Package: Rcompadre 1.3.0.9000
Rcompadre: Utilities for using the 'COM(P)ADRE' Matrix Model Database
Utility functions for interacting with the 'COMPADRE' and 'COMADRE' databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Authors:
Rcompadre_1.3.0.9000.tar.gz
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Rcompadre.pdf |Rcompadre.html✨
Rcompadre/json (API)
NEWS
| # Install 'Rcompadre' in R: |
| install.packages('Rcompadre', repos = c('https://jonesor.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jonesor/rcompadre/issues
- Comadre - Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples
- Compadre - Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples
- CompadreLegacy - Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examples
Last updated 9 months agofrom:eb6cc60ade. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 23 2024 |
| R-4.5-win | NOTE | Aug 23 2024 |
| R-4.5-linux | NOTE | Aug 23 2024 |
| R-4.4-win | NOTE | Aug 23 2024 |
| R-4.4-mac | NOTE | Aug 23 2024 |
| R-4.3-win | NOTE | Aug 23 2024 |
| R-4.3-mac | NOTE | Aug 23 2024 |
Exports:as_cdbcdb_build_cdbcdb_check_speciescdb_collapsecdb_comparecdb_fetchcdb_flagcdb_flattencdb_idcdb_id_stagescdb_id_studiescdb_mean_matFcdb_metadatacdb_rbindcdb_unflattencdb_unnestCompadreDataDateCreatedmat_elementwise_applymat_meanmat_medianmat_sdmat_to_stringmatAmatCmatFmatrixClassMatrixClassAuthorMatrixClassNumberMatrixClassOrganizedmatUmpm_elementwise_applympm_first_activempm_has_activempm_has_dormmpm_has_propmpm_meanmpm_medianmpm_sdNumberAcceptedSpeciesNumberMatricesNumberStudiesstring_to_matstring_to_vecvec_to_stringVersionVersionData
Dependencies:clicodaexpmfansigluelatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackpillarpkgconfigpopdemoquantregrlangSparseMsurvivaltibbleutf8vctrs
Getting started with Rcompadre
Rendered froma01_GettingStarted.Rmdusingknitr::rmarkdownon Aug 23 2024.Last update: 2023-09-02
Started: 2021-02-21
Obtaining references
Rendered froma04_ObtainingReferences.Rmdusingknitr::rmarkdownon Aug 23 2024.Last update: 2023-09-02
Started: 2021-02-21
Using Rcompadre with the tidyverse
Rendered froma02_RcompadreTidy.Rmdusingknitr::rmarkdownon Aug 23 2024.Last update: 2023-09-02
Started: 2021-02-21
Using your own matrix data
Rendered froma05_UsingYourOwnData.Rmdusingknitr::rmarkdownon Aug 23 2024.Last update: 2023-09-02
Started: 2021-06-20
Vectorising with Rcompadre
Rendered froma03_VectorisingRcompadre.Rmdusingknitr::rmarkdownon Aug 23 2024.Last update: 2023-09-02
Started: 2021-03-13
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert legacy COM(P)ADRE database object to CompadreDB | as_cdb |
| Create a CompadreDB object from user-specified data | cdb_build_cdb |
| Check whether a COM(P)ADRE database contains one or more species of interest | cdb_check_species |
| Collapse a COM(P)ADRE database by averaging matrices over levels of one or more grouping variables | cdb_collapse |
| Compare two versions or subsets of a COM(P)ADRE database | cdb_compare |
| Fetch the COM(P)ADRE database from compadre-db.org or a local file | cdb_fetch |
| Flag potential issues in matrices of a COM(P)ADRE database | cdb_flag |
| Convert a COM(P)ADRE database to a flat data frame with matrices and vectors stored in string representation | cdb_flatten |
| Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of a given set of columns | cdb_id |
| Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of species and matrix stage class definitions | cdb_id_stages |
| Create a vector of unique study identifiers from a COM(P)ADRE database | cdb_id_studies |
| Calculate a population-specific mean fecundity matrix for each set of matrices in a COM(P)ADRE database | cdb_mean_matF |
| Extract metadata from a COM(P)ADRE database | cdb_metadata |
| Merge two COM(P)ADRE databases via row-bind | cdb_rbind |
| Reconstitute a flattened COM(P)ADRE database (created by cdb_flatten) as a CompadreDB object | cdb_unflatten |
| Unnest a COM(P)ADRE database by spreading the components of CompadreMat into separate list-columns | cdb_unnest |
| Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples | Comadre Compadre |
| CompadreDB Class | $,CompadreDB-method $<-,CompadreDB-method CompadreData CompadreData,CompadreDB-method CompadreDB DateCreated DateCreated,CompadreDB-method Version Version,CompadreDB-method VersionData VersionData,CompadreDB-method [[,CompadreDB,ANY,missing-method [[<-,CompadreDB,ANY,missing-method |
| Methods for CompadreDB objects | as.data.frame.CompadreDB as_tibble.CompadreDB CompadreDB-Methods dim.CompadreDB head.CompadreDB merge.CompadreDB names.CompadreDB NumberAcceptedSpecies NumberAcceptedSpecies,CompadreDB-method NumberMatrices NumberMatrices,CompadreDB-method NumberStudies NumberStudies,CompadreDB-method tail.CompadreDB |
| Subsetting CompadreDB objects | CompadreDB-Subsetting subset.CompadreDB [,CompadreDB,ANY,ANY,ANY-method |
| Tidyverse methods for CompadreDB objects | arrange.CompadreDB CompadreDB-Tidyverse filter.CompadreDB fortify.CompadreDB full_join.CompadreDB group_by.CompadreDB inner_join.CompadreDB left_join.CompadreDB mutate.CompadreDB rename.CompadreDB right_join.CompadreDB select.CompadreDB slice.CompadreDB summarise.CompadreDB summarize.CompadreDB ungroup.CompadreDB |
| Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examples | CompadreLegacy |
| Methods for working with matrices in com(p)adre | CompadreMatrixMethods matA matA,CompadreDB-method matA,CompadreMat-method matA,list-method matC matC,CompadreDB-method matC,CompadreMat-method matC,list-method matF matF,CompadreDB-method matF,CompadreMat-method matF,list-method matrixClass matrixClass,CompadreDB-method matrixClass,CompadreMat-method matrixClass,list-method MatrixClassAuthor MatrixClassAuthor,CompadreDB-method MatrixClassAuthor,CompadreMat-method MatrixClassAuthor,list-method MatrixClassNumber MatrixClassNumber,CompadreDB-method MatrixClassNumber,CompadreMat-method MatrixClassNumber,list-method MatrixClassOrganized MatrixClassOrganized,CompadreDB-method MatrixClassOrganized,CompadreMat-method MatrixClassOrganized,list-method matU matU,CompadreDB-method matU,CompadreMat-method matU,list-method |
| Apply a function element-wise to a list of matrices | mat_elementwise_apply mpm_elementwise_apply |
| Calculate a mean over a list of matrices or CompadreMat objects | mat_mean mpm_mean |
| Calculate a median over a list of matrices or CompadreMat objects | mat_median mpm_median |
| Extract stage-class information from CompadreMat or CompadreDB objects | mpm_first_active mpm_first_active,CompadreDB-method mpm_first_active,CompadreMat-method mpm_has_active mpm_has_active,CompadreDB-method mpm_has_active,CompadreMat-method mpm_has_dorm mpm_has_dorm,CompadreDB-method mpm_has_dorm,CompadreMat-method mpm_has_prop mpm_has_prop,CompadreDB-method mpm_has_prop,CompadreMat-method mpm_methods |
| Calculate a standard deviation over a list of matrices or CompadreMat objects | mat_sd mpm_sd |
| Convert vectors or square numeric matrices to and from string representation | mat_to_string string_representation string_to_mat string_to_vec vec_to_string |
