-
Notifications
You must be signed in to change notification settings - Fork 20
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Restructure documents and vignettes for website (#398)
- Loading branch information
Showing
52 changed files
with
1,632 additions
and
486 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,6 @@ | ||
| inst/website | ||
| inst/docs/*.md | ||
| inst/docs/figure | ||
| inst/doc | ||
| inst/doc* | ||
| gh-pages | ||
| *Rproj* | ||
| *.Rhistory* | ||
| ^plant.Rcheck$ | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -36,6 +36,8 @@ Imports: | |
| purrr | ||
| Suggests: | ||
| testthat, | ||
| pkgdown, | ||
| here, | ||
| deSolve, | ||
| numDeriv, | ||
| parallel, | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,183 @@ | ||
| url: https://traitecoevo.github.io/plant/ | ||
|
|
||
| destination: gh-pages | ||
|
|
||
| template: | ||
| bootstrap: 5 | ||
| bootswatch: cosmo | ||
|
|
||
| navbar: | ||
| title: "plant" | ||
| type: inverse | ||
| left: | ||
| - text: "Home" | ||
| icon: fa-home | ||
| href: index.html | ||
| - text: "Getting Started" | ||
| icon: fa-tree | ||
| href: articles/plant.html | ||
| - text: "Package functions" | ||
| icon: fa-list | ||
| href: reference/index.html | ||
| - text: "Articles" | ||
| icon: fa-book | ||
| menu: | ||
| - text: ------- | ||
| - text: "Theory" | ||
| - text: "Demography of individuals, patches, and metacommunities" | ||
| href: articles/demography.html | ||
| - text: "Numerical methods for solving equations" | ||
| href: articles/methods/solving_dynamics.html | ||
| - text: "The node spacing algorithm" | ||
| href: articles/blog/node_spacing.html | ||
| - text: ------- | ||
| - text: "Models" | ||
| - text: "The TF24 model" | ||
| href: articles/models/strategy_TF24.html | ||
| - text: "The FF16 model" | ||
| href: articles/models/strategy_FF16.html | ||
| - text: "The K93 model" | ||
| href: articles/models/strategy_K93.html | ||
| - text: ------- | ||
| - text: "Examples" | ||
| - text: "Example analysis" | ||
| href: articles/example_analysis.html | ||
| - text: "Changing parameters" | ||
| href: articles/parameters.html | ||
| - text: "Self thinning" | ||
| href: articles/self_thinning.html | ||
| - text: "Individual plants" | ||
| href: articles/individuals.html | ||
| - text: "Patches of competing plants" | ||
| href: articles/patch.html | ||
| - text: "Emergent properties of patches" | ||
| href: articles/emergent.html | ||
| - text: "Utilising Extrinsic Drivers" | ||
| href: articles/extrinsic_drivers.html | ||
| - text: ------- | ||
| - text: "Developer Notes" | ||
| - text: "Organisation of the package" | ||
| href: articles/package_organisation.html | ||
| - text: "Implementing a new strategy" | ||
| href: articles/strategy_new.html | ||
| - text: "Blog" | ||
| icon: fa-terminal | ||
| desc: > | ||
| These articles are used to record experiments, that are not expected to continue working into the future. | ||
| menu: | ||
| - text: "2021-water_bucket_model" | ||
| href: articles/blog/2021-water_bucket_model.html | ||
|
|
||
| right: | ||
| - text: "News" | ||
| icon: fa-newspaper-o | ||
| href: news/index.html | ||
| - text: "Github" | ||
| icon: fa-github fa-lg | ||
| href: https://github.com/traitecoevo/plant | ||
|
|
||
| reference: | ||
|
|
||
| - title: Setup | ||
| desc: | ||
| contents: | ||
| - Control | ||
| - scm_base_control | ||
| - fast_control | ||
| - build_schedule | ||
| - plant_log_console | ||
| - scm_base_parameters | ||
| - trait_matrix | ||
| - expand_parameters | ||
| - strategy_list | ||
| - make_hyperpar | ||
| - Disturbance_Regime | ||
| - Weibull_Disturbance_Regime | ||
| - No_Disturbance | ||
|
|
||
| - title: Growing individuals | ||
| contents: | ||
| - Individual | ||
| - grow_individual_to_size | ||
| - grow_individual_to_time | ||
| - optimise_individual_rate_at_size_by_trait | ||
| - resource_compensation_point | ||
|
|
||
| - title: Running patches | ||
| desc: | ||
| contents: | ||
| - run_scm | ||
| - run_scm_collect | ||
| - run_stochastic_collect | ||
|
|
||
| - title: Manipulating outputs | ||
| contents: | ||
| - tidy_env | ||
| - tidy_individual | ||
| - tidy_patch | ||
| - tidy_species | ||
| - integrate_over_size_distribution | ||
| - interpolate_to_heights | ||
| - interpolate_to_times | ||
| - plot_size_distribution | ||
|
|
||
| - title: FF16 model | ||
| desc: Functions for runnign the FF16 model | ||
| contents: | ||
| - contains("FF16_") | ||
|
|
||
| - title: FF16r model | ||
| desc: Functions for runnign the FF16r model | ||
| contents: | ||
| - contains("FF16r_") | ||
|
|
||
| - title: FF16w model | ||
| desc: Functions for runnign the FF16w model | ||
| contents: | ||
| - contains("FF16w_") | ||
|
|
||
|
|
||
| - title: K93 model | ||
| desc: Functions for runnign the K93 model | ||
| contents: | ||
| - contains("K93_") | ||
|
|
||
| - title: TF24 model | ||
| desc: Functions for runnign the TF24 model | ||
| contents: | ||
| - contains("TF24_") | ||
|
|
||
| - title: Development & testing | ||
| contents: | ||
| - run_plant_benchmarks | ||
| - validate | ||
|
|
||
| - title: Helpers | ||
| desc: Small function used in vignettes. Remove from package? | ||
| contents: | ||
| - bounds | ||
| - clamp_domain | ||
| - seq_log | ||
| - rbind_list | ||
| - make_transparent | ||
| - splinefun_log | ||
|
|
||
| - title: Numerical methods | ||
| desc: You're unlikely to run these unless you're diving deep into the code | ||
| contents: | ||
| - environment_type | ||
| - Internals | ||
| - Interpolator | ||
| - OdeControl | ||
| - NodeSchedule | ||
| - QK | ||
| - nlsolve | ||
|
|
||
| - title: Review if still needed | ||
| contents: | ||
| - make_scm_integrate | ||
| - node_schedule_times_default | ||
| - make_reference_plant | ||
| - make_reference_plant_FF16 | ||
| - make_patch | ||
|
|
Oops, something went wrong.