Concept | Workflow | Import the relevant data | Generate the analysis objects | Fit the models | Extract the results | Traceable and auditable | Portable | Efficient | Metadata | Definition of the model | Scheme, species and location | Time-stamp | Used packages | Linked analyses | Available models | n2k_import() | n2k_inla() | n2k_inla_comparison() | n2k_composite() | n2k_hurdle_imputed() | n2k_aggregate() | n2k_modelimputed() | Manifest | Docker
Package: n2kanalysis 0.4.1
Thierry Onkelinx
n2kanalysis: Generic Functions to Analyse Data from the 'Natura 2000' Monitoring
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'.
Authors:
n2kanalysis_0.4.1.tar.gz
n2kanalysis_0.4.1.zip(r-4.7)n2kanalysis_0.4.1.zip(r-4.6)n2kanalysis_0.4.1.zip(r-4.5)
n2kanalysis_0.4.1.tgz(r-4.6-any)n2kanalysis_0.4.1.tgz(r-4.5-any)
n2kanalysis_0.4.1.tar.gz(r-4.7-any)n2kanalysis_0.4.1.tar.gz(r-4.6-any)
n2kanalysis_0.4.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
n2kanalysis/json (API)
| # Install 'n2kanalysis' in R: |
| install.packages('n2kanalysis', repos = c('https://inbo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/inbo/n2kanalysis/issues
Pkgdown/docs site:https://inbo.github.io
Last updated from:1a76ccfbf5. Checks:6 OK, 1 ERROR, 2 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 334 | ||
| source / vignettes | OK | 320 | ||
| linux-release-x86_64 | OK | 358 | ||
| macos-release-arm64 | ERROR | 135 | ||
| macos-oldrel-arm64 | OK | 306 | ||
| windows-devel | FAIL | 193 | ||
| windows-release | FAIL | 120 | ||
| windows-oldrel | OK | 262 | ||
| wasm-release | OK | 170 |
Exports:combineconnect_inbo_s3delete_modeldisplayextractfit_every_modelfit_modelget_analysis_dateget_analysis_versionget_anomalyget_dataget_datafield_idget_file_fingerprintget_formulaget_location_group_idget_modelget_model_parameterget_model_typeget_parentsget_resultget_scheme_idget_seedget_species_group_idget_status_fingerprintinla_inversemake_amanifest_yaml_to_bashmark_obsolete_datasetmoving_averagemoving_differencemoving_trendn2k_aggregaten2k_compositen2k_hurdle_imputedn2k_importn2k_inlan2k_inla_comparisonn2k_manifestn2k_model_imputedn2k_spdeorder_manifestparent_statusparent_status<-read_manifestread_modelread_resultresult_estimateresult_metadataselect_factor_count_non_zeroselect_factor_thresholdselect_observed_rangesession_packagesha1spdespde2maternspde2meshstatusstatus<-store_manifeststore_manifest_yamlstore_modelunionvalidObject
Dependencies:askpassassertthataws.s3aws.signaturebase64encbitbit64blobbootclicpp11curlDBIdigestdplyrfsgenericsgit2rgit2rdatagluehmshttrINLAjsonlitelatticelazyevallifecyclelme4lubridatemagrittrMASSMatrixmimeminqamultimputmvtnormn2khelpernlmenloptrodbcopensslpillarpkgconfigplyrpurrrR6rbibutilsRcppRcppEigenRdpackreformulasrlangRODBCRPostgreSQLstringistringrsystibbletidyrtidyselecttimechangeutf8vctrswithrxml2yaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Combine multiple n2k objects | combine combine,n2kAnalysisVersion-method combine,n2kAnalysisVersion-methods combine,n2kAnamoly-methods combine,n2kAnomaly-method combine,n2kParameter-method combine,n2kParameter-methods combine,n2kResult-method combine,n2kResult-methods |
| Set environment variables for INBO S3 bucket | connect_inbo_s3 |
| Delete an 'n2kModel' object | delete_model delete_model,ANY,character-method delete_model,ANY,s3_bucket-method |
| Display a message. | display |
| Extract the relevant coefficients | extract extract,ANY,character-method extract,ANY,n2kInla-method extract,ANY,n2kModelImputed-method extract,character-methods extract,n2kInla-methods extract,n2kModelImputed-methods |
| Fit the model to the analysis files | fit_every_model |
| Fit an 'n2kModel' object | fit_model fit_model,character-method fit_model,n2kAggregate-method fit_model,n2kComposite-method fit_model,n2kHurdleImputed-method fit_model,n2kInla-method fit_model,n2kInlaComparison-method fit_model,n2kManifest-method fit_model,n2kModelImputed-method fit_model,n2kSpde-method fit_model,s3_object-method |
| Get the analysis date of an 'n2kModel' object | get_analysis_date get_analysis_date,n2kAnalysisMetadata-method get_analysis_date,n2kModel-methods |
| Get an analysis version | get_analysis_version get_analysis_version,data.frame-method get_analysis_version,n2kAnalysisMetadata-method get_analysis_version,n2kAnalysisMetadata-methods get_analysis_version,sessionInfo-method get_analysis_version,sessionInfo-methods |
| Get the anomalies from a model | get_anomaly get_anomaly,n2kInla-method get_anomaly,n2kInla-methods get_anomaly,n2kModel-method |
| Get the data of an 'n2kModel' object | get_data get_data,n2kInla-method get_data,n2kInla-methods |
| Get the data field id | get_datafield_id |
| Get the file fingerprint of an 'n2kModel' object | get_file_fingerprint get_file_fingerprint,n2kAnalysisMetadata-method get_file_fingerprint,n2kAnalysisMetadata-methods get_file_fingerprint,n2kManifest-method get_file_fingerprint,n2kManifest-methods |
| Get the formula of an 'n2kModel' object | get_formula get_formula,n2kAnalysisMetadata-method get_formula,n2kAnalysisMetadata-methods |
| Get the location group id of an 'n2kModel' object | get_location_group_id get_location_group_id,n2kAnalysisMetadata-method get_location_group_id,n2kAnalysisMetadata-methods |
| Get the model of a 'n2kModel' object | get_model get_model,character-method get_model,character-methods get_model,n2kInla-method get_model,n2kInla-methods |
| Add the model parameters from a model | get_model_parameter get_model_parameter,n2kAggregate-method get_model_parameter,n2kComposite-method get_model_parameter,n2kHurdleImputed-method get_model_parameter,n2kInla-method get_model_parameter,n2kInlaComparison-method get_model_parameter,n2kModelImputed-method |
| Get the model type of an 'n2kModel' object | get_model_type get_model_type,n2kAnalysisMetadata-method get_model_type,n2kAnalysisMetadata-methods |
| Get the object of the parent analyses of an 'n2kModel' object | get_parents |
| Add the results from an analysis | get_result get_result,character,character-method get_result,character,s3_bucket-method get_result,n2kInla,ANY-method get_result,n2kManifest,character-method get_result,n2kManifest,s3_bucket-method get_result,n2kModel,ANY-method get_result,s3_object,ANY-method |
| Get the 'scheme_id' of an 'n2kModel' object | get_scheme_id get_scheme_id,n2kAnalysisMetadata-method get_scheme_id,n2kAnalysisMetadata-methods |
| Get the seed of an 'n2kModel' object | get_seed get_seed,n2kAnalysisMetadata-method get_seed,n2kAnalysisMetadata-methods |
| Get the species group id of an 'n2kModel' object | get_species_group_id get_species_group_id,n2kAnalysisMetadata-method get_species_group_id,n2kAnalysisMetadata-methods |
| Get the status fingerprint of an 'n2kModel' object | get_status_fingerprint get_status_fingerprint,n2kAnalysisMetadata-method get_status_fingerprint,n2kAnalysisMetadata-methods |
| Calculate the mean and 95\ marginal | inla_inverse |
| Convert an 'Spde' object to a A object | make_a make_a,Spde-method |
| Convert a manifest yaml file into a bash script | manifest_yaml_to_bash manifest_yaml_to_bash,character-method manifest_yaml_to_bash,s3_bucket-method |
| Find and mark obsolete datasets | mark_obsolete_dataset |
| Calculate moving trend coefficients | moving_average |
| Calculate coefficients for a moving difference | moving_difference |
| Calculate moving trend coefficients | moving_trend |
| Create an 'n2kAggregate' object | n2k_aggregate n2k_aggregate,ANY-method n2k_aggregate,n2kAggregate-methods |
| Create an 'n2kComposite' object | n2k_composite n2k_composite,data.frame-method n2k_composite,n2kComposite-methods |
| Create an 'n2kHurdleImputed' object | n2k_hurdle_imputed n2k_hurdle_imputed,n2kHurdleImputed-methods n2k_hurdle_imputed,n2kInla-method |
| Create an 'n2kImport' object | n2k_import n2k_import,ANY-method |
| Create an 'n2kInla' object | n2k_inla n2k_inla,data.frame,ANY-method n2k_inla,n2kInla,inla-method n2k_inla,n2kInla-methods |
| Create an 'n2kInlaComparison' object | n2k_inla_comparison n2k_inla_comparison,data.frame-method n2k_inla_comparison,n2kInlaComparison-methods |
| Create an 'n2kManifest' object | n2k_manifest n2k_manifest,data.frame-method n2k_manifest,n2kManifest-methods |
| Create an 'n2kModelImputed' object | n2k_model_imputed n2k_model_imputed,ANY-method n2k_model_imputed,n2kModelImputed-methods |
| Create an 'n2kSpde' object | n2k_spde n2k_spde,data.frame,ANY-method n2k_spde,n2kSpde,inla-method n2k_spde,n2kSpde-methods |
| The 'n2kAggregate' class | n2kAggregate-class |
| The 'n2kAnalysisMetadata' class | n2kAnalysisMetadata-class |
| The 'n2kAnalysisVersion' class | n2kAnalysisVersion-class |
| The 'n2kAnomaly' class | n2kAnomaly-class |
| The 'n2kComposite' class | n2kComposite-class |
| The 'n2kContrast' class | n2kContrast-class |
| The 'n2kHurdleImputed' class | n2kHurdleImputed-class |
| The 'n2kImport' class | n2kImport-class |
| The 'n2kInla' class | n2kInla-class |
| The 'n2kInlaComparison' class | n2kInlaComparison-class |
| The 'n2kManifest' class | n2kManifest-class |
| The 'n2kModel' class | n2kModel-class |
| The 'n2kModelImputed' class | n2kModelImputed-class |
| The 'n2kParameter' class | n2kParameter-class |
| The 'n2kResult' class | n2kResult-class |
| The 'n2kSpde' class | n2kSpde-class |
| Convert a manifest in vector of analysis fingerprints | order_manifest |
| Get the parent status of an 'n2kModel' | parent_status parent_status,n2kAnalysisMetadata-method parent_status,n2kAnalysisMetadata-methods |
| Overwrite the status of an 'n2kAnalysisMetadata' | parent_status<- parent_status<-,n2kComposite-method |
| Read a 'n2kManifest' object | read_manifest read_manifest,character-method read_manifest,s3_bucket-method |
| Read an 'n2kModel' object | read_model read_model,ANY,ANY-method read_model,ANY,character-method read_model,ANY,s3_bucket-method |
| Read an 'n2kResult' object | read_result read_result,ANY,ANY-method read_result,ANY,character-method read_result,ANY,s3_bucket-method |
| Aggregate all results estimates in a single dataframe | result_estimate result_estimate,character-method result_estimate,n2kResult-method |
| Aggregate all results meta data in a single dataframe | result_metadata result_metadata,character-method result_metadata,n2kResult-method |
| Select data based on the number of presences per category | select_factor_count_non_zero |
| Select the observations based on the average of a factor | select_factor_threshold |
| Limit the observation to the range in which the species is present | select_observed_range |
| Convert a 'sessionInfo()' to a data.frame of packages | session_package session_package,sessionInfo-method session_package,sessionInfo-methods |
| Create an 'Spde' object | spde |
| The 'spde' class | Spde-class |
| Convert an 'Spde' object to a 'matern' object | spde2matern |
| Convert an 'Spde' object to a mesh object | spde2matern,Spde-method spde2mesh spde2mesh,Spde-method |
| Get the status of an 'n2kModel' | status status,character-method status,character-methods status,n2kAnalysisMetadata-method status,n2kAnalysisMetadata-methods |
| Overwrite the status of an 'n2kAnalysisMetadata' | status<- status<-,n2kAggregate-method status<-,n2kComposite-method status<-,n2kHurdleImputed-method status<-,n2kInla-method status<-,n2kInlaComparison-method status<-,n2kModelImputed-method |
| Store an 'n2kManifest' object | store_manifest store_manifest,ANY,character-method store_manifest,ANY,s3_bucket-method |
| Store a Docker configuration | store_manifest_yaml store_manifest_yaml,ANY,character-method store_manifest_yaml,ANY,s3_bucket-method |
| Store an 'n2kModel' object | store_model store_model,ANY,character-method store_model,ANY,s3_bucket-method |
| Make a union of 'AnalysisVersions' | union |
| Get the validity of objects in files | validObject,character-method validObject,character-methods |
