Removing unused functions; downstream updates to docs

ashander · Jan 9, 2015 · a5cdfd0 · a5cdfd0
1 parent 71e554a
commit a5cdfd0
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Showing 27 changed files with 77 additions and 546 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,12 +1,11 @@
-# Generated by roxygen2 (4.0.1): do not edit by hand
+# Generated by roxygen2 (4.0.2): do not edit by hand
 
 export(Beta)
 export(Env_shift)
 export(Env_shift_cpp)
 export(Env_smooth)
 export(G)
 export(Log_R_bar)
-export(Log_R_bar_dd)
 export(Log_W_bar)
 export(Log_W_bar_lethal)
 export(Pheno_demo)
@@ -17,10 +16,6 @@ export(R_bar)
 export(R_bar_dd)
 export(Va)
 export(W_bar)
-export(pdLande)
-export(pdLandeLRG)
-export(pdLandeT)
-export(pdRespVarLoad)
 export(pdTS)
 export(stab_curve)
 import(MASS)

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -54,17 +54,6 @@ R_bar_dd <- function(R0, Wbar, N, K, thetaL) {
     .Call('phenoecosim_R_bar_dd', PACKAGE = 'phenoecosim', R0, Wbar, N, K, thetaL)
 }
 
-#' Compute LOG population growth rate under stabilizing selection
-#' @inheritParams R_bar_dd
-#' @param logWbar log average fitness
-#' @details Assumes theta-logistic population regulation
-#' would be good to have separate DD function specified after
-#' chevin and lande 2010
-#' @export
-Log_R_bar_dd <- function(R0, logWbar, N, K, thetaL) {
-    .Call('phenoecosim_Log_R_bar_dd', PACKAGE = 'phenoecosim', R0, logWbar, N, K, thetaL)
-}
-
 #' Selection on plasticity as as function of environment assuming stabilizing selection
 #' @param gamma = 1/(Oz2 + Vz2), with Vz2 phenotypic variance
 #' @param A the environmental optimum RN int
@@ -99,78 +88,13 @@ Env_shift_cpp <- function(t, env_args) {
     .Call('phenoecosim_Env_shift_cpp', PACKAGE = 'phenoecosim', t, env_args)
 }
 
-#' Compute change in fitness over one generation after stabilizing selection
-#' function of environment (after Lande Chevin)
-#' @param t timestep
-#' @param X parameters (a, b, env, logN)
-#' @param params a list with (Oz2, AB, R0, K, theta)
-#' @param G the (constant) G matrix
-#' @param env_args extra args for env.fn
-#' @details function signature as for use with deSolve
-#' imposes fitness based on Lande
-#' and demography after CL 2010
-#' @return rowvector: log R bar, delta R bar, variance load
-#' @export
-pdRespVarLoad <- function(t, X, params, G, env_args) {
-    .Call('phenoecosim_pdRespVarLoad', PACKAGE = 'phenoecosim', t, X, params, G, env_args)
-}
-
-#' Compute trait + demographic change over one generation under stabilizing selection as 
-#' function of environment (after Lande Chevin)
-#' @param t timestep
-#' @param X parameters (a, b, env, logN)
-#' @param params a list with (Oz2, AB, R0, K, theta)
-#' @param G the (constant) G matrix
-#' @param env_args extra args for env.fn
-#' @details function signature as for use with deSolve
-#' imposes fitness based on Lande
-#' and demography after CL 2010
-#' @export
-pdLande <- function(t, X, params, G, env_args) {
-    .Call('phenoecosim_pdLande', PACKAGE = 'phenoecosim', t, X, params, G, env_args)
-}
-
-#' Compute trait + demographic change over T generations under stabilizing selection as 
-#' function of environment (after Lande Chevin)
-#' @param T end time, assuming start time of 1
-#' @param X parameters (a, b, env, logN)
-#' @param params a list with (Oz2, AB, R0, K, theta)
-#' @param G the (constant) G matrix
-#' @param env_args extra args for env.fn
-#' @details function signature as for use with deSolve
-#' imposes fitness based on Lande
-#' and demography after CL 2010
-#' @export
-pdLandeT <- function(T, X, params, G, env_args) {
-    .Call('phenoecosim_pdLandeT', PACKAGE = 'phenoecosim', T, X, params, G, env_args)
-}
-
-#' Compute trait + demographic change over over T generations and
-#' long run growth rate over last N_lam generations
-#' under stabilizing selection as 
-#' function of environment (after Lande Chevin)
-#' @param T end time, assuming start time of 1
-#' @param N_lam number of gens over which to compute long-run growth  -- must be less than T
-#' @param X parameters (a, b, env, logN)
-#' @param params a list with (Oz2, AB, R0, K, theta)
-#' @param G the (constant) G matrix
-#' @param env_args extra args for env.fn
-#' @details function signature as for use with deSolve
-#' imposes fitness based on Lande
-#' and demography after CL 2010
-#' @export
-pdLandeLRG <- function(T, N_lam, X, params, G, env_args) {
-    .Call('phenoecosim_pdLandeLRG', PACKAGE = 'phenoecosim', T, N_lam, X, params, G, env_args)
-}
-
 #' Compute phenotypic dynamic Time Series of trait + demographic change under stabilizing selection as 
 #' function of environment (after Lande Chevin)
 #' @param T end time, assuming start time of 1
 #' @param X parameters (z, a, b, wbar, logN, theta)
-#' @param params a list with (Oz2, AB, R0, K, theta)
+#' @param params a list with (gamma_sh, omegaz, A, B, R0, Va, Vb, delta, sigma_xi, rho_tau, fractgen)
 #' @param env_args extra args for env.fn
-#' @details NB - for now assume Tchange = 0
-#' and demography after CL 2010
+#' @details NB - for now assume Tchange = 0 and demography after CL 2010
 #' @export
 pdTS <- function(T, X, params, env_args) {
     .Call('phenoecosim_pdTS', PACKAGE = 'phenoecosim', T, X, params, env_args)

diff --git a/R/traitfitpop.R b/R/traitfitpop.R
@@ -56,8 +56,8 @@ Pheno_lande <- function(t, X, p, G, env.fn, env.args) {
   X <- c(a, b) + G %*% beta
   va <- Va(e.plast, G) 
   list(c(X, env, z.bar, va))
-
 }
+
 #' Compute trait + demographic change under stabilizing selection as function of environment
 #' @param t timestep
 #' @param X parameters (a, b, env, N)

diff --git a/man/Beta.Rd b/man/Beta.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Beta}
 \alias{Beta}
 \title{Selection on plasticity as as function of environment assuming stabilizing selection}

diff --git a/man/Env_shift.Rd b/man/Env_shift.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Env_shift}
 \alias{Env_shift}
 \title{Compute a white noise environment with a shift}

diff --git a/man/Env_shift_cpp.Rd b/man/Env_shift_cpp.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Env_shift_cpp}
 \alias{Env_shift_cpp}
 \title{Compute a white noise environment with a shift}

diff --git a/man/Env_smooth.Rd b/man/Env_smooth.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Env_smooth}
 \alias{Env_smooth}
 \title{Simulate one step of a linearly changing environment, possibly with noise}

diff --git a/man/G.Rd b/man/G.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{G}
 \alias{G}
 \title{G matrix}

diff --git a/man/Log_R_bar.Rd b/man/Log_R_bar.Rd
@@ -1,14 +1,14 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Log_R_bar}
 \alias{Log_R_bar}
 \title{Compute LOG population growth rate under stabilizing selection}
 \usage{
 Log_R_bar(R0, logWbar)
 }
 \arguments{
-\item{logWbar}{log average fitness}
-
 \item{R0}{basic reproductive number}
+
+\item{logWbar}{log average fitness}
 }
 \description{
 Compute LOG population growth rate under stabilizing selection

diff --git a/man/Log_W_bar.Rd b/man/Log_W_bar.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Log_W_bar}
 \alias{Log_W_bar}
 \title{Compute mean fitness under stabilizing selection}

diff --git a/man/Log_W_bar_lethal.Rd b/man/Log_W_bar_lethal.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Log_W_bar_lethal}
 \alias{Log_W_bar_lethal}
 \title{Mean fitness -- with constraint, need to make as function of environment...}

diff --git a/man/Pheno_demo.Rd b/man/Pheno_demo.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Pheno_demo}
 \alias{Pheno_demo}
 \title{Compute trait + demographic change under stabilizing selection as function of environment}

diff --git a/man/Pheno_demo_econ.Rd b/man/Pheno_demo_econ.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Pheno_demo_econ}
 \alias{Pheno_demo_econ}
 \title{Compute trait + demographic change under stabilizing selection as function of environment via Lande Chevin

diff --git a/man/Pheno_demo_lande.Rd b/man/Pheno_demo_lande.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Pheno_demo_lande}
 \alias{Pheno_demo_lande}
 \title{Compute trait + demographic change under stabilizing selection as function of environment via Lande Chevin}

diff --git a/man/Pheno_lande.Rd b/man/Pheno_lande.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Pheno_lande}
 \alias{Pheno_lande}
 \title{Compute trait change under stabilizing selection as function of environment}

diff --git a/man/R_bar.Rd b/man/R_bar.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{R_bar}
 \alias{R_bar}
 \title{Compute population growth rate under stabilizing selection}

diff --git a/man/R_bar_dd.Rd b/man/R_bar_dd.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{R_bar_dd}
+\alias{R_bar_dd}
+\title{Compute population growth rate under stabilizing selection}
+\usage{
+R_bar_dd(R0, Wbar, N, K, thetaL)
+}
+\arguments{
+\item{R0}{basic reproductive number}
+
+\item{Wbar}{average fitness}
+
+\item{N}{number of individuals in this generation}
+
+\item{K}{carrying capacity}
+
+\item{thetaL}{theta-logistic parameter for density dependence}
+}
+\description{
+Compute population growth rate under stabilizing selection
+}
+\details{
+Assumes theta-logistic population regulation
+would be good to have separate DD function specified after
+chevin and lande 2010
+}
+
diff --git a/man/Va.Rd b/man/Va.Rd
@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{Va}
 \alias{Va}
 \title{Va additive genetic variance in the phenotype as a function of the environment}

diff --git a/man/W_bar.Rd b/man/W_bar.Rd
@@ -1,20 +1,20 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{W_bar}
 \alias{W_bar}
 \title{Compute mean fitness under stabilizing selection}
 \usage{
 W_bar(zbar, theta, Oz2, gamma, LOG)
 }
 \arguments{
-\item{LOG}{(=TRUE) whether to return the log of fitness}
-
 \item{zbar}{mean trait prior to selection}
 
 \item{theta}{enironmental optimum}
 
 \item{Oz2}{strength of stabilizing selection}
 
 \item{gamma}{1/(Oz2 + Vz2), with Vz2 phenotypic variance}
+
+\item{LOG}{(=TRUE) whether to return the log of fitness}
 }
 \description{
 Compute mean fitness under stabilizing selection

diff --git a/man/pdLande.Rd b/man/pdLande.Rd
diff --git a/man/pdLandeT.Rd b/man/pdLandeT.Rd
diff --git a/man/pdRespVarLoad.Rd b/man/pdRespVarLoad.Rd