In EvoLandEco/eve: Evolution Emulator, phylogenetically dependent

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

library(eve)

eve

Overview

The package eve is an evolution emulator which provides pipelines to do phylogenetic-diversity-dependent simulation, analyse outputs and generate publication-ready plots and statistics conveniently.

eve supports mainly three different scenarios, the species diversification process is regulated by phylogenetic diversity (PD) or evolutionary distinctiveness (ED) or nearest neighbor distance (NND) respectively.

eve supports parallel computing , this feature is implemented with furrr, read through its documentation before using this feature. Note that parralel computing may use a huge amount of memory and may have large overhead.

Installation

You can install the developmental version from GitHub by running the following commands in R console:

# install.packages("remotes")
remotes::install_github("EvoLandEco/eve")

Example

library(eve)

# make a combo of parameter sets
combo <- edd_combo_maker(
  la = c(0.5, 0.8),
  mu = c(0.1, 0.2),
  beta_n = c(-0.001, 0),
  beta_phi = c(-0.001, 0.001),
  gamma_n = c(-0.001, 0.001),
  gamma_phi = c(-0.001, 0.001),
  age = 5,
  model = "dsde2",
  metric = c("ed"),
  offset = "none"
)

# have a look at the combo
combo[1:3]

All the unique and possible combinations of parameters will be created automatically.

eve supports parallel simulation, the following example shows how to do an 8-session parallel EDD simulation given the combo, with 3 replications for each parameter set . The result will be saved to /result/example. If name is not specified, a folder will be created according to time and date at the moment.

# result will be save as .RData file
# edd_go(
#   combo = combo,
#   nrep = 3,
#   name = "example",
#   strategy = future::multisession,
#   workers = 8
# )

edd_go will not return any object unless you set name = "no_save".

# set name = "no_save" if you want to assign the output to a variable
# output <- edd_go(
#   combo = combo,
#   nrep = 3,
#   name = "no_save",
#   strategy = future::multisession,
#   workers = 8
# )

# examine the result
# output[[1]]

Sequential simulation is also possible:

# edd <- edd_go(
#     combo = combo,
#     nrep = 3,
#     name = "example2",
#     strategy = future::sequential,
#     workers = 8
#   )

EvoLandEco/eve documentation built on Sept. 14, 2024, 12:04 a.m.