Package: Rpadrino 0.0.5

Sam Levin

Rpadrino: Interact with the 'PADRINO' IPM Database

'PADRINO' houses textual representations of Integral Projection Models which can be converted from their table format into full kernels to reproduce or extend an already published analysis. 'Rpadrino' is an R interface to this database. For more information on Integral Projection Models, see Easterling et al. (2000) <doi:10.1890/0012-9658(2000)081[0694:SSSAAN]2.0.CO;2>, Merow et al. (2013) <doi:10.1111/2041-210X.12146>, Rees et al. (2014) <doi:10.1111/1365-2656.12178>, and Metcalf et al. (2015) <doi:10.1111/2041-210X.12405>. See Levin et al. (2021) for more information on 'ipmr', the engine that powers model reconstruction <doi:10.1111/2041-210X.13683>.

Authors:Sam Levin [aut, cre], Aldo Compagnoni [aut], Dylan Childs [aut], Sanne Evers [aut], Tomos Potter [aut], Roberto Salguero-Gomez [aut], Tiffany Knight [aut]

Rpadrino_0.0.5.tar.gz
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Rpadrino.pdf |Rpadrino.html
Rpadrino/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/padrinodb/rpadrino/issues

Datasets:
  • pdb - Selected models from the Padrino Database

On CRAN:

56 exports 2 stars 1.02 score 56 dependencies 15 scripts 252 downloads

Last updated 12 months agofrom:2a9a784d89. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-winOKAug 28 2024
R-4.5-linuxOKAug 28 2024
R-4.4-winOKAug 28 2024
R-4.4-macOKAug 28 2024
R-4.3-winOKAug 28 2024
R-4.3-macOKAug 28 2024

Exports::=.data%>%as_labelas_nameenquoenquosexprpdb_altitudepdb_angio_gymonpdb_appendix_linkpdb_authorspdb_citationspdb_classpdb_commentspdb_continentpdb_countrypdb_dicot_monocotpdb_doipdb_downloadpdb_durationpdb_ecoregionpdb_end_monthpdb_end_yearpdb_evict_typepdb_eviction_usedpdb_familypdb_genuspdb_has_agepdb_has_time_lagpdb_journalpdb_kingdompdb_latpdb_loadpdb_lonpdb_make_ipmpdb_make_proto_ipmpdb_new_fun_formpdb_number_populationspdb_orderpdb_org_typepdb_periodicitypdb_phylumpdb_population_namepdb_pub_yearpdb_reportpdb_savepdb_species_acceptedpdb_species_authorpdb_start_monthpdb_start_yearpdb_studied_sexpdb_subsetpdb_treatmentsymsyms

Dependencies:base64encbslibcachemclicolorspacecurldigestevaluateevdfansifarverfastmapfontawesomefsggplot2gluegtablehighrhtmltoolsipmrisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellmvtnormnlmepillarpkgconfigpurrrR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalestibbletinytextruncdistutf8vctrsviridisLitewithrxfunyaml

Data Cleaning and Troubleshooting

Rendered fromdata-cleaning.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2021-11-08
Started: 2021-10-26

Messages and Warnings in PADRINO

Rendered frompdb-msgs.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2022-04-28
Started: 2022-04-28

Modifying Stochastic IPMs in PADRINO

Rendered fromstoch-ipms.rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2023-09-09
Started: 2022-03-03

Rpadrino Introduction

Rendered frompadrino-intro.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2023-09-09
Started: 2019-01-13

Readme and manuals

Help Manual

Help pageTopics
Selected models from the Padrino Databasepdb
Access pieces of metadata from a 'pdb' objectpdb_altitude pdb_angio_gymon pdb_appendix_link pdb_authors pdb_citations pdb_class pdb_comments pdb_continent pdb_country pdb_dicot_monocot pdb_doi pdb_duration pdb_ecoregion pdb_end_month pdb_end_year pdb_eviction_used pdb_evict_type pdb_family pdb_genus pdb_has_age pdb_has_time_lag pdb_journal pdb_kingdom pdb_lat pdb_lon pdb_number_populations pdb_order pdb_org_type pdb_periodicity pdb_phylum pdb_population_name pdb_pub_year pdb_report pdb_species_accepted pdb_species_author pdb_start_month pdb_start_year pdb_studied_sex pdb_treatment
Download PADRINO 'pdb' objectspdb_download pdb_load pdb_save
Generate IPMs from Padrino objectspdb_make_ipm
Generate proto_ipms from Padrino objectspdb_make_proto_ipm
Subset a Padrino database objectpdb_subset
Print a 'pdb' object.print.pdb print.pdb_proto_ipm_list
Padrino methods for `ipmr` generic functionsconv_plot.pdb_ipm domains.pdb_ipm domains.pdb_proto_ipm_list int_mesh.pdb_ipm is_conv_to_asymptotic.pdb_ipm kernel_formulae.pdb_ipm kernel_formulae.pdb_proto_ipm_list kernel_formulae<-.pdb_proto_ipm_list lambda.pdb_ipm left_ev.pdb_ipm make_iter_kernel.pdb_ipm mean_kernel.pdb_ipm parameters.pdb_ipm parameters.pdb_proto_ipm_list parameters<-.pdb_proto_ipm_list pdb_new_fun_form pop_state.pdb_ipm pop_state.pdb_proto_ipm_list right_ev.pdb_ipm vital_rate_exprs.pdb_ipm vital_rate_exprs.pdb_proto_ipm_list vital_rate_exprs<-.pdb_proto_ipm_list vital_rate_funs.pdb_ipm [.pdb_ipm