Fixed Chan to Chen, added citations to metaM

Author: droglenc

R/metaM.R

@@ -24,7 +24,7 @@
 #'    \item \code{method="RikhterEfanov1"}: The \dQuote{Rikhter and Efanov (1976) equation (#2)} as given in the second column of page 541 of Kenchington (2014) and in Table 6.4 of Miranda and Bettoli (2007). Requires only \code{t50}.
 #'    \item \code{method="RikhterEfanov2"}: The \dQuote{Rikhter and Efanov (1976) equation (#1)} as given in the first column of page 541 of Kenchington (2014). Requires \code{t50}, \code{K}, \code{t0}, and \code{b}.
 #'    \item \code{method="QuinnDeriso"}: The \dQuote{Quinn & Derison (1999)} equation as given in the FAMS manual as equation 4:18. Requires \code{PS} and \code{tmax}. Included only for use with \code{rFAMS} package.
-#'    \item \code{method="ChanWatanabe"}: The \dQuote{Chan & Watanabe (1989)} equation as given in the FAMS manual as equation 4:24. As suggested in FAMS manual used \code{tmax} for final time and 1 as initial time. Requires \code{tmax}, \code{K}, and \code{t0}. Included only for use with \code{rFAMS} package.
+#'    \item \code{method="ChenWatanabe"}: The \dQuote{Chen & Watanabe (1989)} equation as given in the FAMS manual as equation 4:24. As suggested in FAMS manual used \code{tmax} for final time and 1 as initial time. Requires \code{tmax}, \code{K}, and \code{t0}. Included only for use with \code{rFAMS} package.
 #'    \item \code{method="PetersonWroblewski"}: The \dQuote{Peterson & Wroblewski (1984)} equation as given in the FAMS manual as equation 4:22. As suggested in FAMS manual used \code{Winf} for weight. Requires \code{Winf}. Included only for use with \code{rFAMS} package.
 #'  } 
 #' 
@@ -68,6 +68,8 @@
 #' 
 #' Alverson, D.L. and M.J. Carney. 1975. A graphic review of the growth and decay of population cohorts. Journal du Conseil International pour l'Exploration de la Mer. 36:133-143.
 #' 
+#' Chen, S. and S. Watanabe. 1989. Age dependence of natural mortality coefficient in fish population dynamics. Nippon Suisan Gakkaishi 55:205-208.
+#' 
 #' Charnov, E.L., H. Gislason, and J.G. Pope. 2013. Evolutionary assembly rules for fish life histories. Fish and Fisheries. 14:213-224.
 #' 
 #' 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.
@@ -84,8 +86,14 @@
 #' 
 #' 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.]
 #' 
+#' Peterson, I. and J.S. Wroblewski. 1984. Mortality rate of fishes in the pelagic ecosystem. Canadian Journal of Fisheries and Aquatic Sciences. 41:1117-1120.
+#' 
+#' Quinn III, T.J. and R.B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York.
+#' 
 #' 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. 
 #' 
+#' Slipke, J.W. and M.J. Maceina. 2013. Fisheries Analysis and Modeling Simulator (FAMS 1.64). American Fisheries Society.
+#' 
 #' 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 information on over 200 fish species. ICES Journal of Marine Science. 72:82-92.
 #' 
 #' 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 Society. 135-620-633. [Was (is?) from http://www.pmel.noaa.gov/foci/publications/2006/zhan0531.pdf.]
@@ -148,7 +156,7 @@ Mmethods <- function(method=c("all","tmax","K","Hoenig","Pauly","FAMS")) {
                 "AlversonCarney","Charnov",
                 "ZhangMegreyD","ZhangMegreyP",
                 "RikhterEfanov1","RikhterEfanov2",
-                "QuinnDeriso","ChanWatanabe","PetersonWroblewski")
+                "QuinnDeriso","ChenWatanabe","PetersonWroblewski")
   H_meth <- all_meth[grep("Hoenig",all_meth)]
   P_meth <- 
   switch(method,
@@ -158,7 +166,7 @@ Mmethods <- function(method=c("all","tmax","K","Hoenig","Pauly","FAMS")) {
          Hoenig = { meths <- H_meth},
          Pauly  = { meths <- all_meth[grep("Pauly",all_meth)] },
          FAMS   = { meths <- c("QuinnDeriso","HoenigOF","JensenK1",
-                               "PetersonWroblewski","PaulyL","ChanWatanabe")}
+                               "PetersonWroblewski","PaulyL","ChenWatanabe")}
          )
   meths
 }
@@ -350,16 +358,16 @@ metaM1 <- function(method,tmax,K,Linf,t0,b,L,Temp,t50,Winf,PS,...) {
            givens <- c(PS=PS,tmax=tmax)
            M <- -log(PS)/tmax
          },
-         ChanWatanabe = {
-           ## from Chan and Watanabe (1989) as described in FAMS manual
+         ChenWatanabe = {
+           ## from Chen and Watanabe (1989) as described in FAMS manual
            ##   equation 4:24 in FAMS manual
            ##   here followed FAMS notes and used ti=1 and tf=tmax
            ti <- 1    # initial age
            tf <- tmax # final age
            iCheck_K(K)
            iCheck_t0(t0)
            iCheck_tmax(tmax)
-           name <- "Chan & Watanabe (1989) from FAMS"
+           name <- "Chen & Watanabe (1989) from FAMS"
            givens <- c(tmax=tmax,K=K,t0=t0)
            M <- (1/(tf-ti))*log((exp(-K*tf)-exp(-K*t0))/(exp(-K*ti)-exp(-K*t0)))
          },