Package: portalr 0.4.5

Glenda M. Yenni

portalr: Create Useful Summaries of the Portal Data

Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahuan desert. The raw data files can be found at <https://github.com/weecology/portaldata>.

Authors:Glenda M. Yenni [aut, cre], Hao Ye [aut], Erica M. Christensen [aut], Juniper L. Simonis [aut], Ellen K. Bledsoe [aut], Renata M. Diaz [aut], Shawn D. Taylor [aut], Ethan P, White [aut], S.K. Morgan Ernest [aut], Weecology [cph]

portalr_0.4.5.tar.gz
portalr_0.4.5.zip(r-4.7)portalr_0.4.5.zip(r-4.6)portalr_0.4.5.zip(r-4.5)
portalr_0.4.5.tgz(r-4.6-any)portalr_0.4.5.tgz(r-4.5-any)
portalr_0.4.5.tar.gz(r-4.7-any)portalr_0.4.5.tar.gz(r-4.6-any)
portalr_0.4.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
portalr/json (API)

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

Bug tracker:https://github.com/weecology/portalr/issues

Pkgdown/docs site:https://weecology.github.io

On CRAN:

Conda:

community-ecologyecologysmall-mammal-trapping

6.98 score 12 stars 79 scripts 894 downloads 41 exports 52 dependencies

Last updated from:1178c20e23. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK282
source / vignettesOK299
linux-release-x86_64OK272
macos-release-arm64OK223
macos-oldrel-arm64OK319
windows-develOK262
windows-releaseOK256
windows-oldrelOK244
wasm-releaseOK156

Exports:%>%abundanceadd_seasonsbait_presence_absencebiomasscheck_default_data_pathcheck_for_newer_dataclean_plant_dataclean_rodent_datacolony_presence_absencedownload_observationsenergyfcast_ndvifill_missing_ndvifind_incomplete_censusesforecasting_speciesget_dataset_citationget_default_data_pathget_future_newmoonsload_ant_dataload_datafileload_plant_dataload_rodent_dataload_trapping_datana_conformerndviphenocamplant_abundanceratesreturn_if_nullrodent_speciesshrub_coversummarise_individual_rodentssummarise_plant_datasummarise_rodent_datasummarize_individual_rodentssummarize_plant_datasummarize_rodent_datause_default_data_pathweatheryearly

Dependencies:askpassclicliprcolorspacecpp11curldplyrfarverforecastfracdiffgenericsggplot2gluegtablehttrisobandjsonlitelabelinglatticelifecyclelmtestlubridatelunarmagrittrmimenlmennetopensslpillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadillorlangS7scalesstringistringrsystibbletidyrtidyselecttimechangetimeDateurcautf8vctrsviridisLitewithrzoo

Portal Rodent Abundance Demo
Introduction | Package Setup | Retrieving the Data | Rodent Abundances | Figure: abundance over time | Next Steps | Plot Treatments | Figure: plot treatments over time | Identifying control plots | Which plots have always been control plots? | Abundances over control plots | Abundances over rodent exclosures | Comparison Figure
Rendered fromrodent-abundance-demo.Rmdusingknitr::rmarkdown

Last update: 2025-06-26
Started: 2017-11-15

Examples of How Portal Researchers Are Using the Package
Introduction | Installing the Package | Rodent Biomass Ratios between Plot Treatment Types | Getting the Data We Want | Working with the Data | Plotting the Ratios | Working with Plant Data | Happy coding!
Rendered fromportal_researcher_examples.Rmdusingknitr::rmarkdown

Last update: 2021-02-11
Started: 2018-07-09

Readme and manuals

Help Manual

Help pageTopics
Add Seasonsadd_seasons yearly
Ant Bait Presence Absencebait_presence_absence
Manage the default path for downloading Portal Data intocheck_default_data_path get_default_data_path use_default_data_path
Check for latest version of data filescheck_for_newer_data
Do basic cleaning of Portal plant dataclean_plant_data
Do basic cleaning of Portal rodent dataclean_rodent_data
Ant Colony Presence Absencecolony_presence_absence
Download the PortalData repodownload_observations
Forecast ndvi using a seasonal auto ARIMAfcast_ndvi
Fill in historic ndvi data to the complete timeseries being fitfill_missing_ndvi
Period code for incomplete censusesfind_incomplete_censuses
Return Citation for Portal Dataget_dataset_citation
Get future newmoon dates and numbersget_future_newmoons
read in a raw datafile from the downloaded data or the GitHub repoload_datafile
Read in the Portal data filesload_ant_data load_plant_data load_rodent_data load_trapping_data
Conform NA entries to "NA" entriesna_conformer
NDVI by calendar month or lunar monthndvi
Phenocam data products by day, calendar month, or lunar monthphenocam
Prints a portal_data_list objectprint print.portal_data_list
If a Value is NULL, Trigger the Parent Function's Returnreturn_if_null
Rodent species abbreviationsforecasting_species rodent_species
Generate percent cover from Portal plant transect datashrub_cover
Return cleaned Portal rodent individual datasummarise_individual_rodents summarize_individual_rodents
Generate summaries of Portal plant dataplant_abundance summarise_plant_data summarize_plant_data
Generate summaries of Portal rodent dataabundance biomass energy rates summarise_rodent_data summarize_rodent_data
Weather by day, calendar month, or lunar monthweather