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First commit with examples contributed by Ken Andersen.
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^mizerExamples\.Rproj$ | ||
^\.Rproj\.user$ | ||
^LICENSE\.md$ | ||
^README\.Rmd$ | ||
^cran-comments\.md$ |
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.Rproj.user | ||
.Rhistory | ||
.RData | ||
.Ruserdata |
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Package: mizerExamples | ||
Title: A crowd-sourced repository of mizer size-spectrum models for various ecosystems | ||
Version: 0.0.0.9000 | ||
Author: mizer users worldwide | ||
Maintainer: Gustav Delius <[email protected]> | ||
Description: Please contribute your mizer model for others to explore and give feedback on | ||
License: GPL-3 | ||
Imports: | ||
mizer (>= 1.0.1.9001) | ||
Suggests: | ||
pkgdown, | ||
rmarkdown, | ||
roxygen2, | ||
testthat | ||
Collate: | ||
data.R | ||
Encoding: UTF-8 | ||
Roxygen: list(markdown = TRUE) | ||
RoxygenNote: 7.0.2 | ||
URL: https://github.com/sizespectrum/mizerExamples | ||
BugReports: https://github.com/sizespectrum/mizerExamples/issues |
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# Generated by roxygen2: do not edit by hand | ||
|
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# Benguela current ---- | ||
#' Example MizerParams object for the Benguela current | ||
#' | ||
#' Created with purely size-based predation, i.e., no species-specific | ||
#' interactions. Set up with three fishing gears targeting small, medium and | ||
#' large species. Vulnerabilities are represented by changing the clearance rate | ||
#' constant (gamma) between species. Calibrated to efforts | ||
#' \code{effort = c(small = 0.13, medium = 0.05, large = 0.45)}. | ||
#' @examples | ||
#' \dontrun{ | ||
#' sim = project(Benguela_params, effort = c(small = 0.13, medium = 0.05, large = 0.45)) | ||
#' plot(sim) | ||
#' } | ||
#' @format A MizerParams object | ||
#' @source{N.S. Jacobsen, M. Burgess and K.H. Andersen (2017): | ||
#' Efficiency of fisheries is increasing at the ecosystem level. | ||
#' Fish and Fisheries 18(2) 199- 211. doi:10.1111/faf.12171.} | ||
#' @docType data | ||
#' @name Benguela_params | ||
#' @family example parameter objects | ||
NULL | ||
|
||
# Baltic Sea ---- | ||
#' Example MizerParams object for the Central Baltic Sea | ||
#' | ||
#' Created with purely size-based predation, i.e., no species-specific | ||
#' interactions. Set up with three fishing gears targeting small, medium and | ||
#' large species. Vulnerabilities are represented by changing the clearance rate | ||
#' constant (gamma) between species. Calibrated to efforts | ||
#' \code{effort = c(small = 0.3, medium = 0.3, large = 0.7)}. | ||
#' @examples | ||
#' \dontrun{ | ||
#' sim = project(Baltic_params, effort = c(small = 0.3, medium = 0.3, large = 0.7)) | ||
#' plot(sim) | ||
#' } | ||
#' @format A MizerParams object | ||
#' @source{N.S. Jacobsen, M. Burgess and K.H. Andersen (2017): | ||
#' Efficiency of fisheries is increasing at the ecosystem level. | ||
#' Fish and Fisheries 18(2) 199- 211. doi:10.1111/faf.12171.} | ||
#' @docType data | ||
#' @name Baltic_params | ||
#' @family example parameter objects | ||
NULL | ||
|
||
# Barents Sea ---- | ||
#' Example MizerParams object for the Barents Sea | ||
#' | ||
#' Created with purely size-based predation, i.e., no species-specific | ||
#' interactions. Set up with three fishing gears targeting small, medium and | ||
#' large species. Vulnerabilities are represented by changing the clearance rate | ||
#' constant (gamma) between species. Calibrated to efforts | ||
#' \code{effort = c(small = 1.1, medium = 0.5, large = 0.75)}. | ||
#' @examples | ||
#' \dontrun{ | ||
#' sim = project(Barents_params, effort = c(small = 1.1, medium = 0.5, large = 0.75)) | ||
#' plot(sim) | ||
#' } | ||
#' @format A MizerParams object | ||
#' @source{N.S. Jacobsen, M. Burgess and K.H. Andersen (2017): | ||
#' Efficiency of fisheries is increasing at the ecosystem level. | ||
#' Fish and Fisheries 18(2) 199- 211. doi:10.1111/faf.12171.} | ||
#' @docType data | ||
#' @name Barents_params | ||
#' @family example parameter objects | ||
NULL | ||
|
||
# North-East US ---- | ||
#' Example MizerParams object for the North East US Continental Shelf (NEUSCS) with 24 species. | ||
#' | ||
#' Created with purely size-based predation, i.e., no species-specific | ||
#' interactions. Set up with three fishing gears targeting small, medium and | ||
#' large species. Vulnerabilities are represented by changing the clearance rate | ||
#' constant (gamma) between species. Calibrated to efforts | ||
#' \code{effort = c(small = 0.4, medium = 0.3, large = 0.25)}. | ||
#' @examples | ||
#' \dontrun{ | ||
#' sim = project(NEUSCS_params, effort = c(small = 0.4, medium = 0.3, large = 0.25)) | ||
#' plot(sim) | ||
#' } | ||
#' @format A MizerParams object | ||
#' @source{N.S. Jacobsen, M. Burgess and K.H. Andersen (2017): | ||
#' Efficiency of fisheries is increasing at the ecosystem level. | ||
#' Fish and Fisheries 18(2) 199- 211. doi:10.1111/faf.12171.} | ||
#' @docType data | ||
#' @name NEUSCS_params | ||
#' @family example parameter objects | ||
NULL | ||
|
||
# North Sea 10 species ---- | ||
#' Example MizerParams object for the North Sea with 10 species. | ||
#' | ||
#' Created with purely size-based predation, i.e., no species-specific | ||
#' interactions. Set up with three fishing gears targeting small, medium and | ||
#' large species. Vulnerabilities are represented by changing the clearance rate | ||
#' constant (gamma) between species. Calibrated to efforts | ||
#' \code{effort = c(small = 0.6, medium = 0.6, large = 1.25)}. | ||
#' @examples | ||
#' \dontrun{ | ||
#' sim = project(NorthSea_params, effort = c(small = 0.6, medium = 0.6, large = 1.25)) | ||
#' plot(sim) | ||
#' } | ||
#' @format A MizerParams object | ||
#' @source{N.S. Jacobsen, M. Burgess and K.H. Andersen (2017): | ||
#' Efficiency of fisheries is increasing at the ecosystem level. | ||
#' Fish and Fisheries 18(2) 199- 211. doi:10.1111/faf.12171.} | ||
#' @docType data | ||
#' @name NorthSea_params | ||
#' @family example parameter objects | ||
NULL | ||
|
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--- | ||
output: github_document | ||
--- | ||
|
||
<!-- README.md is generated from README.Rmd. Please edit that file --> | ||
|
||
```{r, include = FALSE} | ||
knitr::opts_chunk$set( | ||
collapse = TRUE, | ||
comment = "#>", | ||
fig.path = "man/figures/README-", | ||
out.width = "100%" | ||
) | ||
``` | ||
|
||
# mizerExamples | ||
|
||
<!-- badges: start --> | ||
[](https://www.tidyverse.org/lifecycle/#experimental) | ||
[](https://CRAN.R-project.org/package=mizerExamples) | ||
<!-- badges: end --> | ||
|
||
The goal of mizerExamples is to provide mizer users a way to share their | ||
models. | ||
|
||
If you have a model to contribute, just email [email protected]. | ||
|
||
## Installation | ||
|
||
You can install the current version from [GitHub](https://github.com/) with: | ||
|
||
``` r | ||
# install.packages("devtools") | ||
devtools::install_github("sizespectrum/mizerExamples") | ||
``` | ||
## Example | ||
|
||
```{r example} | ||
library(mizer) | ||
library(mizerExamples) | ||
data("Benguela_params") | ||
plot(Benguela_params) | ||
``` | ||
|
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|
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<!-- README.md is generated from README.Rmd. Please edit that file --> | ||
|
||
# mizerExamples | ||
A crowd-sourced repository of mizer size-spectrum models for various ecosystems | ||
|
||
<!-- badges: start --> | ||
|
||
[](https://www.tidyverse.org/lifecycle/#experimental) | ||
[](https://CRAN.R-project.org/package=mizerExamples) | ||
<!-- badges: end --> | ||
|
||
The goal of mizerExamples is to provide mizer users a way to share their | ||
models. | ||
|
||
If you have a model to contribute, just email | ||
<[email protected]>. | ||
|
||
## Installation | ||
|
||
You can install the current version from [GitHub](https://github.com/) | ||
with: | ||
|
||
``` r | ||
# install.packages("devtools") | ||
devtools::install_github("sizespectrum/mizerExamples") | ||
``` | ||
|
||
## Example | ||
|
||
``` r | ||
library(mizer) | ||
library(mizerExamples) | ||
data("Benguela_params") | ||
plot(Benguela_params) | ||
``` | ||
|
||
<img src="man/figures/README-example-1.png" width="100%" /> |
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## Test environments | ||
* local OS X install, R 3.6.3 | ||
* ubuntu 14.04 (on travis-ci), R 3.6.3 | ||
* win-builder (devel and release) | ||
|
||
## R CMD check results | ||
|
||
0 errors | 0 warnings | 1 note | ||
|
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* This is a new release. |
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