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Full simulator with Luis
Features: simulate autocorrelated environment with trait and population dynamics. Also ceiling density regulation. Expand README and add LICENSE (MIT) Add Luis as package author Add testing: - unit testing at highest (ts simulation) level - env sim - stub for tests - a regression test Ignore build and autosave files - Add rds files to ignore
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‎.gitignore‎

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.Rhistory
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*.rds
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..Rcheck
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*.o
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*.so
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.\#*
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\#*\#

‎DESCRIPTION‎

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@@ -4,15 +4,16 @@ Description: A set of codes to simulate evolutionary, plastic and ecological
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constantly moving optima
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Title: Simulations of eco-evo trait and demographic dynamics under changing
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environments
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Version: 0.0-1
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Date: 2013-10-31
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Version: 0.1.0
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Date: 2015-11-17
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Authors@R: c(person("Jaime", "Ashander", role = c("aut", "cre"), email=
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'jashander@ucdavis.edu'))
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"jashander@ucdavis.edu"), person("Luis-Miguel", "Chevin", role=c("aut"),
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email="luis-miguel.chevin@cefe.cnrs.fr"))
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Depends:
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RcppArmadillo (>= 0.4.3)
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Imports:
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Rcpp,
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deSolve,
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MASS
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Rcpp
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LinkingTo: Rcpp, RcppArmadillo
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License: BSD
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License: MIT
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Suggests:
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testthat

‎LICENSE‎

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The MIT License (MIT)
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Copyright (c) 2015 Jaime Ashander and Luis-Miguel Chevin
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎NAMESPACE‎

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# Generated by roxygen2 (4.0.2): do not edit by hand
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export(Beta)
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export(Env_shift)
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export(Env_shift_cpp)
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export(Env_smooth)
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export(G)
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export(Log_R_bar)
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export(Log_W_bar)
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export(Log_W_bar_lethal)
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export(Pheno_demo)
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export(Pheno_demo_econ)
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export(Pheno_demo_lande)
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export(Pheno_lande)
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export(R_bar)
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export(R_bar_dd)
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export(R_bar_ceiling)
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export(R_bar_thetalog)
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export(Va)
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export(W_bar)
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export(pdTS)
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export(stab_curve)
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import(MASS)
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import(deSolve)
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export(make_env)
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export(simulate_pheno_ts)
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useDynLib(phenoecosim)

‎R/RcppExports.R‎

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# This file was generated by Rcpp::compileAttributes
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# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
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#' Compute a white noise environment with a shift
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#' @param t the time point
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#' @param env_args other args:
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#' t.jump the location for the jump,
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#' delta env change that takes place at t.jump
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#' sd noise in env
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#' sdc noise in cue
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#' @details nada
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NULL
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#' Compute mean fitness under stabilizing selection
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#' @param zbar mean trait prior to selection
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#' @param theta enironmental optimum
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#' @param Oz2 strength of stabilizing selection
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#' @param gamma 1/(Oz2 + Vz2), with Vz2 phenotypic variance
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#' @details no details
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#' @param oz2 strength of stabilizing selection
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#' @param gamma 1/(oz2 + Vz2), with Vz2 phenotypic variance
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#' @details IN USE
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#' @export
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Log_W_bar <- function(zbar, theta, Oz2, gamma) {
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.Call('phenoecosim_Log_W_bar', PACKAGE = 'phenoecosim', zbar, theta, Oz2, gamma)
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Log_W_bar <- function(zbar, theta, oz2, gamma) {
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.Call('phenoecosim_Log_W_bar', PACKAGE = 'phenoecosim', zbar, theta, oz2, gamma)
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}
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#' Compute mean fitness under stabilizing selection
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#' @inheritParams Log_W_bar
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#' @param LOG (=TRUE) whether to return the log of fitness
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#' @details no details
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#' @param LOG (=TRUE) whether to return the log of fitness
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#' @details IN USE
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#' @export
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W_bar <- function(zbar, theta, Oz2, gamma, LOG) {
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.Call('phenoecosim_W_bar', PACKAGE = 'phenoecosim', zbar, theta, Oz2, gamma, LOG)
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W_bar <- function(zbar, theta, oz2, gamma, LOG) {
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.Call('phenoecosim_W_bar', PACKAGE = 'phenoecosim', zbar, theta, oz2, gamma, LOG)
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}
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#' Compute population growth rate under stabilizing selection
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#' Compute population growth rate under stabilizing selection and no regulation
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#' @param R0 basic reproductive number
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#' @param Wbar average fitness
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#' @details Assumes density-independent
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#' @export
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R_bar <- function(R0, Wbar) {
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.Call('phenoecosim_R_bar', PACKAGE = 'phenoecosim', R0, Wbar)
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}
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#' Compute LOG population growth rate under stabilizing selection
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#' @inheritParams R_bar
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#' @param logWbar log average fitness
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#' @details Assumes theta-logistic population regulation
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#' @param N number of individuals in this generation
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#' @param K carrying capacity
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#' @details Assumes ceiling population regulation
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#' would be good to have separate DD function specified after
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#' chevin and lande 2010
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#' @export
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Log_R_bar <- function(R0, logWbar) {
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.Call('phenoecosim_Log_R_bar', PACKAGE = 'phenoecosim', R0, logWbar)
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R_bar <- function(R0, Wbar, N) {
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.Call('phenoecosim_R_bar', PACKAGE = 'phenoecosim', R0, Wbar, N)
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}
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#' Compute population growth rate under stabilizing selection
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#' @inheritParams R_bar
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#' Compute population growth rate under stabilizing selection and ceiling regulation
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#' @param R0 basic reproductive number
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#' @param Wbar average fitness
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#' @param N number of individuals in this generation
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#' @param K carrying capacity
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#' @param thetaL theta-logistic parameter for density dependence
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#' @details Assumes theta-logistic population regulation
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#' @details Assumes ceiling population regulation
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#' would be good to have separate DD function specified after
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#' chevin and lande 2010
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#' @export
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R_bar_dd <- function(R0, Wbar, N, K, thetaL) {
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.Call('phenoecosim_R_bar_dd', PACKAGE = 'phenoecosim', R0, Wbar, N, K, thetaL)
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R_bar_ceiling <- function(R0, Wbar, N, K) {
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.Call('phenoecosim_R_bar_ceiling', PACKAGE = 'phenoecosim', R0, Wbar, N, K)
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}
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#' Selection on plasticity as as function of environment assuming stabilizing selection
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#' @param gamma = 1/(Oz2 + Vz2), with Vz2 phenotypic variance
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#' @param A the environmental optimum RN int
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#' @param B the environmental optimum RN slope
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#' @param a current value of RN int
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#' @param b current value of RN slope
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#' @param e_t environment now
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#' @param e_plast env that cues plasticity
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#' Compute population growth rate under stabilizing selection and theta-logistic regulation
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#' @inheritParams R_bar_ceiling
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#' @param thetaL theta-logistic parameter for density dependence
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#' @details Assumes theta-logistic population regulation
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#' would be good to have separate DD function specified after
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#' chevin and lande 2010
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#' @export
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Beta <- function(gamma, A, B, a, b, e_t, e_plast) {
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.Call('phenoecosim_Beta', PACKAGE = 'phenoecosim', gamma, A, B, a, b, e_t, e_plast)
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R_bar_thetalog <- function(R0, Wbar, N, K, thetaL) {
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.Call('phenoecosim_R_bar_thetalog', PACKAGE = 'phenoecosim', R0, Wbar, N, K, thetaL)
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}
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#' Va additive genetic variance in the phenotype as a function of the environment
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.Call('phenoecosim_Va', PACKAGE = 'phenoecosim', env, GG)
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}
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#' Compute a white noise environment with a shift
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#' @param t the time point
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#' @param env_args other args:
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#' t.jump the location for the jump,
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#' delta env change that takes place at t.jump
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#' sd noise in env
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#' sdc noise in cue
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#' @details nada
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#' Compute correctly-scaled environment of development and selection
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#' @param env_args environment args
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#' @param T how many gens
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#' @details given a pre-generated vector of random environments
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#' @export
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Env_shift_cpp <- function(t, env_args) {
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.Call('phenoecosim_Env_shift_cpp', PACKAGE = 'phenoecosim', t, env_args)
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make_env <- function(T, env_args) {
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.Call('phenoecosim_make_env', PACKAGE = 'phenoecosim', T, env_args)
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}
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#' Compute phenotypic dynamic Time Series of trait + demographic change under stabilizing selection as
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#' Compute phenotypic dynamic Time Series of trait + demographic change under stabilizing selection as
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#' function of environment (after Lande Chevin)
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#' @param T end time, assuming start time of 1
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#' @param X parameters (z, a, b, wbar, logN, theta)
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#' @param params a list with (gamma_sh, omegaz, A, B, R0, Va, Vb, delta, sigma_xi, rho_tau, fractgen)
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#' @param params a list with (gamma_sh, omegaz, A, B, R0, var_a, Vb, delta, sigma_xi, rho_tau, fractgen)
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#' @param env_args extra args for env.fn
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#' @details NB - for now assume Tchange = 0 and demography after CL 2010
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#' @value a long matrix
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#' @export
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pdTS <- function(T, X, params, env_args) {
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.Call('phenoecosim_pdTS', PACKAGE = 'phenoecosim', T, X, params, env_args)
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simulate_pheno_ts <- function(T, X, params, env_args) {
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.Call('phenoecosim_simulate_pheno_ts', PACKAGE = 'phenoecosim', T, X, params, env_args)
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}
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‎R/envsim.R‎

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