eve

Evolution emulator, phylogenetically dependent.

https://github.com/evolandeco/eve

Repository

Evolution emulator, phylogenetically dependent.

README.Rmd

---
output: github_document
editor_options: 
  chunk_output_type: console
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

```{r, echo=FALSE, message=FALSE, warning=FALSE}
library(eve)
```

# eve 

[![CRAN
status](https://www.r-pkg.org/badges/version/eve)](https://cran.r-project.org/package=eve)
[![R build
status](https://github.com/DEvoLandEco/eve/workflows/R-CMD-check/badge.svg)](https://github.com/EvoLandEco/eve/actions)
[![DOI](https://zenodo.org/badge/382378337.svg)](https://zenodo.org/badge/latestdoi/382378337)

## 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](https://furrr.futureverse.org/), 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](https://github.com/) by running the following commands in R console:

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


## Example


```{r combo}
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.

```{r edd_go}
# 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"`.

```{r}
# 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:

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

Owner

Citation (CITATION.cff)

cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Qin
    given-names: Tianjian
    orcid: https://orcid.org/0000-0003-2540-1778
title: "eve - Evolution emulator, phylogenetically dependent"
version: 0.1.0
doi: 10.5281/zenodo.8475
date-released: 2023-05-31

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