Package: urbioconnect 0.1.0.9000

Nicholas Tierney

urbioconnect: Urban Habitat Connectivity Analysis

Analyse and visualise habitat connectivity in urban landscapes, accounting for barriers and buffer distances. Includes Shiny app for interactive analysis and report generation. Based on methods developed by Kirk et al (2023) <doi:10.1016/j.mex.2022.101989>.

Authors:Nicholas Tierney [aut, cre], Holly Kirk [aut, cph]

urbioconnect_0.1.0.9000.tar.gz
urbioconnect_0.1.0.9000.zip(r-4.7-any)urbioconnect_0.1.0.9000.zip(r-4.6-any)urbioconnect_0.1.0.9000.zip(r-4.5-any)
urbioconnect_0.1.0.9000.tgz(r-4.6-any)urbioconnect_0.1.0.9000.tgz(r-4.5-any)
urbioconnect_0.1.0.9000.tar.gz(r-4.7-any)urbioconnect_0.1.0.9000.tar.gz(r-4.6-any)
urbioconnect_0.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
urbioconnect/json (API)

# Install 'urbioconnect' in R:
install.packages('urbioconnect', repos = c('https://urbio-ecology.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/urbio-ecology/urbioconnect/issues

Pkgdown/docs site:https://urbio-ecology.github.io

Datasets:

On CRAN:

Conda:

ecologyshinyspatial-analysisurban-ecologyquarto

4.82 score 15 scripts 72 exports 89 dependencies

Last updated from:f95672b883. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE322
source / vignettesOK266
linux-releaseNOTE255
macos-releaseNOTE240
macos-oldrelNOTE241
windows-develNOTE249
windows-releaseNOTE257
windows-oldrelNOTE250
wasm-releaseOK138

Exports:add_patch_areaaggregate_connected_patchesassign_patches_to_fragmentscleancol2hexcompare_connectivitycompare_scenariosconnectivity_displayconnectivity_file_stemconnectivity_probabilityconnectivity_report_datacreate_barrier_maskdisplay_idsdrop_habitat_under_barriereffective_mesh_sizeempty_gridexample_barrierexample_barrier_scenarioexample_barrier_shpexample_habitatexample_wren_barrierexample_wren_barrier_scenarioexample_wren_habitatexample_wren_habitat_scenarioformat_byformat_resolutionfragment_habitatgenerate_connectivity_reportgg_barrier_habitat_interpatch_distgg_layerhabitat_bufferhabitat_connectivityhabitat_connectivity_comparisonhabitat_connectivity_fullhabitat_connectivity_scenariosmean_patch_sizen_patchesnew_patch_size_tblonto_gridpatch_size_tblpatch_sizespc_interpatch_distancepc_patchespc_respc_speciesplot_barrier_habitat_interpatch_distplot_connectivityplot_patchesprepare_rastersquarto_availableread_geometryread_report_datarender_connectivity_reportround_byrun_connectivity_appscenario_layersf_add_patch_areasf_aggregate_connected_patchessf_assign_patches_to_fragmentssf_drop_habitat_under_barriersf_fragment_habitatsf_habitat_buffersf_habitat_connectivitysummarise_connectivitytotal_habitat_areaurbio_coloursurbio_figure_sizewrite_connectivity_assetswrite_connectivity_reportwrite_report_datazip_connectivity_assetszip_connectivity_reports

Dependencies:base64encbitbit64bslibcachemclassclassIntclicliprcolorspacecommonmarkcpp11crayondata.tableDBIdigestdplyre1071evaluatefarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshttpuvisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlifecyclemagrittrmemoisemimeotelpillarpkgconfigprettyunitsprocessxprogresspromisesproxypspurrrquartoR6rappdirsRColorBrewerRcppreadrrlangrmarkdownrstudioapis2S7sassscalesscicosfshinysourcetoolsstringistringrterratibbletidyrtidyselecttidyterratinytextzdbunitsutf8vctrsviridisLitevroomwithrwkxfunxtableyamlzip

Using raster vs vector
Rasters and vectors | Running raster and vector models on the same data | Prepare the example data | Raster approach | Vector approach | Comparing raster vs vector | Summarising connectivity metrics | Which approach should you use? | Raster approach trade-offs | Vector approach trade-offs | Converting between raster and vector | Analysis step-by-step | References
Rendered fromraster-vs-vector.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2026-04-14

Using urbioconnect in a targets pipeline
Why use targets for connectivity analysis? | A minimal _targets.R | What each section does | Running and inspecting the pipeline | Running | Inspecting results | Visualising the dependency graph | Example workflows
Rendered fromtargets-pipeline.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2026-04-14

Getting started
Overview | The example data | The pipeline, step-by-step | Step 1: Create the barrier mask | Step 2: Remove habitat under barriers | Step 3: Buffer the habitat | Step 4: Fragment habitat along barriers | Step 5: Assign patch IDs | Step 6: Summarise patch areas | Computing connectivity metrics | Run the pipeline as a single step | Comparing multiple interpatch distances | Summary
Rendered fromurbioconnect.Rmdusingknitr::rmarkdown

Last update: 2026-07-22
Started: 2026-07-22

Interpatch distance and raster resolution
Interpatch distance | Buffering happens on a grid | A sub-cell radius does nothing - and habitat_buffer() warns | Why it matters: the same distance, two resolutions | Choosing a resolution | What about vector (sf) data?
Rendered frominterpatch-distance-and-resolution.Rmdusingknitr::rmarkdown

Last update: 2026-06-05
Started: 2026-06-05

Readme and manuals

Help Manual

Help pageTopics
Add patch area layeradd_patch_area
Aggregate connected patch areasaggregate_connected_patches
Assign patches to fragmentsassign_patches_to_fragments
Clean any spatial data layer (shape file)clean
Convert color name to hexadecimalcol2hex
Compare the connectivity of two scenarioscompare_connectivity
Compare several scenarios against one baselinecompare_scenarios
Prepare a result for displayconnectivity_display connectivity_display.compare_connectivity connectivity_display.connectivity connectivity_display.default connectivity_display.patch_size_tbl
The name to give a download: species and dateconnectivity_file_stem
Calculate connectivity probabilityconnectivity_probability
Everything one connectivity analysis producesconnectivity_report_data
Create barrier maskcreate_barrier_mask
Which display columns identify a row rather than measure itdisplay_ids
Remove habitat under barriersdrop_habitat_under_barrier
Calculate effective mesh sizeeffective_mesh_size
Create Empty terra raster gridempty_grid
Lizard Habitat and Barrier Data from Melbourne.example-lizard-data example_barrier example_barrier_scenario example_barrier_shp example_habitat
Fair Wren Habitat, Barrier, and scenario Data from City of Knox.example-wren-data example_wren_barrier example_wren_barrier_scenario example_wren_habitat example_wren_habitat_scenario
Format a raster resolution for readingformat_resolution
Fragment habitatfragment_habitat
Render a connectivity reportgenerate_connectivity_report
Plot barrier, habitat, and interpatch distance layersgg_barrier_habitat_interpatch_dist
Plot one layer on its owngg_layer
Buffer habitat rasterhabitat_buffer
Calculate habitat connectivity using terrahabitat_connectivity
Compare habitat connectivity of a scenario against a baselinehabitat_connectivity_comparison
Calculate habitat connectivity with visualization datahabitat_connectivity_full
Compare several scenarios against one baseline, starting from layershabitat_connectivity_scenarios
Connected habitat patch areas for Blue-tongued Lizardlizard_areas_connected
Calculate mean patch sizemean_patch_size
Count number of habitat patchesn_patches
A set of connected habitat patchesnew_patch_size_tbl patch_size_tbl
Put a layer on a grid, whichever form it arrives inonto_grid
Extract the per-patch tables from a 'connectivity' objectpatch_sizes
Metadata from a 'patch_size_tbl' objectpc-getters pc_interpatch_distance pc_patches pc_res pc_species
Save barrier habitat interpatch distance plotplot_barrier_habitat_interpatch_dist
Plot connectivity metrics across interpatch distancesplot_connectivity
Plot connected habitat patchesplot_patches
Prepare habitat and barrier rastersprepare_rasters
Is the Quarto command line tool installed?quarto_available
Read shapefile geometryread_geometry read_geometry.default read_geometry.sf
Render a connectivity report's sourcerender_connectivity_report
Apply the rounding a display describesformat_by round_by
Launch the Connectivity Shiny Apprun_connectivity_app
The layer a scenario changedscenario_layer
Add patch area columnsf_add_patch_area
Aggregate connected patch areassf_aggregate_connected_patches
Assign habitat patches to fragment IDssf_assign_patches_to_fragments
Remove habitat underneath barrierssf_drop_habitat_under_barrier
Fragment habitat along barrierssf_fragment_habitat
Buffer habitat by distancesf_habitat_buffer
Calculate habitat connectivitysf_habitat_connectivity
Summarise connectivity metricssummarise-connectivity summarise_connectivity summarise_connectivity.default
Calculate total habitat areatotal_habitat_area
The urbioconnect map coloursurbio_colours
The default figure size for urbioconnect maps and plotsurbio_figure_size
Write the downloadable assets for one analysiswrite_connectivity_assets
Write a connectivity report's source, so you can render it yourselfwrite_connectivity_report
Save and reload a connectivity analysisread_report_data write_report_data
Write the downloadable assets as a single zipzip_connectivity_assets
Write the reports as a single zipzip_connectivity_reports