Fix site

.gitignore

@@ -1,12 +1,8 @@
 .Rhistory
 .Rapp.history
 .DS_Store
-Ancillary/EnvironmentalData/CreateEnviro/Data/GEBCO_2014_2D.nc
 .Rproj.user
-RawOutput/*
-Ancillary/*
 
 inst/doc
-docs
 /doc/
 /Meta/

README.Rmd

@@ -29,7 +29,7 @@ knitr::opts_chunk$set(
 
 The Zooplankton Model of Size Spectra (ZooMSS) is a functional size-spectrum model of the marine ecosystem (following Heneghan et al. 2016) to resolve phytoplankton, nine zooplankton functional groups (heterotrophic flagellates and ciliates, omnivorous and carnivorous copepods, larvaceans, euphausiids, salps, chaetognaths and jellyfish) and three size-based fish groups. Zooplankton functional groups are resolved using their body-size ranges, size-based feeding characteristics and carbon content, and the zooplankton community emerges from the model across global environmental gradients, depending on the functional traits of the different groups.
 
-We developed the Zooplankton Model of Size Spectra (ZooMSSv2) based on the prototype of Heneghan et al. (2016). ZooMSS uses the functional size-spectrum framework (Blanchard et al., 2017) to resolve the body size ranges, size-based feeding characteristics and carbon content of nine zooplankton groups and three fish groups. The model supports time-varying environmental conditions enabling studies of seasonal cycles, climate change scenarios, and ecosystem responses to environmental variability.
+We developed the Zooplankton Model of Size Spectra ZooMSS based on the prototype of Heneghan et al. (2016). ZooMSS uses the functional size-spectrum framework (Blanchard et al., 2017) to resolve the body size ranges, size-based feeding characteristics and carbon content of nine zooplankton groups and three fish groups. The model supports time-varying environmental conditions enabling studies of seasonal cycles, climate change scenarios, and ecosystem responses to environmental variability.
 
 ZooMSS represents the marine ecosystem as three communities: phytoplankton, zooplankton and fish. The zooplankton community consists of nine of the most abundant zooplankton groups, and the fish community was made up of a small, medium and large group. Dynamics of the phytoplankton are not explicitly resolved in the model, rather the mean size structure of the phytoplankton community is estimated directly from satellite chlorophyll a observations (Brewin et al., 2010; Barnes et al., 2011; Hirata et al., 2011). Abundances of the zooplankton and fish communities are driven by size-dependent processes of growth and mortality, with the temporal dynamics of each functional group governed by separate second-order McKendrick-von Foerster equations.
 

README.md

@@ -31,8 +31,8 @@ characteristics and carbon content, and the zooplankton community
 emerges from the model across global environmental gradients, depending
 on the functional traits of the different groups.
 
-We developed the Zooplankton Model of Size Spectra (ZooMSSv2) based on
-the prototype of Heneghan et al. (2016). ZooMSS uses the functional
+We developed the Zooplankton Model of Size Spectra ZooMSS based on the
+prototype of Heneghan et al. (2016). ZooMSS uses the functional
 size-spectrum framework (Blanchard et al., 2017) to resolve the body
 size ranges, size-based feeding characteristics and carbon content of
 nine zooplankton groups and three fish groups. The model supports

_pkgdown.yml

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 url: ~
 template:
   bootstrap: 5
-  bootswatch: lumen
   bslib:
     toc: true
     toc-expand: 3
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   desc: Functions to be unexported
 - contents:
   - untibble
-navbar:
-  structure:
-    right: [github, search]