.R | 2 +- R/growthModels.R | 22 +++++++++++----------- R/metaM.R | 12 ++++++------ R/mrClosed.R | 2 +- R/mrOpen.R | 2 +- R/psdAdd.R | 6 +++--- R/psdCI.R | 2 +- R/psdCalc.R | 6 +++--- R/psdPlot.R | 6 +++--- R/psdVal.R | 6 +++--- R/removal.R | 2 +- R/srStarts.R | 2 +- R/stockRecruitment.R | 2 +- cran-comments/cran-comments-v0_8_2.md | 7 +++++++ man/BluegillJL.Rd | 2 +- man/BrookTroutTH.Rd | 2 +- man/ChinookArg.Rd | 2 +- man/CutthroatAL.Rd | 5 ++++- man/SpotVA1.Rd | 2 +- man/WhitefishLC.Rd | 2 +- man/ageBias.Rd | 6 +++--- man/agePrecision.Rd | 10 +++++----- man/alkIndivAge.Rd | 2 +- man/bcFuns.Rd | 7 +++---- man/capHistConvert.Rd | 2 +- man/catchCurve.Rd | 2 +- man/chapmanRobson.Rd | 2 +- man/depletion.Rd | 2 +- man/growthModels.Rd | 22 +++++++++++----------- man/metaM.Rd | 12 ++++++------ man/mrClosed.Rd | 2 +- man/mrOpen.Rd | 2 +- man/psdAdd.Rd | 6 +++--- man/psdCI.Rd | 2 +- man/psdCalc.Rd | 6 +++--- man/psdPlot.Rd | 6 +++--- man/psdVal.Rd | 6 +++--- man/removal.Rd | 2 +- man/srStarts.Rd | 2 +- man/stockRecruitment.Rd | 2 +- 53 files changed, 127 insertions(+), 116 deletions(-) create mode 100644 cran-comments/cran-comments-v0_8_2.md diff --git a/NEWS.md b/NEWS.md index a38bfe7d..43c62eca 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ -# FSA 0.8.2 ongoing +# FSA 0.8.2 21-Oct-15 * Converted all files in `data-raw` to CSV files. +* Removed all `\href{}{}` and `\url{}` codes to websites that I don't control. The addresses are now "naked" such that the user will need to copy-and-paste them into a browser to view the web page rather than clicking on a hyper link. Hopefully this will eliminate problems with R CMD CHECK. * `ChinookArg`: Updated help documentation. * `Ecoli`: Added a Topics section. * `Mirex`: Added a Topics section. diff --git a/R/BluegillJL.R b/R/BluegillJL.R index 0163d71a..dd14c104 100644 --- a/R/BluegillJL.R +++ b/R/BluegillJL.R @@ -24,7 +24,7 @@ #' #' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' Petersen 'Capture History' #' -#' @source From example 8.1 in Schneider, J.C. 1998. \href{http://www.michigandnr.com/publications/pdfs/IFR/manual/SMII\%20Chapter08.pdf}{Lake fish population estimates by mark-and-recapture methods.} Chapter 8 in Schneider, J.C. (ed.) 2000. Manual of fisheries survey methods II: with periodic updates. Michigan Department of Natural Resources, Fisheries Special Report 25, Ann Arbor. +#' @source From example 8.1 in Schneider, J.C. 1998. Lake fish population estimates by mark-and-recapture methods. Chapter 8 in Schneider, J.C. (ed.) 2000. Manual of fisheries survey methods II: with periodic updates. Michigan Department of Natural Resources, Fisheries Special Report 25, Ann Arbor. [Was (is?) from http://www.michigandnr.com/publications/pdfs/IFR/manual/SMII\%20Chapter08.pdf.] #' #' @keywords datasets #' diff --git a/R/BrookTroutTH.R b/R/BrookTroutTH.R index c01be896..ec410cc3 100644 --- a/R/BrookTroutTH.R +++ b/R/BrookTroutTH.R @@ -21,7 +21,7 @@ #' #' @concept Mortality 'Catch Curve' #' -#' @source Quinlan, H.R. 1999. Biological Characteristics of Coaster Brook Trout at Isle Royale National Park, Michigan, 1996-98. U.S. Fish and Wildlife Service Ashland Fishery Resources Office report. November 1999. Was originally available at \url{www.fws.gov/midwest/ashland/brook/biochar/biolchar.html}. +#' @source Quinlan, H.R. 1999. Biological Characteristics of Coaster Brook Trout at Isle Royale National Park, Michigan, 1996-98. U.S. Fish and Wildlife Service Ashland Fishery Resources Office report. November 1999. [Was (is?) from http://www.fws.gov/midwest/ashland/brook/biochar/biolchar.html.] #' #' @keywords datasets #' diff --git a/R/ChinookArg.R b/R/ChinookArg.R index 044c5972..7cafd64c 100644 --- a/R/ChinookArg.R +++ b/R/ChinookArg.R @@ -20,7 +20,7 @@ #' #' @concept 'Weight-Length' #' -#' @source From Figure 4 in Soto, D., I. Arismendi, C. Di Prinzio, and F. Jara. 2007. \href{http://www.scielo.cl/pdf/rchnat/v80n1/art07.pdf}{Establishment of Chinook salmon (\emph{Oncorhynchus tshawytscha}) in Pacific basins of southern South America and its potential ecosystem implications}. Revista Chilena d Historia Natural, 80:81-98. +#' @source From Figure 4 in Soto, D., I. Arismendi, C. Di Prinzio, and F. Jara. 2007. Establishment of Chinook salmon (\emph{Oncorhynchus tshawytscha}) in Pacific basins of southern South America and its potential ecosystem implications. Revista Chilena d Historia Natural, 80:81-98. [Was (is?) from http://www.scielo.cl/pdf/rchnat/v80n1/art07.pdf.] #' #' @keywords datasets #' diff --git a/R/CutthroatAL.R b/R/CutthroatAL.R index f329c1cf..eafbc438 100644 --- a/R/CutthroatAL.R +++ b/R/CutthroatAL.R @@ -32,7 +32,9 @@ #' #' @concept Abundance 'Population Size' 'Mark-Recapture' 'Capture-Recapture' 'Jolly-Seber' 'Capture History' #' -#' @source Entered from Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010. \href{http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf}{Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006}. Alaska Department of Fish and Game Fisheries Data Series No. 10-82 into \dQuote{RMark} format (see \code{\link[FSAdata]{CutthroatALf}} in \pkg{FSAdata}) and then converted to individual format with \code{\link{capHistConvert}}. +#' @source From Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010. Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006. Alaska Department of Fish and Game Fisheries Data Series No. 10-82. [Was (is?) from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf.] +#' +#' @note Entered into \dQuote{RMark} format (see \code{\link[FSAdata]{CutthroatALf}} in \pkg{FSAdata}) and then converted to individual format with \code{\link{capHistConvert}} #' #' @seealso See \code{\link{mrOpen}} for an example analysis. #' diff --git a/R/SpotVA1.R b/R/SpotVA1.R index 261b3266..9caa3c20 100644 --- a/R/SpotVA1.R +++ b/R/SpotVA1.R @@ -24,7 +24,7 @@ #' #' @seealso See \code{\link[FSAdata]{SpotVA2}} in \pkg{FSAdata} for related data. #' -#' @source Extracted from Table 1 in Chapter 8 (Spot) of the VMRC Final Report on Finfish Ageing, 2002 by the \href{http://www.odu.edu/sci/research/cqfe}{Center for Quantitative Fisheries Ecology} at Old Dominion University. +#' @source Extracted from Table 1 in Chapter 8 (Spot) of the VMRC Final Report on Finfish Ageing, 2002 by the Center for Quantitative Fisheries Ecology at Old Dominion University. #' #' @keywords datasets #' diff --git a/R/WhitefishLC.R b/R/WhitefishLC.R index 05fe47aa..2034b005 100644 --- a/R/WhitefishLC.R +++ b/R/WhitefishLC.R @@ -32,7 +32,7 @@ #' #' @concept Age Precision Bias 'Ageing Error' 'Age Comparisons' #' -#' @source Data from Herbst, S.J. and J.E. Marsden. 2011. \href{http://www.uvm.edu/rsenr/emarsden/documents/Herbst\%20and\%20Marsden\%20whitefish\%20age\%20structure\%20comparison.pdf}{Comparison of precision and bias of scale, fin ray, and otolith age estimates for lake whitefish (\emph{Coregonus clupeaformis}) in Lake Champlain.} Journal of Great Lakes Research. 37:386-389. Contributed by Seth Herbst. \bold{Do not use for other than educational purposes without permission from the author.} +#' @source Data from Herbst, S.J. and J.E. Marsden. 2011. Comparison of precision and bias of scale, fin ray, and otolith age estimates for lake whitefish (\emph{Coregonus clupeaformis}) in Lake Champlain. Journal of Great Lakes Research. 37:386-389. Contributed by Seth Herbst. \bold{Do not use for other than educational purposes without permission from the author.} [Was (is?) from http://www.uvm.edu/rsenr/emarsden/documents/Herbst\%20and\%20Marsden\%20whitefish\%20age\%20structure\%20comparison.pdf.] #' #' @keywords datasets #' diff --git a/R/ageComparisons.R b/R/ageComparisons.R index 3d4b7417..ab8a1ba4 100644 --- a/R/ageComparisons.R +++ b/R/ageComparisons.R @@ -72,7 +72,7 @@ #' #' The \code{summary} returns the result if \code{what=} contains one item, otherwise it returns nothing. Nothing is returned by \code{plot}, but see details for a description of the plot that is produced. #' -#' @section Testing: Tested all symmetry test results against results in Evans and Hoenig (2008), the McNemar and Evans-Hoenig results against results from \code{\link[fishmethods]{compare2}} in \pkg{fishmethods}, and all results using the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from \url{http://www.nefsc.noaa.gov/fbp/age-prec/}. +#' @section Testing: Tested all symmetry test results against results in Evans and Hoenig (2008), the McNemar and Evans-Hoenig results against results from \code{\link[fishmethods]{compare2}} in \pkg{fishmethods}, and all results using the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from the online resource at http://www.nefsc.noaa.gov/fbp/age-prec/. #' #' @author Derek H. Ogle, \email{derek@@derekogle.com} #' @@ -82,7 +82,7 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. \href{http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf}{Graphical and statistical methods for determining the consistency of age determinations.} Transactions of the American Fisheries Society 124:131-138. +#' Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. Graphical and statistical methods for determining the consistency of age determinations. Transactions of the American Fisheries Society 124:131-138. [Was (is?) available from http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf.] #' #' Evans, G.T. and J.M. Hoenig. 1998. Testing and viewing symmetry in contingency tables, with application to readers of fish ages. Biometrics 54:620-629. #' @@ -90,7 +90,7 @@ #' #' McBride, R.S. 2015. Diagnosis of paired age agreement: A simulation approach of accuracy and precision effects. ICES Journal of Marine Science, XX:XXX-XXX. #' -#' Muir, A.M., M.P. Ebener, J.X. He, and J.E. Johnson. 2008. \href{http://www.tandfonline.com/doi/abs/10.1577/M06-160.1}{A comparison of the scale and otolith methods of age estimation for lake whitefish in Lake Huron.} North American Journal of Fisheries Management 28:625-635. +#' Muir, A.M., M.P. Ebener, J.X. He, and J.E. Johnson. 2008. A comparison of the scale and otolith methods of age estimation for lake whitefish in Lake Huron. North American Journal of Fisheries Management 28:625-635. [Was (is?) available from http://www.tandfonline.com/doi/abs/10.1577/M06-160.1] #' #' @aliases ageBias plot.ageBias summary.ageBias #' @@ -591,7 +591,7 @@ iabAxisLmts <- function(d,xlim,ylim,difference,show.range,show.pts,show.CIs=TRUE #' #' The \code{summary} returns the result if \code{what=} contains one item, otherwise it returns nothing. See details for what is printed. #' -#' @section Testing: Tested all precision results against published results in Herbst and Marsden (2011) for the \code{\link{WhitefishLC}} data and the results for the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from \url{http://www.nefsc.noaa.gov/fbp/age-prec/}. +#' @section Testing: Tested all precision results against published results in Herbst and Marsden (2011) for the \code{\link{WhitefishLC}} data and the results for the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from the online resource at http://www.nefsc.noaa.gov/fbp/age-prec/. #' #' @author Derek H. Ogle, \email{derek@@derekogle.com} #' @@ -601,13 +601,13 @@ iabAxisLmts <- function(d,xlim,ylim,difference,show.range,show.pts,show.CIs=TRUE #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Beamish, R.J. and D.A. Fournier. 1981. \href{http://www.pac.dfo-mpo.gc.ca/science/people-gens/beamish/PDF_files/compareagecjfas1981.pdf}{A method for comparing the precision of a set of age determinations.} Canadian Journal of Fisheries and Aquatic Sciences 38:982-983. +#' Beamish, R.J. and D.A. Fournier. 1981. A method for comparing the precision of a set of age determinations. Canadian Journal of Fisheries and Aquatic Sciences 38:982-983. [Was (is?) available from http://www.pac.dfo-mpo.gc.ca/science/people-gens/beamish/PDF_files/compareagecjfas1981.pdf.] #' -#'Campana, S.E. 1982. \href{http://www.denix.osd.mil/nr/crid/Coral_Reef_Iniative_Database/References_for_Reef_Assessment_files/Campana,\%202001.pdf}{Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods.} Journal of Fish Biology 59:197-242. +#'Campana, S.E. 1982. Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods. Journal of Fish Biology 59:197-242. [Was (is?) available from http://www.denix.osd.mil/nr/crid/Coral_Reef_Iniative_Database/References_for_Reef_Assessment_files/Campana,\%202001.pdf.] #' -#'Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. \href{http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf}{Graphical and statistical methods for determining the consistency of age determinations.} Transactions of the American Fisheries Society 124:131-138. +#'Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. Graphical and statistical methods for determining the consistency of age determinations. Transactions of the American Fisheries Society 124:131-138. [Was (is?) available from http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf.] #' -#'Chang, W.Y.B. 1982. \href{http://www.nrcresearchpress.com/doi/abs/10.1139/f82-158}{A statistical method for evaluating the reproducibility of age determination.} Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210. +#'Chang, W.Y.B. 1982. A statistical method for evaluating the reproducibility of age determination. Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210. [Was (is?) available from http://www.nrcresearchpress.com/doi/abs/10.1139/f82-158.] #' #' McBride, R.S. 2015. Diagnosis of paired age agreement: A simulation approach of accuracy and precision effects. ICES Journal of Marine Science, XX:XXX-XXX. #' diff --git a/R/alkIndivAge.R b/R/alkIndivAge.R index 6b1f12a2..df541d24 100644 --- a/R/alkIndivAge.R +++ b/R/alkIndivAge.R @@ -29,7 +29,7 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Isermann, D.A. and C.T. Knight. 2005. \href{http://www.tandfonline.com/doi/abs/10.1577/M04-130.1}{A computer program for age-length keys incorporating age assignment to individual fish.} North American Journal of Fisheries Management, 25:1153-1160. +#' 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.] #' #' @keywords manip #' diff --git a/R/bcFuns.R b/R/bcFuns.R index b191f887..2f9acbd2 100644 --- a/R/bcFuns.R +++ b/R/bcFuns.R @@ -37,11 +37,10 @@ #' #' @author Derek H. Ogle, \email{derek@@derekogle.com} #' -#' @section fishR vignette: \url{https://sites.google.com/site/fishrfiles/gnrl/Backcalculation.pdf}, -#'\url{https://sites.google.com/site/fishrfiles/gnrl/BackcalculationExtra.pdf} +#' @section IFAR Supplement: \url{http://derekogle.com/IFAR/supplements/backcalculation/} #' #' @references -#' Vigliola, L. and M.G. Meekan. 2009. The back-calculation of fish growth from otoliths. pp. 174-211. in B.S. Green et al. (editors). \href{https://www.researchgate.net/publication/226394736_The_Back-Calculation_of_Fish_Growth_From_Otoliths}{Tropical Fish Otoliths: Information for Assessment, Management and Ecology.} Review: Methods and Technologies in Fish Biology and Fisheries 11. Springer. +#' Vigliola, L. and M.G. Meekan. 2009. The back-calculation of fish growth from otoliths. pp. 174-211. in B.S. Green et al. (editors). Tropical Fish Otoliths: Information for Assessment, Management and Ecology. Review: Methods and Technologies in Fish Biology and Fisheries 11. Springer. [Was (is?) available from https://www.researchgate.net/publication/226394736_The_Back-Calculation_of_Fish_Growth_From_Otoliths.] #' #' @keywords manip #' diff --git a/R/capHistConvert.R b/R/capHistConvert.R index b5837711..47459e12 100644 --- a/R/capHistConvert.R +++ b/R/capHistConvert.R @@ -37,7 +37,7 @@ #' 20 \tab 4 \cr #'} #' -#' \href{http://www.phidot.org/software/mark/index.html}{MARK} is the \dQuote{gold-standard} software for analyzing complex capture history information. In the \dQuote{MARK} format the 0s and 1s of the capture histories are combined together as a string without any spaces. Thus, the \dQuote{MARK} format has the capture history strings in one column with an additional column that contains the frequency of individuals that exhibited the capture history of that row. The final column ends with a semi-colon. The same data from above looks like: +#' MARK (http://www.phidot.org/software/mark/index.html) is the \dQuote{gold-standard} software for analyzing complex capture history information. In the \dQuote{MARK} format the 0s and 1s of the capture histories are combined together as a string without any spaces. Thus, the \dQuote{MARK} format has the capture history strings in one column with an additional column that contains the frequency of individuals that exhibited the capture history of that row. The final column ends with a semi-colon. The same data from above looks like: #' #' \tabular{cc}{ #' ch \tab freq \cr diff --git a/R/catchCurve.R b/R/catchCurve.R index a1d1deb9..caa6efe9 100644 --- a/R/catchCurve.R +++ b/R/catchCurve.R @@ -48,7 +48,7 @@ #' #' Maceina, M.J., and P.W. Bettoli. 1998. Variation in largemouth bass recruitment in four mainstream impoundments on the Tennessee River. North American Journal of Fisheries Management 18:998-1003. #' -#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] #' #' @keywords hplot htest manip #' diff --git a/R/chapmanRobson.R b/R/chapmanRobson.R index d8be1101..7002c3bb 100644 --- a/R/chapmanRobson.R +++ b/R/chapmanRobson.R @@ -51,7 +51,7 @@ #' #' Hoenig, J.M. and W.D. Lawing, and N.A. Hoenig. 1983. Using mean age, mean length and median length data to estimate the total mortality rate. International Council for the Exploration of the Sea, CM 1983/D:23, Copenhagen. #' -#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] #' #' Robson, D.S. and D.G. Chapman. 1961. Catch curves and mortality rates. Transactions of the American Fisheries Society. 90:181-189. #' diff --git a/R/depletion.R b/R/depletion.R index 826a1d4b..a45a2c46 100644 --- a/R/depletion.R +++ b/R/depletion.R @@ -56,7 +56,7 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] #' #' Seber, G.A.F. 2002. The Estimation of Animal Abundance. Edward Arnold, Second edition (reprinted). #' diff --git a/R/growthModels.R b/R/growthModels.R index 866ac24f..a8924f40 100644 --- a/R/growthModels.R +++ b/R/growthModels.R @@ -51,7 +51,7 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Campana, S.E. and C.M. Jones. 1992. \href{http://www.dfo-mpo.gc.ca/Library/141734.pdf}{Analysis of otolith microstructure data}. Pages 73-100 In D.K. Stevenson and S.E. Campana, editors. Otolith microstructure examination and analysis. Canadian Special Publication of Fisheries and Aquatic Sciences 117. +#' Campana, S.E. and C.M. Jones. 1992. Analysis of otolith microstructure data. Pages 73-100 In D.K. Stevenson and S.E. Campana, editors. Otolith microstructure examination and analysis. Canadian Special Publication of Fisheries and Aquatic Sciences 117. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/141734.pdf.] #' #' Fabens, A. 1965. Properties and fitting of the von Bertalanffy growth curve. Growth 29:265-289. #' @@ -59,13 +59,13 @@ #' #' Gallucci, V.F. and T.J. Quinn II. 1979. Reparameterizing, fitting, and testing a simple growth model. Transactions of the American Fisheries Society, 108:14-25. #' -#' Garcia-Berthou, E., G. Carmona-Catot, R. Merciai, and D.H. Ogle. \href{https://www.researchgate.net/publication/257658359_A_technical_note_on_seasonal_growth_models}{A technical note on seasonal growth models.} Reviews in Fish Biology and Fisheries 22:635-640. +#' Garcia-Berthou, E., G. Carmona-Catot, R. Merciai, and D.H. Ogle. A technical note on seasonal growth models. Reviews in Fish Biology and Fisheries 22:635-640. [Was (is?) from https://www.researchgate.net/publication/257658359_A_technical_note_on_seasonal_growth_models.] #' #' Gompertz, B. 1825. On the nature of the function expressive of the law of human mortality, and on a new method of determining the value of life contingencies. Philosophical Transactions of the Royal Society of London. 115:513-583. #' -#' Haddon, M., C. Mundy, and D. Tarbath. 2008. \href{http://aquaticcommons.org/8857/1/haddon_Fish_Bull_2008.pdf}{Using an inverse-logistic model to describe growth increments of blacklip abalone (\emph{Haliotis rubra}) in Tasmania}. Fishery Bulletin 106:58-71. +#' Haddon, M., C. Mundy, and D. Tarbath. 2008. Using an inverse-logistic model to describe growth increments of blacklip abalone (\emph{Haliotis rubra}) in Tasmania. Fishery Bulletin 106:58-71. [Was (is?) from http://aquaticcommons.org/8857/1/haddon_Fish_Bull_2008.pdf.] #' -#' Karkach, A. S. 2006. \href{http://www.demographic-research.org/volumes/vol15/12/15-12.pdf}{Trajectories and models of individual growth}. Demographic Research 15:347-400. +#' Karkach, A. S. 2006. Trajectories and models of individual growth. Demographic Research 15:347-400. [Was (is?) from http://www.demographic-research.org/volumes/vol15/12/15-12.pdf.] #' #' Katsanevakis, S. and C.D. Maravelias. 2008. Modelling fish growth: multi-model inference as a better alternative to a priori using von Bertalanffy equation. Fish and Fisheries 9:178-187. #' @@ -79,25 +79,25 @@ #' #' Richards, F. J. 1959. A flexible growth function for empirical use. Journal of Experimental Biology 10:290-300. #' -#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] #' -#' Ricker, W.E. 1979. \href{https://books.google.com/books?id=CB1qu2VbKwQC&pg=PA705&lpg=PA705&dq=Gompertz+fish&source=bl&ots=y34lhFP4IU&sig=EM_DGEQMPGIn_DlgTcGIi_wbItE&hl=en&sa=X&ei=QmM4VZK6EpDAgwTt24CABw&ved=0CE8Q6AEwBw#v=onepage&q=Gompertz\%20fish&f=false}{Growth rates and models}. Pages 677-743 In W.S. Hoar, D.J. Randall, and J.R. Brett, editors. Fish Physiology, Vol. 8: Bioenergetics and Growth. Academic Press, NY, NY. +#' Ricker, W.E. 1979. Growth rates and models. Pages 677-743 In W.S. Hoar, D.J. Randall, and J.R. Brett, editors. Fish Physiology, Vol. 8: Bioenergetics and Growth. Academic Press, NY, NY. [Was (is?) from https://books.google.com/books?id=CB1qu2VbKwQC&pg=PA705&lpg=PA705&dq=Gompertz+fish&source=bl&ots=y34lhFP4IU&sig=EM_DGEQMPGIn_DlgTcGIi_wbItE&hl=en&sa=X&ei=QmM4VZK6EpDAgwTt24CABw&ved=0CE8Q6AEwBw#v=onepage&q=Gompertz\%20fish&f=false.] #' #' Schnute, J. 1981. A versatile growth model with statistically stable parameters. Canadian Journal of Fisheries and Aquatic Sciences, 38:1128-1140. #' -#' Somers, I. F. 1988. \href{http://www.worldfishcenter.org/Naga/na_2914.pdf}{On a seasonally oscillating growth function.} Fishbyte 6(1):8-11. +#' Somers, I. F. 1988. On a seasonally oscillating growth function. Fishbyte 6(1):8-11. [Was (is?) from http://www.worldfishcenter.org/Naga/na_2914.pdf.] #' -#' Tjorve, E. and K. M. C. Tjorve. 2010. \href{https://www.researchgate.net/profile/Even_Tjorve/publication/46218377_A_unified_approach_to_the_Richards-model_family_for_use_in_growth_analyses_why_we_need_only_two_model_forms/links/54ba83b80cf29e0cb04bd24e.pdf}{A unified approach to the Richards-model family for use in growth analyses: Why we need only two model forms.} Journal of Theoretical Biology 267:417-425. +#' Tjorve, E. and K. M. C. Tjorve. 2010. A unified approach to the Richards-model family for use in growth analyses: Why we need only two model forms. Journal of Theoretical Biology 267:417-425. [Was (is?) from https://www.researchgate.net/profile/Even_Tjorve/publication/46218377_A_unified_approach_to_the_Richards-model_family_for_use_in_growth_analyses_why_we_need_only_two_model_forms/links/54ba83b80cf29e0cb04bd24e.pdf.] #' -#' Troynikov, V. S., R. W. Day, and A. M. Leorke. \href{https://www.researchgate.net/profile/Robert_Day2/publication/249340562_Estimation_of_seasonal_growth_parameters_using_a_stochastic_gompertz_model_for_tagging_data/links/54200fa30cf203f155c2a08a.pdf}{Estimation of seasonal growth parameters using a stochastic Gompertz model for tagging data}. Journal of Shellfish Research 17:833-838. +#' Troynikov, V. S., R. W. Day, and A. M. Leorke. Estimation of seasonal growth parameters using a stochastic Gompertz model for tagging data. Journal of Shellfish Research 17:833-838. [Was (is?) from https://www.researchgate.net/profile/Robert_Day2/publication/249340562_Estimation_of_seasonal_growth_parameters_using_a_stochastic_gompertz_model_for_tagging_data/links/54200fa30cf203f155c2a08a.pdf.] #' -#' Vaughan, D. S. and T. E. Helser. 1990. \href{http://docs.lib.noaa.gov/noaa_documents/NMFS/SEFSC/TM_NMFS_SEFSC/NMFS_SEFSC_TM_263.pdf}{Status of the red drum stock of the Atlantic coast: Stock assessment report for 1989}. NOAA Technical Memorandum NMFS-SEFC-263, 117 p. +#' Vaughan, D. S. and T. E. Helser. 1990. Status of the red drum stock of the Atlantic coast: Stock assessment report for 1989. NOAA Technical Memorandum NMFS-SEFC-263, 117 p. [Was (is?) from http://docs.lib.noaa.gov/noaa_documents/NMFS/SEFSC/TM_NMFS_SEFSC/NMFS_SEFSC_TM_263.pdf.] #' #' Wang, Y.-G. 1998. An improved Fabens method for estimation of growth parameters in the von Bertalanffy model with individual asymptotes. Canadian Journal of Fisheries and Aquatic Sciences 55:397-400. #' #' Weisberg, S., G.R. Spangler, and L. S. Richmond. 2010. Mixed effects models for fish growth. Canadian Journal of Fisheries And Aquatic Sciences 67:269-277. #' -#' Winsor, C.P. 1932. \href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1076153/pdf/pnas01729-0009.pdf}{The Gompertz curve as a growth curve}. Proceedings of the National Academy of Sciences. 18:1-8. +#' Winsor, C.P. 1932. The Gompertz curve as a growth curve. Proceedings of the National Academy of Sciences. 18:1-8. [Was (is?) from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1076153/pdf/pnas01729-0009.pdf.] #' #' @keywords manip hplot #' diff --git a/R/metaM.R b/R/metaM.R index 1567059f..0473480e 100644 --- a/R/metaM.R +++ b/R/metaM.R @@ -69,23 +69,23 @@ #' #' Gislason, H., N. Daan, J.C. Rice, and J.G. Pope. 2010. Size, growth, temperature and the natural mortality of marine fish. Fish and Fisheries 11:149-158. #' -#' Hewitt, D.A. and J.M. Hoenig. 2005. \href{http://fishbull.noaa.gov/1032/hewitt.pdf}{Comparison of two approaches for estimating natural mortality based on longevity}. Fishery Bulletin. 103:433-437. +#' Hewitt, D.A. and J.M. Hoenig. 2005. Comparison of two approaches for estimating natural mortality based on longevity. Fishery Bulletin. 103:433-437. [Was (is?) from http://fishbull.noaa.gov/1032/hewitt.pdf.] #' -#' Hoenig, J.M. 1983. \href{http://www.afsc.noaa.gov/REFM/age/Docs/Hoenig_EmpiricalUseOfLongevityData.pdf}{Empirical use of longevity data to estimate mortality rates}. Fishery Bulletin. 82:898-903. +#' Hoenig, J.M. 1983. Empirical use of longevity data to estimate mortality rates. Fishery Bulletin. 82:898-903. [Was (is?) from http://www.afsc.noaa.gov/REFM/age/Docs/Hoenig_EmpiricalUseOfLongevityData.pdf.] #' -#' Jensen, A.L. 1996. Beverton and Holt life history invariants result from optimal trade-off of reproduction and survival. Canadian Journal of Fisheries and Aquatic Sciences. 53:820-822. +#' Jensen, A.L. 1996. Beverton and Holt life history invariants result from optimal trade-off of reproduction and survival. Canadian Journal of Fisheries and Aquatic Sciences. 53:820-822. [Was (is?) from .] #' -#' Jensen, A.L. 2001. \href{http://deepblue.lib.umich.edu/bitstream/handle/2027.42/35236/487_ftp.pdf}{Comparison of theoretical derivations, simple linear regressions, multiple linear regression and principal components for analysis of fish mortality, growth and environmental temperature data}. Environometrics. 12:591-598. +#' Jensen, A.L. 2001. Comparison of theoretical derivations, simple linear regressions, multiple linear regression and principal components for analysis of fish mortality, growth and environmental temperature data. Environometrics. 12:591-598. [Was (is?) from http://deepblue.lib.umich.edu/bitstream/handle/2027.42/35236/487_ftp.pdf.] #' #' Kenchington, T.J. 2014. Natural mortality estimators for information-limited fisheries. Fish and Fisheries. 14:533-562. #' -#' Pauly, D. 1980. \href{http://innri.unuftp.is/pauly/On\%20the\%20interrelationships\%20betwe.pdf}{On the interrelationships between natural mortality, growth parameters, and mean environmental temperature in 175 fish stocks}. Journal du Conseil International pour l'Exploration de la Mer. 39:175-192. +#' Pauly, D. 1980. On the interrelationships between natural mortality, growth parameters, and mean environmental temperature in 175 fish stocks. Journal du Conseil International pour l'Exploration de la Mer. 39:175-192. [Was (is?) from http://innri.unuftp.is/pauly/On\%20the\%20interrelationships\%20betwe.pdf.] #' #' Rikhter, V.A., and V.N. Efanov. 1976. On one of the approaches for estimating natural mortality in fish populations (in Russian). ICNAF Research Document 76/IV/8, 12pp. #' #' Then, A.Y., J.M. Hoenig, N.G. Hall, and D.A. Hewitt. 2015. Evaluating the predictive performance of empirical estimators of natural mortality rate using informatno on over 200 fish species. ICES Journal of Marine Science. 72:82-92. #' -#' Zhang, C-I and B.A. Megrey. 2006. \href{http://www.pmel.noaa.gov/foci/publications/2006/zhan0531.pdf}{A revised Alverson and Carney model for estimating the instantaneous rate of natural mortality}. Transactions of the American Fisheries Socity. 135-620-633. +#' Zhang, C-I and B.A. Megrey. 2006. A revised Alverson and Carney model for estimating the instantaneous rate of natural mortality. Transactions of the American Fisheries Socity. 135-620-633. [Was (is?) from http://www.pmel.noaa.gov/foci/publications/2006/zhan0531.pdf.] #' #' @keywords manip #' diff --git a/R/mrClosed.R b/R/mrClosed.R index 08dfc7f6..9c6d4b87 100644 --- a/R/mrClosed.R +++ b/R/mrClosed.R @@ -97,7 +97,7 @@ #' #' Krebs, C.J. 1989. Ecological Methodology. Addison-Welsey Educational Publishing. #' -#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] #' #' Seber, G.A.F. 2002. The Estimation of Animal Abundance and Related Parameters. Edward Arnold, second edition. #' diff --git a/R/mrOpen.R b/R/mrOpen.R index d4c099d9..9d8e18db 100644 --- a/R/mrOpen.R +++ b/R/mrOpen.R @@ -35,7 +35,7 @@ #' #' @section Testing: The formulas have been triple-checked against formulas in Pollock et al. (1990), Manly (1984), and Seber (2002). #' -#' The results for the \code{\link{CutthroatAL}} data file (as analyzed in the example) was compared to results from the JOLLY program available at \url{http://www.mbr-pwrc.usgs.gov/software/jolly.html}. The r and z values matched, all M and N estimates match at one decimal place, all phi are within 0.001, and all B are within 0.7. The SE match for M except for two estimates that are within 0.1, match for N except for one estimate that is within 0.1, are within 0.001 for phi, and are within 1.3 for B (except for for the first estimate which is dramatically off). +#' The results for the \code{\link{CutthroatAL}} data file (as analyzed in the example) was compared to results from the JOLLY program available at http://www.mbr-pwrc.usgs.gov/software/jolly.html. The r and z values matched, all M and N estimates match at one decimal place, all phi are within 0.001, and all B are within 0.7. The SE match for M except for two estimates that are within 0.1, match for N except for one estimate that is within 0.1, are within 0.001 for phi, and are within 1.3 for B (except for for the first estimate which is dramatically off). #' #' The results of \code{mrOpen} related to Table 4.4 of Pollock et al. (1990) match (to one decimal place) except for three estimates that are within 0.1\% for N, match (to two decimal places) for phi except for where Pollock set phi>1 to phi=1, match for B except for Pollock set B<0 to B=0. The SE match (to two decimal places) for N except for N15 (which is within 0.5, <5\%), match (to three decimal places) for phi except for phi15 (which is within 0.001, <0.5\%), match (to two decimal places) for B except for B17 and B20 which are within 0.2 (<0.2\%) #' diff --git a/R/psdAdd.R b/R/psdAdd.R index 63d410ca..49b833d6 100644 --- a/R/psdAdd.R +++ b/R/psdAdd.R @@ -26,11 +26,11 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. \href{http://pubstorage.sdstate.edu/wfs/415-F.pdf}{New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS).} Fisheries 31:86-87. +#' 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. \href{http://pubstorage.sdstate.edu/wfs/450-F.pdf}{Proportional size distribution (PSD): A further refinement of population size structure index terminology.} Fisheries 32:348. +#' 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. \href{http://web1.cnre.vt.edu/murphybr/web/Readings/Willis\%20et\%20al.pdf}{Stock density indices: development, use, and limitations.} Reviews in Fisheries Science 1:203-222. +#' 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.] #' #' @keywords manip #' diff --git a/R/psdCI.R b/R/psdCI.R index 245f1796..5c530ea3 100644 --- a/R/psdCI.R +++ b/R/psdCI.R @@ -29,7 +29,7 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Brenden, T.O., T. Wagner, and B.R. Murphy. 2008. \href{http://qfc.fw.msu.edu/Publications/Publication\%20List/2008/Novel\%20Tools\%20for\%20Analyzing\%20Proportional\%20Size\%20Distribution_Brenden.pdf}{Novel tools for analyzing proportional size distribution index data.} North American Journal of Fisheries Management 28:1233-1242. +#' Brenden, T.O., T. Wagner, and B.R. Murphy. 2008. Novel tools for analyzing proportional size distribution index data. North American Journal of Fisheries Management 28:1233-1242. [Was (is?) from http://qfc.fw.msu.edu/Publications/Publication\%20List/2008/Novel\%20Tools\%20for\%20Analyzing\%20Proportional\%20Size\%20Distribution_Brenden.pdf.] #' #' @keywords hplot #' diff --git a/R/psdCalc.R b/R/psdCalc.R index 7da790d1..1ff6cfbd 100644 --- a/R/psdCalc.R +++ b/R/psdCalc.R @@ -32,13 +32,13 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. \href{http://pubstorage.sdstate.edu/wfs/415-F.pdf}{New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS).} Fisheries 31:86-87. +#' 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. \href{http://pubstorage.sdstate.edu/wfs/450-F.pdf}{Proportional size distribution (PSD): A further refinement of population size structure index terminology.} Fisheries 32:348. +#' 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.] #' #' Neumann, R. M. and Allen, M. S. 2007. Size structure. In Guy, C. S. and Brown, M. L., editors, Analysis and Interpretation of Freshwater Fisheries Data, Chapter 9, pages 375-421. American Fisheries Society, Bethesda, MD. #' -#' Willis, D.W., B.R. Murphy, and C.S. Guy. 1993. \href{http://web1.cnre.vt.edu/murphybr/web/Readings/Willis\%20et\%20al.pdf}{Stock density indices: development, use, and limitations.} Reviews in Fisheries Science 1:203-222. +#' 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.] #' #' @keywords hplot #' diff --git a/R/psdPlot.R b/R/psdPlot.R index c4e0ab40..a560ce07 100644 --- a/R/psdPlot.R +++ b/R/psdPlot.R @@ -39,11 +39,11 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. \href{http://pubstorage.sdstate.edu/wfs/415-F.pdf}{New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS).} Fisheries 31:86-87. +#' 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. \href{http://pubstorage.sdstate.edu/wfs/450-F.pdf}{Proportional size distribution (PSD): A further refinement of population size structure index terminology.} Fisheries 32:348. +#' 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. \href{http://web1.cnre.vt.edu/murphybr/web/Readings/Willis\%20et\%20al.pdf}{Stock density indices: development, use, and limitations.} Reviews in Fisheries Science 1:203-222. +#' 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.] #' #' @keywords hplot #' diff --git a/R/psdVal.R b/R/psdVal.R index 79a80ef3..2d6217d1 100644 --- a/R/psdVal.R +++ b/R/psdVal.R @@ -24,11 +24,11 @@ #' #' @references Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. \href{http://pubstorage.sdstate.edu/wfs/415-F.pdf}{New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS).} Fisheries 31:86-87. +#' 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. \href{http://pubstorage.sdstate.edu/wfs/450-F.pdf}{Proportional size distribution (PSD): A further refinement of population size structure index terminology.} Fisheries 32:348. +#' 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. \href{http://web1.cnre.vt.edu/murphybr/web/Readings/Willis\%20et\%20al.pdf}{Stock density indices: development, use, and limitations.} Reviews in Fisheries Science 1:203-222. +#' 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.] #' #' @keywords manip #' diff --git a/R/removal.R b/R/removal.R index 5556b412..a2b40e1d 100644 --- a/R/removal.R +++ b/R/removal.R @@ -80,7 +80,7 @@ #' #' Seber, G.A.F. 2002. The Estimation of Animal Abundance. Edward Arnold, second edition (Reprint). #' -#' van Dishoeck, P. 2009. \href{http://rem-main.rem.sfu.ca/theses/vanDishoeckPier_2009_MRM483.pdf}{Effects of catchability variation on performance of depletion estimators: Application to an adaptive management experiment.} Masters Thesis, Simon Fraser University. +#' van Dishoeck, P. 2009. Effects of catchability variation on performance of depletion estimators: Application to an adaptive management experiment. Masters Thesis, Simon Fraser University. [Was (is?) from http://rem-main.rem.sfu.ca/theses/vanDishoeckPier_2009_MRM483.pdf.] #' #' @keywords manip #' diff --git a/R/srStarts.R b/R/srStarts.R index edf272e0..5aff29da 100644 --- a/R/srStarts.R +++ b/R/srStarts.R @@ -46,7 +46,7 @@ #' #' Ricker, W.E. 1954. Stock and recruitment. Journal of the Fisheries Research Board of Canada 11:559-623. #' -#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] #' #' Shepherd, J. 1982. A versatile new stock-recruitment relationship for fisheries and construction of sustainable yield curves. Journal du Conseil International pour l'Exploration de la Mar 40:67-75. #' diff --git a/R/stockRecruitment.R b/R/stockRecruitment.R index a903d3cd..82d0d0a1 100644 --- a/R/stockRecruitment.R +++ b/R/stockRecruitment.R @@ -30,7 +30,7 @@ #' #' Ricker, W.E. 1954. Stock and recruitment. Journal of the Fisheries Research Board of Canada 11:559-623. #' -#' Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +#' Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] #' #' Shepherd, J. 1982. A versatile new stock-recruitment relationship for fisheries and construction of sustainable yield curves. Journal du Conseil International pour l'Exploration de la Mar 40:67-75. #' diff --git a/cran-comments/cran-comments-v0_8_2.md b/cran-comments/cran-comments-v0_8_2.md new file mode 100644 index 00000000..158109e5 --- /dev/null +++ b/cran-comments/cran-comments-v0_8_2.md @@ -0,0 +1,7 @@ +* This is an update to an existing package. + +* It passed the release and development versions on win-builder. + +* Upon confirming submission there was an error for the "r-devel-windows-ix86+x86_64" flavor that appeared to be related to missing gdata and testthat packages. I am not sure what to do about this because the package did pass the win-builder tests for both the release and development versions of R. + +* Additionally there were notes about a missing RMark package for the "r-patched-solaris-sparc" and "r-patched-solaris-x86" flavors. Again, I am not sure what to do about these notes. diff --git a/man/BluegillJL.Rd b/man/BluegillJL.Rd index c43b5ddb..b35ba5a9 100644 --- a/man/BluegillJL.Rd +++ b/man/BluegillJL.Rd @@ -10,7 +10,7 @@ \item{second}{a numeric vector of indicator variables for the second sample (1=captured)} }} \source{ -From example 8.1 in Schneider, J.C. 1998. \href{http://www.michigandnr.com/publications/pdfs/IFR/manual/SMII\%20Chapter08.pdf}{Lake fish population estimates by mark-and-recapture methods.} Chapter 8 in Schneider, J.C. (ed.) 2000. Manual of fisheries survey methods II: with periodic updates. Michigan Department of Natural Resources, Fisheries Special Report 25, Ann Arbor. +From example 8.1 in Schneider, J.C. 1998. Lake fish population estimates by mark-and-recapture methods. Chapter 8 in Schneider, J.C. (ed.) 2000. Manual of fisheries survey methods II: with periodic updates. Michigan Department of Natural Resources, Fisheries Special Report 25, Ann Arbor. [Was (is?) from http://www.michigandnr.com/publications/pdfs/IFR/manual/SMII\%20Chapter08.pdf.] } \description{ Each line consists of the capture history over two samples of Bluegill (\emph{Lepomis macrochirus}) in Jewett Lake (MI). This file contains the capture histories for only Bluegill larger thatn 6-in. diff --git a/man/BrookTroutTH.Rd b/man/BrookTroutTH.Rd index 956dc22f..b450b54f 100644 --- a/man/BrookTroutTH.Rd +++ b/man/BrookTroutTH.Rd @@ -10,7 +10,7 @@ \item{catch}{A numeric vector of number of Brook Trout caught} }} \source{ -Quinlan, H.R. 1999. Biological Characteristics of Coaster Brook Trout at Isle Royale National Park, Michigan, 1996-98. U.S. Fish and Wildlife Service Ashland Fishery Resources Office report. November 1999. Was originally available at \url{www.fws.gov/midwest/ashland/brook/biochar/biolchar.html}. +Quinlan, H.R. 1999. Biological Characteristics of Coaster Brook Trout at Isle Royale National Park, Michigan, 1996-98. U.S. Fish and Wildlife Service Ashland Fishery Resources Office report. November 1999. [Was (is?) from http://www.fws.gov/midwest/ashland/brook/biochar/biolchar.html.] } \description{ Catch-at-age in fyke nets from 1996-1998 for \dQuote{Coaster} Brook Trout (\emph{Salvelinus fontinalis}) in Tobin Harbor, Isle Royale, Lake Superior. diff --git a/man/ChinookArg.Rd b/man/ChinookArg.Rd index 724a6110..c9e26419 100644 --- a/man/ChinookArg.Rd +++ b/man/ChinookArg.Rd @@ -11,7 +11,7 @@ \item{loc}{Capture location (\code{Argentina}, \code{Petrohue}, \code{Puyehue})} }} \source{ -From Figure 4 in Soto, D., I. Arismendi, C. Di Prinzio, and F. Jara. 2007. \href{http://www.scielo.cl/pdf/rchnat/v80n1/art07.pdf}{Establishment of Chinook salmon (\emph{Oncorhynchus tshawytscha}) in Pacific basins of southern South America and its potential ecosystem implications}. Revista Chilena d Historia Natural, 80:81-98. +From Figure 4 in Soto, D., I. Arismendi, C. Di Prinzio, and F. Jara. 2007. Establishment of Chinook salmon (\emph{Oncorhynchus tshawytscha}) in Pacific basins of southern South America and its potential ecosystem implications. Revista Chilena d Historia Natural, 80:81-98. [Was (is?) from http://www.scielo.cl/pdf/rchnat/v80n1/art07.pdf.] } \description{ Lengths and weights for Chinook Salmon from three locations in Argentina. diff --git a/man/CutthroatAL.Rd b/man/CutthroatAL.Rd index 955c3167..eb520729 100644 --- a/man/CutthroatAL.Rd +++ b/man/CutthroatAL.Rd @@ -18,11 +18,14 @@ \item{y2006}{Indicator variable for whether the fish was captured in 2006 (\code{1}=captured)} }} \source{ -Entered from Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010. \href{http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf}{Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006}. Alaska Department of Fish and Game Fisheries Data Series No. 10-82 into \dQuote{RMark} format (see \code{\link[FSAdata]{CutthroatALf}} in \pkg{FSAdata}) and then converted to individual format with \code{\link{capHistConvert}}. +From Appendix A.3 of Harding, R.D., C.L. Hoover, and R.P. Marshall. 2010. Abundance of Cutthroat Trout in Auke Lake, Southeast Alaska, in 2005 and 2006. Alaska Department of Fish and Game Fisheries Data Series No. 10-82. [Was (is?) from http://www.sf.adfg.state.ak.us/FedAidPDFs/FDS10-82.pdf.] } \description{ Individual capture histories of Cutthroat Trout (\emph{Oncorhynchus clarki}) in Auke Lake, Alaska, from samples taken in 1998-2006. } +\note{ +Entered into \dQuote{RMark} format (see \code{\link[FSAdata]{CutthroatALf}} in \pkg{FSAdata}) and then converted to individual format with \code{\link{capHistConvert}} +} \section{Topic(s)}{ \itemize{ diff --git a/man/SpotVA1.Rd b/man/SpotVA1.Rd index 4212c76f..a0c55742 100644 --- a/man/SpotVA1.Rd +++ b/man/SpotVA1.Rd @@ -10,7 +10,7 @@ \item{age}{Ages assigned from examination of otoliths} }} \source{ -Extracted from Table 1 in Chapter 8 (Spot) of the VMRC Final Report on Finfish Ageing, 2002 by the \href{http://www.odu.edu/sci/research/cqfe}{Center for Quantitative Fisheries Ecology} at Old Dominion University. +Extracted from Table 1 in Chapter 8 (Spot) of the VMRC Final Report on Finfish Ageing, 2002 by the Center for Quantitative Fisheries Ecology at Old Dominion University. } \description{ Ages (from otoliths) and lengths of Virginia Spot (\emph{Leiostomus xanthurus}). diff --git a/man/WhitefishLC.Rd b/man/WhitefishLC.Rd index 113ce6a1..7363c288 100644 --- a/man/WhitefishLC.Rd +++ b/man/WhitefishLC.Rd @@ -19,7 +19,7 @@ \item{otolithC}{Consensus age from otoliths by both reader} }} \source{ -Data from Herbst, S.J. and J.E. Marsden. 2011. \href{http://www.uvm.edu/rsenr/emarsden/documents/Herbst\%20and\%20Marsden\%20whitefish\%20age\%20structure\%20comparison.pdf}{Comparison of precision and bias of scale, fin ray, and otolith age estimates for lake whitefish (\emph{Coregonus clupeaformis}) in Lake Champlain.} Journal of Great Lakes Research. 37:386-389. Contributed by Seth Herbst. \bold{Do not use for other than educational purposes without permission from the author.} +Data from Herbst, S.J. and J.E. Marsden. 2011. Comparison of precision and bias of scale, fin ray, and otolith age estimates for lake whitefish (\emph{Coregonus clupeaformis}) in Lake Champlain. Journal of Great Lakes Research. 37:386-389. Contributed by Seth Herbst. \bold{Do not use for other than educational purposes without permission from the author.} [Was (is?) from http://www.uvm.edu/rsenr/emarsden/documents/Herbst\%20and\%20Marsden\%20whitefish\%20age\%20structure\%20comparison.pdf.] } \description{ Assigned ages from two readers on three structures for Lake Whitefish (\emph{Coregonus clupeaformis}) from Lake Champlain in 2009. diff --git a/man/ageBias.Rd b/man/ageBias.Rd index 6f844c4c..2000b0e0 100644 --- a/man/ageBias.Rd +++ b/man/ageBias.Rd @@ -140,7 +140,7 @@ Individual t-tests to determine if the mean age of the non-reference set at a pa The sample size present in the age-agreement table is found with \code{what="n"}. } \section{Testing}{ - Tested all symmetry test results against results in Evans and Hoenig (2008), the McNemar and Evans-Hoenig results against results from \code{\link[fishmethods]{compare2}} in \pkg{fishmethods}, and all results using the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from \url{http://www.nefsc.noaa.gov/fbp/age-prec/}. + Tested all symmetry test results against results in Evans and Hoenig (2008), the McNemar and Evans-Hoenig results against results from \code{\link[fishmethods]{compare2}} in \pkg{fishmethods}, and all results using the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from the online resource at http://www.nefsc.noaa.gov/fbp/age-prec/. } \section{IFAR Chapter}{ @@ -188,7 +188,7 @@ Derek H. Ogle, \email{derek@derekogle.com} \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. \href{http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf}{Graphical and statistical methods for determining the consistency of age determinations.} Transactions of the American Fisheries Society 124:131-138. +Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. Graphical and statistical methods for determining the consistency of age determinations. Transactions of the American Fisheries Society 124:131-138. [Was (is?) available from http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf.] Evans, G.T. and J.M. Hoenig. 1998. Testing and viewing symmetry in contingency tables, with application to readers of fish ages. Biometrics 54:620-629. @@ -196,7 +196,7 @@ Hoenig, J.M., M.J. Morgan, and C.A. Brown. 1995. Analysing differences between McBride, R.S. 2015. Diagnosis of paired age agreement: A simulation approach of accuracy and precision effects. ICES Journal of Marine Science, XX:XXX-XXX. -Muir, A.M., M.P. Ebener, J.X. He, and J.E. Johnson. 2008. \href{http://www.tandfonline.com/doi/abs/10.1577/M06-160.1}{A comparison of the scale and otolith methods of age estimation for lake whitefish in Lake Huron.} North American Journal of Fisheries Management 28:625-635. +Muir, A.M., M.P. Ebener, J.X. He, and J.E. Johnson. 2008. A comparison of the scale and otolith methods of age estimation for lake whitefish in Lake Huron. North American Journal of Fisheries Management 28:625-635. [Was (is?) available from http://www.tandfonline.com/doi/abs/10.1577/M06-160.1] } \seealso{ See \code{\link{agePrecision}} for measures of precision between pairs of age assignments. See \code{\link[fishmethods]{compare2}} in \pkg{fishmethods} for similar functionality. diff --git a/man/agePrecision.Rd b/man/agePrecision.Rd index d28f5b7b..a55efd8d 100644 --- a/man/agePrecision.Rd +++ b/man/agePrecision.Rd @@ -63,7 +63,7 @@ If \code{what="absolute difference"} is used in \code{summary} then a table that If \code{what="detail"} is used in \code{summary} then a data frame of the original \code{data} along with the intermediate caculations of the average age, standard deviation of age, APE, and ACV for each individual will be printed. These details are generally only used to check or to understand calculations. } \section{Testing}{ - Tested all precision results against published results in Herbst and Marsden (2011) for the \code{\link{WhitefishLC}} data and the results for the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from \url{http://www.nefsc.noaa.gov/fbp/age-prec/}. + Tested all precision results against published results in Herbst and Marsden (2011) for the \code{\link{WhitefishLC}} data and the results for the \code{\link[FSAdata]{AlewifeLH}} data set from \pkg{FSAdata} against results from the online resource at http://www.nefsc.noaa.gov/fbp/age-prec/. } \section{IFAR Chapter}{ @@ -104,13 +104,13 @@ Derek H. Ogle, \email{derek@derekogle.com} \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Beamish, R.J. and D.A. Fournier. 1981. \href{http://www.pac.dfo-mpo.gc.ca/science/people-gens/beamish/PDF_files/compareagecjfas1981.pdf}{A method for comparing the precision of a set of age determinations.} Canadian Journal of Fisheries and Aquatic Sciences 38:982-983. +Beamish, R.J. and D.A. Fournier. 1981. A method for comparing the precision of a set of age determinations. Canadian Journal of Fisheries and Aquatic Sciences 38:982-983. [Was (is?) available from http://www.pac.dfo-mpo.gc.ca/science/people-gens/beamish/PDF_files/compareagecjfas1981.pdf.] -Campana, S.E. 1982. \href{http://www.denix.osd.mil/nr/crid/Coral_Reef_Iniative_Database/References_for_Reef_Assessment_files/Campana,\%202001.pdf}{Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods.} Journal of Fish Biology 59:197-242. +Campana, S.E. 1982. Accuracy, precision and quality control in age determination, including a review of the use and abuse of age validation methods. Journal of Fish Biology 59:197-242. [Was (is?) available from http://www.denix.osd.mil/nr/crid/Coral_Reef_Iniative_Database/References_for_Reef_Assessment_files/Campana,\%202001.pdf.] -Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. \href{http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf}{Graphical and statistical methods for determining the consistency of age determinations.} Transactions of the American Fisheries Society 124:131-138. +Campana, S.E., M.C. Annand, and J.I. McMillan. 1995. Graphical and statistical methods for determining the consistency of age determinations. Transactions of the American Fisheries Society 124:131-138. [Was (is?) available from http://www.bio.gc.ca/otoliths/documents/Campana\%20et\%20al\%201995\%20TAFS.pdf.] -Chang, W.Y.B. 1982. \href{http://www.nrcresearchpress.com/doi/abs/10.1139/f82-158}{A statistical method for evaluating the reproducibility of age determination.} Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210. +Chang, W.Y.B. 1982. A statistical method for evaluating the reproducibility of age determination. Canadian Journal of Fisheries and Aquatic Sciences 39:1208-1210. [Was (is?) available from http://www.nrcresearchpress.com/doi/abs/10.1139/f82-158.] McBride, R.S. 2015. Diagnosis of paired age agreement: A simulation approach of accuracy and precision effects. ICES Journal of Marine Science, XX:XXX-XXX. } diff --git a/man/alkIndivAge.Rd b/man/alkIndivAge.Rd index ae0f8253..387888eb 100644 --- a/man/alkIndivAge.Rd +++ b/man/alkIndivAge.Rd @@ -99,7 +99,7 @@ Derek H. Ogle, \email{derek@derekogle.com}. This is largely an R version of the \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Isermann, D.A. and C.T. Knight. 2005. \href{http://www.tandfonline.com/doi/abs/10.1577/M04-130.1}{A computer program for age-length keys incorporating age assignment to individual fish.} North American Journal of Fisheries Management, 25:1153-1160. +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.] } \seealso{ See \code{\link{alkAgeDist}} and \code{\link{alkMeanVar}} for alternative methods to derived age distributions and mean (and SD) values for each age. See \code{\link{alkPlot}} for methods to visualize age-length keys. diff --git a/man/bcFuns.Rd b/man/bcFuns.Rd index ccf2e878..d200b6b6 100644 --- a/man/bcFuns.Rd +++ b/man/bcFuns.Rd @@ -46,9 +46,8 @@ EBPH \tab 21 \tab Exponential Body Proportional Hypothesis \cr ESPH \tab 22 \tab Exponential Scale Proportional Hypothesis \cr } } -\section{fishR vignette}{ - \url{https://sites.google.com/site/fishrfiles/gnrl/Backcalculation.pdf}, -\url{https://sites.google.com/site/fishrfiles/gnrl/BackcalculationExtra.pdf} +\section{IFAR Supplement}{ + \url{http://derekogle.com/IFAR/supplements/backcalculation/} } \examples{ ## Simple Examples @@ -68,7 +67,7 @@ bcm2(lencap,rad,radcap,2) # demonstrated with a=2 Derek H. Ogle, \email{derek@derekogle.com} } \references{ -Vigliola, L. and M.G. Meekan. 2009. The back-calculation of fish growth from otoliths. pp. 174-211. in B.S. Green et al. (editors). \href{https://www.researchgate.net/publication/226394736_The_Back-Calculation_of_Fish_Growth_From_Otoliths}{Tropical Fish Otoliths: Information for Assessment, Management and Ecology.} Review: Methods and Technologies in Fish Biology and Fisheries 11. Springer. +Vigliola, L. and M.G. Meekan. 2009. The back-calculation of fish growth from otoliths. pp. 174-211. in B.S. Green et al. (editors). Tropical Fish Otoliths: Information for Assessment, Management and Ecology. Review: Methods and Technologies in Fish Biology and Fisheries 11. Springer. [Was (is?) available from https://www.researchgate.net/publication/226394736_The_Back-Calculation_of_Fish_Growth_From_Otoliths.] } \keyword{manip} diff --git a/man/capHistConvert.Rd b/man/capHistConvert.Rd index 541cb3fd..d8b92e37 100644 --- a/man/capHistConvert.Rd +++ b/man/capHistConvert.Rd @@ -75,7 +75,7 @@ fish \tab event \cr 20 \tab 4 \cr } -\href{http://www.phidot.org/software/mark/index.html}{MARK} is the \dQuote{gold-standard} software for analyzing complex capture history information. In the \dQuote{MARK} format the 0s and 1s of the capture histories are combined together as a string without any spaces. Thus, the \dQuote{MARK} format has the capture history strings in one column with an additional column that contains the frequency of individuals that exhibited the capture history of that row. The final column ends with a semi-colon. The same data from above looks like: +MARK (http://www.phidot.org/software/mark/index.html) is the \dQuote{gold-standard} software for analyzing complex capture history information. In the \dQuote{MARK} format the 0s and 1s of the capture histories are combined together as a string without any spaces. Thus, the \dQuote{MARK} format has the capture history strings in one column with an additional column that contains the frequency of individuals that exhibited the capture history of that row. The final column ends with a semi-colon. The same data from above looks like: \tabular{cc}{ ch \tab freq \cr diff --git a/man/catchCurve.Rd b/man/catchCurve.Rd index 00d7d039..e7e5dcce 100644 --- a/man/catchCurve.Rd +++ b/man/catchCurve.Rd @@ -145,7 +145,7 @@ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analy Maceina, M.J., and P.W. Bettoli. 1998. Variation in largemouth bass recruitment in four mainstream impoundments on the Tennessee River. North American Journal of Fisheries Management 18:998-1003. -Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] } \seealso{ See \code{\link[fishmethods]{agesurv}} in \pkg{fishmethods} for similar functionality. See \code{\link{chapmanRobson}} and \code{\link[fishmethods]{agesurvcl}} in \pkg{fishmethods} for alternative methods to estimate mortality rates. See \code{\link{metaM}} for empirical methods to estimate natural mortality. diff --git a/man/chapmanRobson.Rd b/man/chapmanRobson.Rd index 79992d6c..f14ab6a4 100644 --- a/man/chapmanRobson.Rd +++ b/man/chapmanRobson.Rd @@ -121,7 +121,7 @@ Chapman, D.G. and D.S. Robson. 1960. The analysis of a catch curve. Biometrics. Hoenig, J.M. and W.D. Lawing, and N.A. Hoenig. 1983. Using mean age, mean length and median length data to estimate the total mortality rate. International Council for the Exploration of the Sea, CM 1983/D:23, Copenhagen. -Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] Robson, D.S. and D.G. Chapman. 1961. Catch curves and mortality rates. Transactions of the American Fisheries Society. 90:181-189. diff --git a/man/depletion.Rd b/man/depletion.Rd index 7c0f522d..ca445b70 100644 --- a/man/depletion.Rd +++ b/man/depletion.Rd @@ -147,7 +147,7 @@ Derek H. Ogle, \email{derek@derekogle.com} \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] Seber, G.A.F. 2002. The Estimation of Animal Abundance. Edward Arnold, Second edition (reprinted). } diff --git a/man/growthModels.Rd b/man/growthModels.Rd index adc89a96..993c06a3 100644 --- a/man/growthModels.Rd +++ b/man/growthModels.Rd @@ -254,7 +254,7 @@ Derek H. Ogle, \email{derek@derekogle.com}, thanks to Gabor Grothendieck for a h \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Campana, S.E. and C.M. Jones. 1992. \href{http://www.dfo-mpo.gc.ca/Library/141734.pdf}{Analysis of otolith microstructure data}. Pages 73-100 In D.K. Stevenson and S.E. Campana, editors. Otolith microstructure examination and analysis. Canadian Special Publication of Fisheries and Aquatic Sciences 117. +Campana, S.E. and C.M. Jones. 1992. Analysis of otolith microstructure data. Pages 73-100 In D.K. Stevenson and S.E. Campana, editors. Otolith microstructure examination and analysis. Canadian Special Publication of Fisheries and Aquatic Sciences 117. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/141734.pdf.] Fabens, A. 1965. Properties and fitting of the von Bertalanffy growth curve. Growth 29:265-289. @@ -262,13 +262,13 @@ Francis, R.I.C.C. 1988. Are growth parameters estimated from tagging and age-l Gallucci, V.F. and T.J. Quinn II. 1979. Reparameterizing, fitting, and testing a simple growth model. Transactions of the American Fisheries Society, 108:14-25. -Garcia-Berthou, E., G. Carmona-Catot, R. Merciai, and D.H. Ogle. \href{https://www.researchgate.net/publication/257658359_A_technical_note_on_seasonal_growth_models}{A technical note on seasonal growth models.} Reviews in Fish Biology and Fisheries 22:635-640. +Garcia-Berthou, E., G. Carmona-Catot, R. Merciai, and D.H. Ogle. A technical note on seasonal growth models. Reviews in Fish Biology and Fisheries 22:635-640. [Was (is?) from https://www.researchgate.net/publication/257658359_A_technical_note_on_seasonal_growth_models.] Gompertz, B. 1825. On the nature of the function expressive of the law of human mortality, and on a new method of determining the value of life contingencies. Philosophical Transactions of the Royal Society of London. 115:513-583. -Haddon, M., C. Mundy, and D. Tarbath. 2008. \href{http://aquaticcommons.org/8857/1/haddon_Fish_Bull_2008.pdf}{Using an inverse-logistic model to describe growth increments of blacklip abalone (\emph{Haliotis rubra}) in Tasmania}. Fishery Bulletin 106:58-71. +Haddon, M., C. Mundy, and D. Tarbath. 2008. Using an inverse-logistic model to describe growth increments of blacklip abalone (\emph{Haliotis rubra}) in Tasmania. Fishery Bulletin 106:58-71. [Was (is?) from http://aquaticcommons.org/8857/1/haddon_Fish_Bull_2008.pdf.] -Karkach, A. S. 2006. \href{http://www.demographic-research.org/volumes/vol15/12/15-12.pdf}{Trajectories and models of individual growth}. Demographic Research 15:347-400. +Karkach, A. S. 2006. Trajectories and models of individual growth. Demographic Research 15:347-400. [Was (is?) from http://www.demographic-research.org/volumes/vol15/12/15-12.pdf.] Katsanevakis, S. and C.D. Maravelias. 2008. Modelling fish growth: multi-model inference as a better alternative to a priori using von Bertalanffy equation. Fish and Fisheries 9:178-187. @@ -282,25 +282,25 @@ Quist, M.C., M.A. Pegg, and D.R. DeVries. 2012. Age and Growth. Chapter 15 in Richards, F. J. 1959. A flexible growth function for empirical use. Journal of Experimental Biology 10:290-300. -Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] -Ricker, W.E. 1979. \href{https://books.google.com/books?id=CB1qu2VbKwQC&pg=PA705&lpg=PA705&dq=Gompertz+fish&source=bl&ots=y34lhFP4IU&sig=EM_DGEQMPGIn_DlgTcGIi_wbItE&hl=en&sa=X&ei=QmM4VZK6EpDAgwTt24CABw&ved=0CE8Q6AEwBw#v=onepage&q=Gompertz\%20fish&f=false}{Growth rates and models}. Pages 677-743 In W.S. Hoar, D.J. Randall, and J.R. Brett, editors. Fish Physiology, Vol. 8: Bioenergetics and Growth. Academic Press, NY, NY. +Ricker, W.E. 1979. Growth rates and models. Pages 677-743 In W.S. Hoar, D.J. Randall, and J.R. Brett, editors. Fish Physiology, Vol. 8: Bioenergetics and Growth. Academic Press, NY, NY. [Was (is?) from https://books.google.com/books?id=CB1qu2VbKwQC&pg=PA705&lpg=PA705&dq=Gompertz+fish&source=bl&ots=y34lhFP4IU&sig=EM_DGEQMPGIn_DlgTcGIi_wbItE&hl=en&sa=X&ei=QmM4VZK6EpDAgwTt24CABw&ved=0CE8Q6AEwBw#v=onepage&q=Gompertz\%20fish&f=false.] Schnute, J. 1981. A versatile growth model with statistically stable parameters. Canadian Journal of Fisheries and Aquatic Sciences, 38:1128-1140. -Somers, I. F. 1988. \href{http://www.worldfishcenter.org/Naga/na_2914.pdf}{On a seasonally oscillating growth function.} Fishbyte 6(1):8-11. +Somers, I. F. 1988. On a seasonally oscillating growth function. Fishbyte 6(1):8-11. [Was (is?) from http://www.worldfishcenter.org/Naga/na_2914.pdf.] -Tjorve, E. and K. M. C. Tjorve. 2010. \href{https://www.researchgate.net/profile/Even_Tjorve/publication/46218377_A_unified_approach_to_the_Richards-model_family_for_use_in_growth_analyses_why_we_need_only_two_model_forms/links/54ba83b80cf29e0cb04bd24e.pdf}{A unified approach to the Richards-model family for use in growth analyses: Why we need only two model forms.} Journal of Theoretical Biology 267:417-425. +Tjorve, E. and K. M. C. Tjorve. 2010. A unified approach to the Richards-model family for use in growth analyses: Why we need only two model forms. Journal of Theoretical Biology 267:417-425. [Was (is?) from https://www.researchgate.net/profile/Even_Tjorve/publication/46218377_A_unified_approach_to_the_Richards-model_family_for_use_in_growth_analyses_why_we_need_only_two_model_forms/links/54ba83b80cf29e0cb04bd24e.pdf.] -Troynikov, V. S., R. W. Day, and A. M. Leorke. \href{https://www.researchgate.net/profile/Robert_Day2/publication/249340562_Estimation_of_seasonal_growth_parameters_using_a_stochastic_gompertz_model_for_tagging_data/links/54200fa30cf203f155c2a08a.pdf}{Estimation of seasonal growth parameters using a stochastic Gompertz model for tagging data}. Journal of Shellfish Research 17:833-838. +Troynikov, V. S., R. W. Day, and A. M. Leorke. Estimation of seasonal growth parameters using a stochastic Gompertz model for tagging data. Journal of Shellfish Research 17:833-838. [Was (is?) from https://www.researchgate.net/profile/Robert_Day2/publication/249340562_Estimation_of_seasonal_growth_parameters_using_a_stochastic_gompertz_model_for_tagging_data/links/54200fa30cf203f155c2a08a.pdf.] -Vaughan, D. S. and T. E. Helser. 1990. \href{http://docs.lib.noaa.gov/noaa_documents/NMFS/SEFSC/TM_NMFS_SEFSC/NMFS_SEFSC_TM_263.pdf}{Status of the red drum stock of the Atlantic coast: Stock assessment report for 1989}. NOAA Technical Memorandum NMFS-SEFC-263, 117 p. +Vaughan, D. S. and T. E. Helser. 1990. Status of the red drum stock of the Atlantic coast: Stock assessment report for 1989. NOAA Technical Memorandum NMFS-SEFC-263, 117 p. [Was (is?) from http://docs.lib.noaa.gov/noaa_documents/NMFS/SEFSC/TM_NMFS_SEFSC/NMFS_SEFSC_TM_263.pdf.] Wang, Y.-G. 1998. An improved Fabens method for estimation of growth parameters in the von Bertalanffy model with individual asymptotes. Canadian Journal of Fisheries and Aquatic Sciences 55:397-400. Weisberg, S., G.R. Spangler, and L. S. Richmond. 2010. Mixed effects models for fish growth. Canadian Journal of Fisheries And Aquatic Sciences 67:269-277. -Winsor, C.P. 1932. \href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1076153/pdf/pnas01729-0009.pdf}{The Gompertz curve as a growth curve}. Proceedings of the National Academy of Sciences. 18:1-8. +Winsor, C.P. 1932. The Gompertz curve as a growth curve. Proceedings of the National Academy of Sciences. 18:1-8. [Was (is?) from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1076153/pdf/pnas01729-0009.pdf.] } \seealso{ See \code{\link{Schnute}} for an implementation of the Schnute (1981) model. diff --git a/man/metaM.Rd b/man/metaM.Rd index c03b4d25..8946c7e1 100644 --- a/man/metaM.Rd +++ b/man/metaM.Rd @@ -138,23 +138,23 @@ Charnov, E.L., H. Gislason, and J.G. Pope. 2013. Evolutionary assembly rules f Gislason, H., N. Daan, J.C. Rice, and J.G. Pope. 2010. Size, growth, temperature and the natural mortality of marine fish. Fish and Fisheries 11:149-158. -Hewitt, D.A. and J.M. Hoenig. 2005. \href{http://fishbull.noaa.gov/1032/hewitt.pdf}{Comparison of two approaches for estimating natural mortality based on longevity}. Fishery Bulletin. 103:433-437. +Hewitt, D.A. and J.M. Hoenig. 2005. Comparison of two approaches for estimating natural mortality based on longevity. Fishery Bulletin. 103:433-437. [Was (is?) from http://fishbull.noaa.gov/1032/hewitt.pdf.] -Hoenig, J.M. 1983. \href{http://www.afsc.noaa.gov/REFM/age/Docs/Hoenig_EmpiricalUseOfLongevityData.pdf}{Empirical use of longevity data to estimate mortality rates}. Fishery Bulletin. 82:898-903. +Hoenig, J.M. 1983. Empirical use of longevity data to estimate mortality rates. Fishery Bulletin. 82:898-903. [Was (is?) from http://www.afsc.noaa.gov/REFM/age/Docs/Hoenig_EmpiricalUseOfLongevityData.pdf.] -Jensen, A.L. 1996. Beverton and Holt life history invariants result from optimal trade-off of reproduction and survival. Canadian Journal of Fisheries and Aquatic Sciences. 53:820-822. +Jensen, A.L. 1996. Beverton and Holt life history invariants result from optimal trade-off of reproduction and survival. Canadian Journal of Fisheries and Aquatic Sciences. 53:820-822. [Was (is?) from .] -Jensen, A.L. 2001. \href{http://deepblue.lib.umich.edu/bitstream/handle/2027.42/35236/487_ftp.pdf}{Comparison of theoretical derivations, simple linear regressions, multiple linear regression and principal components for analysis of fish mortality, growth and environmental temperature data}. Environometrics. 12:591-598. +Jensen, A.L. 2001. Comparison of theoretical derivations, simple linear regressions, multiple linear regression and principal components for analysis of fish mortality, growth and environmental temperature data. Environometrics. 12:591-598. [Was (is?) from http://deepblue.lib.umich.edu/bitstream/handle/2027.42/35236/487_ftp.pdf.] Kenchington, T.J. 2014. Natural mortality estimators for information-limited fisheries. Fish and Fisheries. 14:533-562. -Pauly, D. 1980. \href{http://innri.unuftp.is/pauly/On\%20the\%20interrelationships\%20betwe.pdf}{On the interrelationships between natural mortality, growth parameters, and mean environmental temperature in 175 fish stocks}. Journal du Conseil International pour l'Exploration de la Mer. 39:175-192. +Pauly, D. 1980. On the interrelationships between natural mortality, growth parameters, and mean environmental temperature in 175 fish stocks. Journal du Conseil International pour l'Exploration de la Mer. 39:175-192. [Was (is?) from http://innri.unuftp.is/pauly/On\%20the\%20interrelationships\%20betwe.pdf.] Rikhter, V.A., and V.N. Efanov. 1976. On one of the approaches for estimating natural mortality in fish populations (in Russian). ICNAF Research Document 76/IV/8, 12pp. Then, A.Y., J.M. Hoenig, N.G. Hall, and D.A. Hewitt. 2015. Evaluating the predictive performance of empirical estimators of natural mortality rate using informatno on over 200 fish species. ICES Journal of Marine Science. 72:82-92. -Zhang, C-I and B.A. Megrey. 2006. \href{http://www.pmel.noaa.gov/foci/publications/2006/zhan0531.pdf}{A revised Alverson and Carney model for estimating the instantaneous rate of natural mortality}. Transactions of the American Fisheries Socity. 135-620-633. +Zhang, C-I and B.A. Megrey. 2006. A revised Alverson and Carney model for estimating the instantaneous rate of natural mortality. Transactions of the American Fisheries Socity. 135-620-633. [Was (is?) from http://www.pmel.noaa.gov/foci/publications/2006/zhan0531.pdf.] } \seealso{ See \code{\link[fishmethods]{M.empirical}} in \pkg{fishmethods} for similar functionality. diff --git a/man/mrClosed.Rd b/man/mrClosed.Rd index 1feb61e6..d4b2b46f 100644 --- a/man/mrClosed.Rd +++ b/man/mrClosed.Rd @@ -232,7 +232,7 @@ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analy Krebs, C.J. 1989. Ecological Methodology. Addison-Welsey Educational Publishing. -Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] Seber, G.A.F. 2002. The Estimation of Animal Abundance and Related Parameters. Edward Arnold, second edition. diff --git a/man/mrOpen.Rd b/man/mrOpen.Rd index 60ef3990..e81bcb2f 100644 --- a/man/mrOpen.Rd +++ b/man/mrOpen.Rd @@ -67,7 +67,7 @@ The level of confidence is not set in the \code{confint} function, in contrast t \section{Testing}{ The formulas have been triple-checked against formulas in Pollock et al. (1990), Manly (1984), and Seber (2002). -The results for the \code{\link{CutthroatAL}} data file (as analyzed in the example) was compared to results from the JOLLY program available at \url{http://www.mbr-pwrc.usgs.gov/software/jolly.html}. The r and z values matched, all M and N estimates match at one decimal place, all phi are within 0.001, and all B are within 0.7. The SE match for M except for two estimates that are within 0.1, match for N except for one estimate that is within 0.1, are within 0.001 for phi, and are within 1.3 for B (except for for the first estimate which is dramatically off). +The results for the \code{\link{CutthroatAL}} data file (as analyzed in the example) was compared to results from the JOLLY program available at http://www.mbr-pwrc.usgs.gov/software/jolly.html. The r and z values matched, all M and N estimates match at one decimal place, all phi are within 0.001, and all B are within 0.7. The SE match for M except for two estimates that are within 0.1, match for N except for one estimate that is within 0.1, are within 0.001 for phi, and are within 1.3 for B (except for for the first estimate which is dramatically off). The results of \code{mrOpen} related to Table 4.4 of Pollock et al. (1990) match (to one decimal place) except for three estimates that are within 0.1\% for N, match (to two decimal places) for phi except for where Pollock set phi>1 to phi=1, match for B except for Pollock set B<0 to B=0. The SE match (to two decimal places) for N except for N15 (which is within 0.5, <5\%), match (to three decimal places) for phi except for phi15 (which is within 0.001, <0.5\%), match (to two decimal places) for B except for B17 and B20 which are within 0.2 (<0.2\%) diff --git a/man/psdAdd.Rd b/man/psdAdd.Rd index 5f520a3f..189bc1a4 100644 --- a/man/psdAdd.Rd +++ b/man/psdAdd.Rd @@ -95,11 +95,11 @@ Derek H. Ogle, \email{derek@derekogle.com} \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. \href{http://pubstorage.sdstate.edu/wfs/415-F.pdf}{New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS).} Fisheries 31:86-87. +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. \href{http://pubstorage.sdstate.edu/wfs/450-F.pdf}{Proportional size distribution (PSD): A further refinement of population size structure index terminology.} Fisheries 32:348. +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. \href{http://web1.cnre.vt.edu/murphybr/web/Readings/Willis\%20et\%20al.pdf}{Stock density indices: development, use, and limitations.} Reviews in Fisheries Science 1:203-222. +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.] } \seealso{ \code{\link{psdVal}}, \code{\link{psdCalc}}, \code{\link{psdPlot}}, \code{\link{PSDlit}}, and \code{\link{wrAdd}} for related functions. See \code{\link{mapvalues}} for help in changing species names to match those in \code{\link{PSDlit}}. diff --git a/man/psdCI.Rd b/man/psdCI.Rd index d300389f..7ea4c4c4 100644 --- a/man/psdCI.Rd +++ b/man/psdCI.Rd @@ -84,7 +84,7 @@ Derek H. Ogle, \email{derek@derekogle.com} \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Brenden, T.O., T. Wagner, and B.R. Murphy. 2008. \href{http://qfc.fw.msu.edu/Publications/Publication\%20List/2008/Novel\%20Tools\%20for\%20Analyzing\%20Proportional\%20Size\%20Distribution_Brenden.pdf}{Novel tools for analyzing proportional size distribution index data.} North American Journal of Fisheries Management 28:1233-1242. +Brenden, T.O., T. Wagner, and B.R. Murphy. 2008. Novel tools for analyzing proportional size distribution index data. North American Journal of Fisheries Management 28:1233-1242. [Was (is?) from http://qfc.fw.msu.edu/Publications/Publication\%20List/2008/Novel\%20Tools\%20for\%20Analyzing\%20Proportional\%20Size\%20Distribution_Brenden.pdf.] } \seealso{ See \code{\link{psdVal}}, \code{\link{psdPlot}}, \code{\link{psdAdd}}, \code{\link{PSDlit}}, \code{\link{tictactoe}}, \code{\link{lencat}}, and \code{\link{rcumsum}} for related functionality. diff --git a/man/psdCalc.Rd b/man/psdCalc.Rd index 0631d135..4847814e 100644 --- a/man/psdCalc.Rd +++ b/man/psdCalc.Rd @@ -114,13 +114,13 @@ Derek H. Ogle, \email{derek@derekogle.com} \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. \href{http://pubstorage.sdstate.edu/wfs/415-F.pdf}{New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS).} Fisheries 31:86-87. +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. \href{http://pubstorage.sdstate.edu/wfs/450-F.pdf}{Proportional size distribution (PSD): A further refinement of population size structure index terminology.} Fisheries 32:348. +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.] Neumann, R. M. and Allen, M. S. 2007. Size structure. In Guy, C. S. and Brown, M. L., editors, Analysis and Interpretation of Freshwater Fisheries Data, Chapter 9, pages 375-421. American Fisheries Society, Bethesda, MD. -Willis, D.W., B.R. Murphy, and C.S. Guy. 1993. \href{http://web1.cnre.vt.edu/murphybr/web/Readings/Willis\%20et\%20al.pdf}{Stock density indices: development, use, and limitations.} Reviews in Fisheries Science 1:203-222. +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.] } \seealso{ See \code{\link{psdVal}}, \code{\link{psdPlot}}, \code{\link{psdAdd}}, \code{\link{PSDlit}}, \code{\link{tictactoe}}, \code{\link{lencat}}, and \code{\link{rcumsum}} for related functionality. diff --git a/man/psdPlot.Rd b/man/psdPlot.Rd index 7927b7b7..55340cc8 100644 --- a/man/psdPlot.Rd +++ b/man/psdPlot.Rd @@ -119,11 +119,11 @@ Derek H. Ogle, \email{derek@derekogle.com} \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. \href{http://pubstorage.sdstate.edu/wfs/415-F.pdf}{New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS).} Fisheries 31:86-87. +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. \href{http://pubstorage.sdstate.edu/wfs/450-F.pdf}{Proportional size distribution (PSD): A further refinement of population size structure index terminology.} Fisheries 32:348. +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. \href{http://web1.cnre.vt.edu/murphybr/web/Readings/Willis\%20et\%20al.pdf}{Stock density indices: development, use, and limitations.} Reviews in Fisheries Science 1:203-222. +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.] } \seealso{ See \code{\link{psdVal}}, \code{\link{psdCalc}}, \code{\link{psdAdd}}, \code{\link{PSDlit}}, \code{\link{lencat}}, \code{\link{tictactoe}}, \code{\link{lencat}}, and \code{\link{rcumsum}} for related functionality. diff --git a/man/psdVal.Rd b/man/psdVal.Rd index 5a254cf7..c5ae0cf4 100644 --- a/man/psdVal.Rd +++ b/man/psdVal.Rd @@ -59,11 +59,11 @@ Derek H. Ogle, \email{derek@derekogle.com} \references{ Ogle, D.H. 2015. \href{http://derekogle.com/IFAR}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. -Guy, C.S., R.M. Neumann, and D.W. Willis. 2006. \href{http://pubstorage.sdstate.edu/wfs/415-F.pdf}{New terminology for proportional stock density (PSD) and relative stock density (RSD): proportional size structure (PSS).} Fisheries 31:86-87. +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. \href{http://pubstorage.sdstate.edu/wfs/450-F.pdf}{Proportional size distribution (PSD): A further refinement of population size structure index terminology.} Fisheries 32:348. +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. \href{http://web1.cnre.vt.edu/murphybr/web/Readings/Willis\%20et\%20al.pdf}{Stock density indices: development, use, and limitations.} Reviews in Fisheries Science 1:203-222. +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.] } \seealso{ See \code{\link{psdCalc}}, \code{\link{psdPlot}}, \code{\link{psdAdd}}, \code{\link{PSDlit}}, \code{\link{tictactoe}}, \code{\link{lencat}}, and \code{\link{rcumsum}} for related functionality. diff --git a/man/removal.Rd b/man/removal.Rd index dc37d34c..7bad41dc 100644 --- a/man/removal.Rd +++ b/man/removal.Rd @@ -208,7 +208,7 @@ Schnute, J. 1983. A new approach to estimating populations by the removal meth Seber, G.A.F. 2002. The Estimation of Animal Abundance. Edward Arnold, second edition (Reprint). -van Dishoeck, P. 2009. \href{http://rem-main.rem.sfu.ca/theses/vanDishoeckPier_2009_MRM483.pdf}{Effects of catchability variation on performance of depletion estimators: Application to an adaptive management experiment.} Masters Thesis, Simon Fraser University. +van Dishoeck, P. 2009. Effects of catchability variation on performance of depletion estimators: Application to an adaptive management experiment. Masters Thesis, Simon Fraser University. [Was (is?) from http://rem-main.rem.sfu.ca/theses/vanDishoeckPier_2009_MRM483.pdf.] } \seealso{ See \code{\link{depletion}} for related functionality. diff --git a/man/srStarts.Rd b/man/srStarts.Rd index 3307ef14..222346bc 100644 --- a/man/srStarts.Rd +++ b/man/srStarts.Rd @@ -112,7 +112,7 @@ Quinn II, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford Univers Ricker, W.E. 1954. Stock and recruitment. Journal of the Fisheries Research Board of Canada 11:559-623. -Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] Shepherd, J. 1982. A versatile new stock-recruitment relationship for fisheries and construction of sustainable yield curves. Journal du Conseil International pour l'Exploration de la Mar 40:67-75. } diff --git a/man/stockRecruitment.Rd b/man/stockRecruitment.Rd index d0f056b7..df9e9f16 100644 --- a/man/stockRecruitment.Rd +++ b/man/stockRecruitment.Rd @@ -92,7 +92,7 @@ Quinn II, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford Univers Ricker, W.E. 1954. Stock and recruitment. Journal of the Fisheries Research Board of Canada 11:559-623. -Ricker, W.E. 1975. \href{http://www.dfo-mpo.gc.ca/Library/1485.pdf}{Computation and interpretation of biological statistics of fish populations}. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. +Ricker, W.E. 1975. Computation and interpretation of biological statistics of fish populations. Technical Report Bulletin 191, Bulletin of the Fisheries Research Board of Canada. [Was (is?) from http://www.dfo-mpo.gc.ca/Library/1485.pdf.] Shepherd, J. 1982. A versatile new stock-recruitment relationship for fisheries and construction of sustainable yield curves. Journal du Conseil International pour l'Exploration de la Mar 40:67-75. }