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Minor cleanup in help page #112

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28 changes: 14 additions & 14 deletions R/growthModels.R
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Expand Up @@ -36,7 +36,7 @@
#' \item Richards
#' \itemize{
#' \item Within FSA, Linf is the mean asymptotic length, ti is the age at the inflection point, k controls the slope at the inflection point (maximum relative growth rate), b is dimensionless but related to the vertical position (i.e., size) of the inflection point, a is dimensionless but related to the horizontal position (i.e., age) of the inflection point, and L0 is the mean length at age-0.
#' \item The parameterizations (1-6) correspond to functions/equations 1, 4, 5, 6, 7, and 8, respectively, in Tjorve and Tjorve (2010). Note that their A, S, k, d, and B are Linf, a, k, b, and L0, respectively, here (in FSA). THeir (Tjorve and Tjorve 2010) K does not appear here.
#' \item The parameterizations (1-6) correspond to functions/equations 1, 4, 5, 6, 7, and 8, respectively, in Tjorve and Tjorve (2010). Note that their A, S, k, d, and B are Linf, a, k, b, and L0, respectively, here (in FSA). Their (Tjorve and Tjorve 2010) K does not appear here.
#' }
#' \item logistic
#' \itemize{
Expand All @@ -52,53 +52,53 @@
#'
#' @references Ogle, D.H. 2016. \href{https://fishr-core-team.github.io/fishR/pages/books.html#introductory-fisheries-analyses-with-r}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL.
#'
#' 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.]
#' 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 https://waves-vagues.dfo-mpo.gc.ca/library-bibliotheque/141734.pdf.]
#'
#' Fabens, A. 1965. Properties and fitting of the von Bertalanffy growth curve. Growth 29:265-289.
#'
#' Francis, R.I.C.C. 1988. Are growth parameters estimated from tagging and age-length data comparable? Canadian Journal of Fisheries and Aquatic Sciences, 45:936-942.
#'
#' 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. 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.]
#' 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.
#'
#' 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.
#' Gompertz, B. 1825. On the nature of the function expressive of the law of human mortality, and on a new mode 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. 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.]
#' 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 https://spo.nmfs.noaa.gov/sites/default/files/pdf-content/2008/1061/haddon.pdf.]
#'
#' 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.]
#' Karkach, A. S. 2006. Trajectories and models of individual growth. Demographic Research 15:347-400. [Was (is?) from https://www.demographic-research.org/volumes/vol15/12/15-12.pdf.]
#'
#' Katsanevakis, S. and C.D. Maravelias. 2008. Modeling fish growth: multi-model inference as a better alternative to a priori using von Bertalanffy equation. Fish and Fisheries 9:178-187.
#'
#' Mooij, W.M., J.M. Van Rooij, and S. Wijnhoven. 1999. Analysis and comparison of fish growth from small samples of length-at-age data: Detection of sexual dimorphism in Eurasian Perch as an example. Transactions of the American Fisheries Society 128:483-490.
#' Mooij, W.M., J.M. Van Rooij, and S. Wijnhoven. 1999. Analysis and comparison of fish growth from small samples of length-at-age data: Detection of sexual dimorphism in Eurasian perch as an example. Transactions of the American Fisheries Society 128:483-490.
#'
#' Polacheck, T., J.P. Eveson, and G.M. Laslett. 2004. Increase in growth rates of southern Bluefin Tuna (\emph{Thunnus maccoyii}) over four decades: 1960 to 2000. Canadian Journal of Fisheries and Aquatic Sciences, 61:307-322.
#' Polacheck, T., J.P. Eveson, and G.M. Laslett. 2004. Increase in growth rates of southern bluefin tuna (\emph{Thunnus maccoyii}) over four decades: 1960 to 2000. Canadian Journal of Fisheries and Aquatic Sciences, 61:307-322.
#'
#' Quinn, T. J. and R. B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York, New York. 542 pages.
#'
#' Quist, M.C., M.A. Pegg, and D.R. DeVries. 2012. Age and Growth. Chapter 15 in A.V. Zale, D.L Parrish, and T.M. Sutton, Editors Fisheries Techniques, Third Edition. American Fisheries Society, Bethesda, MD.
#' Quist, M.C., M.A. Pegg, and D.R. DeVries. 2012. Age and growth. Chapter 15 in A.V. Zale, D.L Parrish, and T.M. Sutton, editors. Fisheries Techniques, Third Edition. American Fisheries Society, Bethesda, MD.
#'
#' Richards, F. J. 1959. A flexible growth function for empirical use. Journal of Experimental Biology 10:290-300.
#'
#' 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. 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 https://publications.gc.ca/collections/collection_2015/mpo-dfo/Fs94-191-eng.pdf.]
#'
#' 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.]
#' 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, New York, 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. On a seasonally oscillating growth function. Fishbyte 6(1):8-11. [Was (is?) from http://www.worldfishcenter.org/Naga/na_2914.pdf.]
#' Somers, I. F. 1988. On a seasonally oscillating growth function. Fishbyte 6(1):8-11. [Was (is?) from https://www.fishbase.us/manual/English/fishbaseSeasonal_Growth.htm.]
#'
#' 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. 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. 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.]
#' 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 https://repository.library.noaa.gov/view/noaa/5927/noaa_5927_DS1.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. 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.]
#' Winsor, C.P. 1932. The Gompertz curve as a growth curve. Proceedings of the National Academy of Sciences. 18:1-8. [Was (is?) from https://pmc.ncbi.nlm.nih.gov/articles/PMC1076153/pdf/pnas01729-0009.pdf.]
#'
#' @keywords manip hplot
#'
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