Package: n2kanalysis
Title: Generic Functions to Analyse Data from the 'Natura 2000' Monitoring
Version: 0.4.0
Authors@R: c(
    person("Thierry", "Onkelinx", , "thierry.onkelinx@inbo.be", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
    person("Research Institute for Nature and Forest (INBO)", , , "info@inbo.be", role = c("cph", "fnd"))
  )
Description: All generic functions and classes for the analysis for the
    'Natura 2000' monitoring. The classes contain all required data and
    definitions to fit the model without the need to access other sources.
    Potentially they might need access to one or more parent objects. An
    aggregation object might for example need the result of an imputation
    object. The actual definition of the analysis, using these generic
    function and classes, is defined in dedictated analysis R packages for
    every monitoring scheme. For example 'abvanalysis' and
    'watervogelanalysis'.
License: GPL-3
URL: https://doi.org/10.5281/zenodo.3576047,
    https://inbo.github.io/n2kanalysis/
BugReports: https://github.com/inbo/n2kanalysis/issues
Depends:
    R (>= 4.2.0)
Imports:
    assertthat (>= 0.2.1),
    aws.s3,
    digest (>= 0.6.23.2),
    dplyr,
    fs,
    git2rdata (>= 0.5.0),
    MASS,
    methods,
    multimput (>= 0.2.14),
    n2khelper (>= 0.5.0),
    purrr,
    rlang,
    RODBC,
    tibble,
    tidyr (>= 0.4.0),
    tools,
    yaml
Suggests:
    fmesher,
    INLA (>= 23.04.24),
    knitr,
    Matrix,
    parallel,
    rmarkdown,
    sf,
    sn,
    testthat (>= 2.0.1)
VignetteBuilder: 
    knitr
Remotes:
    inbo/multimput,
    inbo/n2khelper
Additional_repositories: https://inla.r-inla-download.org/R/stable,
    https://inbo.r-universe.dev
Config/checklist/communities: inbo
Config/checklist/keywords: analysis, reproducible research, natura 2000,
    monitoring
Encoding: UTF-8
Language: en-GB
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Collate: 
    'n2k_parameter_class.R'
    'n2k_anomaly_class.R'
    'n2k_analysis_version_class.R'
    'combine.R'
    'n2k_contrast_class.R'
    'n2k_analysis_metadata_class.R'
    'n2k_result_class.R'
    'combine_result.R'
    'import_s3_classes.R'
    'delete_model.R'
    'display.R'
    'n2k_model_class.R'
    'n2k_inla_comparison_class.R'
    'n2k_inla_class.R'
    'n2k_aggregate_class.R'
    'n2k_model_imputed_class.R'
    'extract.R'
    'fit_every_model.R'
    'fit_model.R'
    'fit_model_character.R'
    'fit_model_n2k_aggregate.R'
    'n2k_composite_class.R'
    'fit_model_n2k_composite.R'
    'n2k_hurdle_imputed_class.R'
    'fit_model_n2k_hurdle_imputed.R'
    'fit_model_n2k_inla.R'
    'fit_model_n2k_inla_comparison.R'
    'n2k_manifest_class.R'
    'fit_model_n2k_manifest.R'
    'fit_model_n2k_model_imputed.R'
    'spde_class.R'
    'n2k_spde_class.R'
    'fit_model_n2k_spde.R'
    'fit_model_s3_object.R'
    'get_analysis_date.R'
    'get_analysis_version.R'
    'get_anomaly.R'
    'get_anomaly_n2k_inla.R'
    'get_anomaly_n2k_model.R'
    'get_data.R'
    'get_datafield_id.R'
    'get_file_fingerprint.R'
    'get_formula.R'
    'get_location_group_id.R'
    'get_model.R'
    'get_model_parameter.R'
    'get_model_parameter_n2k_aggregated.R'
    'get_model_parameter_n2k_composite.R'
    'get_model_parameter_n2k_hurdle_imputed.R'
    'get_model_parameter_n2k_inla.R'
    'get_model_parameter_n2k_inla_comparison.R'
    'get_model_parameter_n2k_model_imputed.R'
    'get_model_type.R'
    'get_parents.R'
    'get_result.R'
    'get_result_character.R'
    'get_result_n2k_inla.R'
    'get_result_n2k_model.R'
    'get_result_n2kmanifest.R'
    'get_result_s3_object.R'
    'get_scheme_id.R'
    'get_seed.R'
    'get_species_group_id.R'
    'get_status_fingerprint.R'
    'inla_inverse.R'
    'make_a.R'
    'manifest_yaml_to_bash.R'
    'mark_obsolete_dataset.R'
    'moving_average.R'
    'moving_difference.R'
    'moving_trend.R'
    'n2k_aggregated.R'
    'n2k_composite.R'
    'n2k_hurdle_imputed.R'
    'n2k_import_class.R'
    'n2k_import.R'
    'n2k_inla.R'
    'n2k_inla_comparison.R'
    'n2k_manifest.R'
    'n2k_model_imputed.R'
    'n2k_spde.R'
    'parent_status.R'
    'read_manifest.R'
    'read_model.R'
    'read_result.R'
    'result_estimate.R'
    'result_estimate_character.R'
    'result_estimate_n2k_result.R'
    'result_metadata.R'
    'result_metadata_character.R'
    'result_metadata_n2k_result.R'
    'select_factor_count_strictly_positive.R'
    'select_factor_treshold.R'
    'select_observed_range.R'
    'session_package.R'
    'sha1.R'
    'spde.R'
    'spde2matern.R'
    'spde2mesh.R'
    'status.R'
    'store_manifest.R'
    'store_manifest_yaml.R'
    'store_model.R'
    'union.R'
    'valid_object.R'
