diff --git a/DESCRIPTION b/DESCRIPTION index 0ad0b2e..77a4138 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -45,7 +45,7 @@ URL: https://github.com/MathMarEcol/zoomss BugReports: https://github.com/MathMarEcol/zoomss/issues Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Suggests: knitr, rmarkdown, diff --git a/README.Rmd b/README.Rmd index 7b930de..01c183a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -13,9 +13,8 @@ knitr::opts_chunk$set( ) ``` -# Zooplankton Model of Size Spectrum (ZooMSS) +# Zooplankton Model of Size Spectrum (ZooMSS) zoomss website - [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![Windows](https://github.com/MathMarEcol/zoomss/actions/workflows/Windows.yaml/badge.svg)](https://github.com/MathMarEcol/zoomss/actions/workflows/Windows.yaml) diff --git a/README.md b/README.md index ea4e321..869e5f6 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,7 @@ -# Zooplankton Model of Size Spectrum (ZooMSS) - - +# Zooplankton Model of Size Spectrum (ZooMSS) zoomss website diff --git a/_pkgdown.yml b/_pkgdown.yml index 136fb39..ced5eb5 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -2,9 +2,10 @@ url: ~ template: bootstrap: 5 bslib: + primary: "#002F61" toc: true toc-expand: 3 - bootswatch: cerulean + bootswatch: flatly reference: - title: Data desc: Data related functions and datasets diff --git a/data-raw/Hex/zoomss.png b/data-raw/Hex/zoomss.png new file mode 100644 index 0000000..e1088ee Binary files /dev/null and b/data-raw/Hex/zoomss.png differ diff --git a/data-raw/Hex/zoomss_hexsticker_ocean.png b/data-raw/Hex/zoomss_hexsticker_ocean.png new file mode 100644 index 0000000..171695e Binary files /dev/null and b/data-raw/Hex/zoomss_hexsticker_ocean.png differ diff --git a/docs/404.html b/docs/404.html index 140edab..d5c7746 100644 --- a/docs/404.html +++ b/docs/404.html @@ -61,7 +61,7 @@

Page not found (404)

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/404.md b/docs/404.md new file mode 100644 index 0000000..5107f89 --- /dev/null +++ b/docs/404.md @@ -0,0 +1,3 @@ +Content not found. Please use links in the navbar. + +# Page not found (404) diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 9648e09..331759e 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -44,7 +44,7 @@

License

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/LICENSE-text.md b/docs/LICENSE-text.md new file mode 100644 index 0000000..8b5daef --- /dev/null +++ b/docs/LICENSE-text.md @@ -0,0 +1,4 @@ +# License + + YEAR: 2025 + COPYRIGHT HOLDER: zoomss authors diff --git a/docs/LICENSE.html b/docs/LICENSE.html index cc23d28..67a7d98 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -48,7 +48,7 @@

MIT License

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/LICENSE.md b/docs/LICENSE.md new file mode 100644 index 0000000..56439fb --- /dev/null +++ b/docs/LICENSE.md @@ -0,0 +1,22 @@ +# MIT License + +Copyright (c) 2025 zoomss authors + +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. diff --git a/docs/articles/index.html b/docs/articles/index.html index c97f642..7c17c9f 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -46,7 +46,7 @@

All vignettes

-

Site built with pkgdown 2.1.3.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/articles/index.md b/docs/articles/index.md new file mode 100644 index 0000000..ea30c44 --- /dev/null +++ b/docs/articles/index.md @@ -0,0 +1,5 @@ +# Articles + +### All vignettes + +- [Getting started with ZooMSS](zoomss.md): diff --git a/docs/articles/zoomss.html b/docs/articles/zoomss.html index ecf7ba5..ba7a60e 100644 --- a/docs/articles/zoomss.html +++ b/docs/articles/zoomss.html @@ -101,7 +101,7 @@

Running the default Model 
 plotEnvironment(env_data)
-

+

Now we run ZooMSS and save every isave timestep to reduce storage requirements.

@@ -127,7 +127,7 @@ 
Time Series Analysisp3 <- plotTimeSeries(mdl, by = "mortality") # Plot predation mortality time series
 
 wrap_plots(p1, p2, p3, nrow = 3, guides = "collect")
-

+

We can also plot total biomass through time.

 p4 <- plotTimeSeries(mdl, by = "biomass", transform = "log10") + theme(legend.position = "none") # Plot biomass 
@@ -135,7 +135,7 @@ 
Time Series Analysisp6 <- plotTimeSeries(mdl, by = "biomass", type = "fill") # Plot proportional stacked biomass 
 
 wrap_plots(p4, p5, p6, nrow = 3, guides = "collect")
-

+

Static Plots for a given model time point @@ -145,11 +145,11 @@

Static Plots for a given mode 
 plotSizeSpectra(mdl, n_years = 10)
 #> Averaging final 10 years (50 saved time steps with isave = 2) of abundance from 500 total saved time steps.
-

+

Plot predator-prey mass ratios for the idx timestep

 plotPPMR(mdl, idx = 500) # Plot final timestep
-

+