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

.gitignore

@@ -1 +1,7 @@
 .Rhistory
+*.rds
+..Rcheck
+*.o
+*.so
+.\#*
+\#*\#

DESCRIPTION

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

LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2015 Jaime Ashander and Luis-Miguel Chevin
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,23 +1,11 @@
 # 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_W_bar)
-export(Log_W_bar_lethal)
-export(Pheno_demo)
-export(Pheno_demo_econ)
-export(Pheno_demo_lande)
-export(Pheno_lande)
-export(R_bar)
-export(R_bar_dd)
+export(R_bar_ceiling)
+export(R_bar_thetalog)
 export(Va)
 export(W_bar)
-export(pdTS)
-export(stab_curve)
-import(MASS)
-import(deSolve)
+export(make_env)
+export(simulate_pheno_ts)
 useDynLib(phenoecosim)

R/RcppExports.R

@@ -1,70 +1,71 @@
 # This file was generated by Rcpp::compileAttributes
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+#' Compute a white noise environment with a shift
+#' @param t the time point
+#' @param env_args other args:
+#' t.jump the location for the jump,
+#' delta env change that takes place at t.jump
+#' sd noise in env
+#' sdc noise in cue
+#' @details nada
+NULL
+
 #' Compute mean fitness under stabilizing selection
 #' @param zbar mean trait prior to selection
 #' @param theta enironmental optimum
-#' @param Oz2 strength of stabilizing selection
-#' @param gamma 1/(Oz2 + Vz2), with Vz2 phenotypic variance 
-#' @details no details
+#' @param oz2 strength of stabilizing selection
+#' @param gamma 1/(oz2 + Vz2), with Vz2 phenotypic variance
+#' @details IN USE
 #' @export
-Log_W_bar <- function(zbar, theta, Oz2, gamma) {
-    .Call('phenoecosim_Log_W_bar', PACKAGE = 'phenoecosim', zbar, theta, Oz2, gamma)
+Log_W_bar <- function(zbar, theta, oz2, gamma) {
+    .Call('phenoecosim_Log_W_bar', PACKAGE = 'phenoecosim', zbar, theta, oz2, gamma)
 }
 
 #' Compute mean fitness under stabilizing selection
 #' @inheritParams Log_W_bar
-#' @param LOG (=TRUE) whether to return the log of fitness  
-#' @details no details
+#' @param LOG (=TRUE) whether to return the log of fitness
+#' @details IN USE
 #' @export
-W_bar <- function(zbar, theta, Oz2, gamma, LOG) {
-    .Call('phenoecosim_W_bar', PACKAGE = 'phenoecosim', zbar, theta, Oz2, gamma, LOG)
+W_bar <- function(zbar, theta, oz2, gamma, LOG) {
+    .Call('phenoecosim_W_bar', PACKAGE = 'phenoecosim', zbar, theta, oz2, gamma, LOG)
 }
 
-#' Compute population growth rate under stabilizing selection
+#' Compute population growth rate under stabilizing selection and no regulation
 #' @param R0 basic reproductive number
 #' @param Wbar average fitness
-#' @details Assumes density-independent
-#' @export
-R_bar <- function(R0, Wbar) {
-    .Call('phenoecosim_R_bar', PACKAGE = 'phenoecosim', R0, Wbar)
-}
-
-#' Compute LOG population growth rate under stabilizing selection
-#' @inheritParams R_bar
-#' @param logWbar log average fitness
-#' @details Assumes theta-logistic population regulation
+#' @param N number of individuals in this generation
+#' @param K carrying capacity
+#' @details Assumes ceiling population regulation
 #' would be good to have separate DD function specified after
 #' chevin and lande 2010
 #' @export
-Log_R_bar <- function(R0, logWbar) {
-    .Call('phenoecosim_Log_R_bar', PACKAGE = 'phenoecosim', R0, logWbar)
+R_bar <- function(R0, Wbar, N) {
+    .Call('phenoecosim_R_bar', PACKAGE = 'phenoecosim', R0, Wbar, N)
 }
 
-#' Compute population growth rate under stabilizing selection
-#' @inheritParams R_bar
+#' Compute population growth rate under stabilizing selection and ceiling regulation
+#' @param R0 basic reproductive number
+#' @param Wbar average fitness
 #' @param N number of individuals in this generation
 #' @param K carrying capacity
-#' @param thetaL theta-logistic parameter for density dependence
-#' @details Assumes theta-logistic population regulation
+#' @details Assumes ceiling population regulation
 #' would be good to have separate DD function specified after
 #' chevin and lande 2010
 #' @export
-R_bar_dd <- function(R0, Wbar, N, K, thetaL) {
-    .Call('phenoecosim_R_bar_dd', PACKAGE = 'phenoecosim', R0, Wbar, N, K, thetaL)
+R_bar_ceiling <- function(R0, Wbar, N, K) {
+    .Call('phenoecosim_R_bar_ceiling', PACKAGE = 'phenoecosim', R0, Wbar, N, K)
 }
 
-#' 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
-#' @param B the environmental optimum RN slope
-#' @param a current value of RN int
-#' @param b current value of RN slope
-#' @param e_t environment now
-#' @param e_plast env that cues plasticity
+#' Compute population growth rate under stabilizing selection and theta-logistic regulation
+#' @inheritParams R_bar_ceiling
+#' @param thetaL theta-logistic parameter for density dependence
+#' @details Assumes theta-logistic population regulation
+#' would be good to have separate DD function specified after
+#' chevin and lande 2010
 #' @export
-Beta <- function(gamma, A, B, a, b, e_t, e_plast) {
-    .Call('phenoecosim_Beta', PACKAGE = 'phenoecosim', gamma, A, B, a, b, e_t, e_plast)
+R_bar_thetalog <- function(R0, Wbar, N, K, thetaL) {
+    .Call('phenoecosim_R_bar_thetalog', PACKAGE = 'phenoecosim', R0, Wbar, N, K, thetaL)
 }
 
 #' Va additive genetic variance in the phenotype as a function of the environment
@@ -75,28 +76,25 @@ Va <- function(env, GG) {
     .Call('phenoecosim_Va', PACKAGE = 'phenoecosim', env, GG)
 }
 
-#' Compute a white noise environment with a shift
-#' @param t the time point
-#' @param env_args other args:
-#' t.jump the location for the jump,
-#' delta env change that takes place at t.jump
-#' sd noise in env
-#' sdc noise in cue
-#' @details nada
+#' Compute correctly-scaled environment of development and selection
+#' @param env_args environment args
+#' @param T how many gens
+#' @details given a pre-generated vector of random environments
 #' @export
-Env_shift_cpp <- function(t, env_args) {
-    .Call('phenoecosim_Env_shift_cpp', PACKAGE = 'phenoecosim', t, env_args)
+make_env <- function(T, env_args) {
+    .Call('phenoecosim_make_env', PACKAGE = 'phenoecosim', T, env_args)
 }
 
-#' Compute phenotypic dynamic Time Series of trait + demographic change under stabilizing selection as 
+#' 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 (gamma_sh, omegaz, A, B, R0, Va, Vb, delta, sigma_xi, rho_tau, fractgen)
+#' @param params a list with (gamma_sh, omegaz, A, B, R0, var_a, 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
+#' @value a long matrix
 #' @export
-pdTS <- function(T, X, params, env_args) {
-    .Call('phenoecosim_pdTS', PACKAGE = 'phenoecosim', T, X, params, env_args)
+simulate_pheno_ts <- function(T, X, params, env_args) {
+    .Call('phenoecosim_simulate_pheno_ts', PACKAGE = 'phenoecosim', T, X, params, env_args)
 }