MathMarEcol · jaseeverett · Mar 10, 2026 · Mar 9, 2026
diff --git 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
@@ -13,9 +13,8 @@ knitr::opts_chunk$set(
 )
 ```
 
-# Zooplankton Model of Size Spectrum (ZooMSS)
+# Zooplankton Model of Size Spectrum (ZooMSS) <a href="https://MathMarEcol.github.io/zoomss"><img src="man/figures/zoomss.png" align="right" height="139" alt="zoomss website"></a>
 
-<!-- # planktonr <a href='https://github.com/MathMarEcol/zoomss'><img src='man/figures/planktonr.png' align="right" width="139px" /></a> -->
 <!-- badges: start -->
 [![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
@@ -1,9 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# Zooplankton Model of Size Spectrum (ZooMSS)
-
-<!-- # planktonr <a href='https://github.com/MathMarEcol/zoomss'><img src='man/figures/planktonr.png' align="right" width="139px" /></a> -->
+# Zooplankton Model of Size Spectrum (ZooMSS) <a href="https://MathMarEcol.github.io/zoomss"><img src="man/figures/zoomss.png" align="right" height="139" alt="zoomss website"></a>
 
 <!-- badges: start -->
 

diff --git 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
diff --git a/data-raw/Hex/zoomss_hexsticker_ocean.png b/data-raw/Hex/zoomss_hexsticker_ocean.png
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/404.md 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
diff --git a/docs/LICENSE-text.md 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
diff --git a/docs/LICENSE.md 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
diff --git a/docs/articles/index.md 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
diff --git a/docs/articles/zoomss.md b/docs/articles/zoomss.md
@@ -0,0 +1,121 @@
+# Getting started with ZooMSS
+
+``` r
+
+library(zoomss)
+library(ggplot2)
+```
+
+## Input Data
+
+ZooMSS requires two sets of input data:
+
+1.  **Groups** - Contains all taxa-specific parameter values for each
+    model group, including size ranges and functional group properties.
+
+2.  **Environmental data** - A Time-series dataframe with time series of
+    environmental conditions with `time`, `sst`, and `chl` columns.
+
+## Running the default Model
+
+Get the default published `Groups` dataframe using:
+
+``` r
+
+Groups <- getGroups()
+#> Using default ZooMSS functional groups. Use getGroups() to customize.
+```
+
+Now create an environmental data time-series using the helper function.
+This time-series uses a constant sea surface temperature (`sst`) and
+chlorophyll *a* (`chl`) with a 0.1 yr-1 timestep (`dt`).
+
+``` r
+
+env_data <- createInputParams(time = seq(0, 100, by = 0.1) ,
+                              sst = 15,
+                              chl = 0.15)
+#> ZooMSS input parameters created:
+#> - Time points: 1001 (time values provided)
+#> - Time steps: 1000 (intervals to simulate)
+#> - Time range: 0 to 100 years
+#> - dt = 0.1 years
+#> - SST range: 15 to 15 deg C
+#> - Chlorophyll range: 0.15 to 0.15 mg/m^3
+```
+
+We can look at the environment data and check everything is ok with:
+
+``` r
+
+plotEnvironment(env_data)
+```
+
+![](zoomss_files/figure-html/unnamed-chunk-5-1.png)
+
+Now we run ZooMSS and save every `isave` timestep to reduce storage
+requirements.
+
+``` r
+
+mdl <- zoomss_model(input_params = env_data, Groups = Groups, isave = 2)
+#> Functional groups validation passed
+#> Calculating phytoplankton parameters from environmental time series
+```
+
+## Plotting
+
+The model includes several built-in plotting functions for analysis and
+visualization.
+
+### Time Series Analysis
+
+These plots display total abundance and mean growth/mortality across all
+size classes through time.
+
+``` r
+
+
+library(patchwork)
+p1 <- plotTimeSeries(mdl, by = "abundance", transform = "log10") # Plot abundance time series
+p2 <- plotTimeSeries(mdl, by = "growth") # Plot growth rate time series
+p3 <- plotTimeSeries(mdl, by = "mortality") # Plot predation mortality time series
+
+wrap_plots(p1, p2, p3, nrow = 3, guides = "collect")
+```
+
+![](zoomss_files/figure-html/unnamed-chunk-7-1.png)
+
+We can also plot total biomass through time.
+
+``` r
+
+p4 <- plotTimeSeries(mdl, by = "biomass", transform = "log10") + theme(legend.position = "none") # Plot biomass 
+p5 <- plotTimeSeries(mdl, by = "biomass", type = "stack", transform = "log10") # Plot stacked biomass 
+p6 <- plotTimeSeries(mdl, by = "biomass", type = "fill") # Plot proportional stacked biomass 
+
+wrap_plots(p4, p5, p6, nrow = 3, guides = "collect")
+```
+
+![](zoomss_files/figure-html/unnamed-chunk-8-1.png)
+
+### Static Plots for a given model time point
+
+Plot mean species-resolved size spectra for the final `n_years`.
+
+``` r
+
+plotSizeSpectra(mdl, n_years = 10)
+#> Averaging final 10 years (50 saved time steps with isave = 2) of abundance from 500 total saved time steps.
+```
+
+![](zoomss_files/figure-html/unnamed-chunk-9-1.png)
+
+Plot predator-prey mass ratios for the `idx` timestep
+
+``` r
+
+plotPPMR(mdl, idx = 500) # Plot final timestep
+```
+
+![](zoomss_files/figure-html/unnamed-chunk-10-1.png)
diff --git a/docs/articles/zoomss_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/zoomss_files/figure-html/unnamed-chunk-8-1.png
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/authors.md b/docs/authors.md
@@ -0,0 +1,31 @@
+# Authors and Citation
+
+## Authors
+
+- **Jason D. Everett**. Author, maintainer.
+  [](https://orcid.org/0000-0002-6681-8054)
+
+- **Ryan F. Heneghan**. Author.
+  [](https://orcid.org/0000-0001-7626-1248)
+
+- **Kieran Murphy**. Author. [](https://orcid.org/0000-0002-9697-2458)
+
+- **Anthony J. Richardson**. Author.
+  [](https://orcid.org/0000-0002-9289-7366)
+
+## Citation
+
+Source:
+[`DESCRIPTION`](https://github.com/MathMarEcol/zoomss/blob/HEAD/DESCRIPTION)
+
+Everett J, Heneghan R, Murphy K, Richardson A (2026). *zoomss:
+Zooplankton Model of Size Spectra*. R package version 0.1.0,
+<https://github.com/MathMarEcol/zoomss>.
+
+    @Manual{,
+      title = {zoomss: Zooplankton Model of Size Spectra},
+      author = {Jason D. Everett and Ryan F. Heneghan and Kieran Murphy and Anthony J. Richardson},
+      year = {2026},
+      note = {R package version 0.1.0},
+      url = {https://github.com/MathMarEcol/zoomss},
+    }
diff --git a/docs/deps/bootstrap-5.3.1/bootstrap.min.css b/docs/deps/bootstrap-5.3.1/bootstrap.min.css
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		Content not found. Please use links in the navbar.

		# Page not found (404)