Spde #29

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged

ThierryO merged 50 commits into main from spde

Jan 30, 2025

.Rbuildignore

-Original file line number
+Diff line change
@@ Expand Up / @@ -14,5 +14,6 @@ @@
     ^data-raw$
     ^docs$
     ^man-roxygen$
+    ^organisation.yml$
     ^pkgdown$
     ^wercker\.yml$

.github/workflows/check_on_branch.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,6 @@ on: @@
       push:
         branches-ignore:
           - main
-          - master
           - ghpages
     name: "check package with checklist"
@@ Expand All / @@ -14,11 +13,11 @@ jobs: @@
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          N2KBUCKET: ${{ secrets.N2KBUCKET }}
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          N2KBUCKET: ${{ secrets.N2KBUCKET }}
         permissions:
           contents: read
         steps:
-          - uses: inbo/actions/check_pkg@checklist-0.3.6
+          - uses: inbo/actions/check_pkg@checklist-0.4.1

.github/workflows/check_on_different_r_os.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -21,6 +21,7 @@ jobs: @@
           matrix:
             config:
               - {os: macOS-latest,   r: 'release'}
+              - {os: windows-latest, r: 'release'}
               - {os: ubuntu-22.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
               - {os: ubuntu-22.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
@@ Expand All / @@ -40,7 +41,7 @@ jobs: @@
           - uses: r-lib/actions/setup-r@v2
             with:
               r-version: ${{ matrix.config.r }}
-              extra-repositories: https://inla.r-inla-download.org/R/testing
+              extra-repositories: https://inla.r-inla-download.org/R/stable
           - uses: r-lib/actions/setup-pandoc@v2
@@ Expand Down @@

.github/workflows/check_on_main.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -15,9 +15,9 @@ jobs: @@
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          N2KBUCKET: ${{ secrets.N2KBUCKET }}
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
           AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          N2KBUCKET: ${{ secrets.N2KBUCKET }}
         steps:
-          - uses: inbo/actions/check_pkg@checklist-0.3.6
+          - uses: inbo/actions/check_pkg@checklist-0.4.1

.github/workflows/release.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -10,32 +10,21 @@ on:
  
          - completed

    jobs:

      prepare:

      publish:

        runs-on: ubuntu-latest

        outputs:

          tag: ${{ steps.gettag.outputs.tag }}

          body: ${{ steps.gettag.outputs.body }}

        permissions:

          contents: write

        steps:

          - uses: actions/checkout@v3

          - name: Get tag

            run: |

              git fetch --tags --force

              TAG=$(git tag --contains $(git rev-parse HEAD))

              echo "tag=$TAG" >> "$GITHUB_OUTPUT"

              TAG_BODY=$(git tag --contains $(git rev-parse HEAD) --format='%(contents)')

              TAG_BODY="${TAG_BODY//'%'/'%25'}"

              TAG_BODY="${TAG_BODY//$'\n'/'%0A'}"

              TAG_BODY="${TAG_BODY//$'\r'/'%0D'}"

              echo "body=$TAG_BODY" >> "$GITHUB_OUTPUT"

            id: gettag

      publish:

        runs-on: ubuntu-latest

        permissions:

          contents: write

        needs: prepare

        steps:

              echo "tag=$TAG" >> $GITHUB_ENV

              echo "$TAG_BODY" > body.md

          - uses: ncipollo/release-action@v1

            with:

              name: Release ${{needs.prepare.outputs.tag}}

              tag: ${{needs.prepare.outputs.tag}}

              body: ${{needs.prepare.outputs.body}}

              name: Release ${{ env.tag }}

              tag: ${{ env.tag }}

              bodyFile: body.md

.gitignore

-Original file line number
+Diff line change
@@ Expand Up / @@ -17,7 +17,7 @@ @@
     .Ruserdata
     .httr-oauth
     docs
+    inst/doc
     libs
     output
     renv/library
-    inst/doc

.zenodo.json

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1,9 +1,9 @@
  
    {

      "title": "n2kanalysis: Generic Functions to Analyse Data from the 'Natura 2000' Monitoring",

      "version": "0.3.2",

      "version": "0.4.0",

      "license": "GPL-3.0",

      "upload_type": "software",

      "description": "<p>All generic functions and classes for the analysis for the ‘Natura\n2000’ monitoring. The classes contain all required data and definitions\nto fit the model without the need to access other sources. Potentially\nthey might need access to one or more parent objects. An aggregation\nobject might for example need the result of an imputation object. The\nactual definition of the analysis, using these generic function and\nclasses, is defined in dedictated analysis R packages for every\nmonitoring scheme. For example ‘abvanalysis’ and\n‘watervogelanalysis’.<\/p>",

      "description": "<p>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’.<\/p>",

      "keywords": [

        "analysis, reproducible research, natura 2000, monitoring"

      ],

    @@ -14,11 +14,11 @@
  
          "name": "Onkelinx, Thierry",

          "affiliation": "Research Institute for Nature and Forest (INBO)",

          "orcid": "0000-0001-8804-4216",

          "type": "ContactPerson"

          "type": "contactperson"

        },

        {

          "name": "Research Institute for Nature and Forest (INBO)",

          "type": "RightsHolder"

          "type": "rightsholder"

        }

      ],

      "creators": [

CITATION.cff

-Original file line number
+Diff line change
@@ Expand Up @@
     identifiers:
     - type: doi
       value: 10.5281/zenodo.3576047
-    version: 0.3.2
+    - type: url
+      value: https://inbo.github.io/n2kanalysis/
+    version: 0.4.0

DESCRIPTION

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1,6 +1,6 @@
  
    Package: n2kanalysis

    Title: Generic Functions to Analyse Data from the 'Natura 2000' Monitoring

    Version: 0.3.2

    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)")),

    @@ -16,7 +16,8 @@ Description: All generic functions and classes for the analysis for the
  
        every monitoring scheme. For example 'abvanalysis' and

        'watervogelanalysis'.

    License: GPL-3

    URL: https://doi.org/10.5281/zenodo.3576047

    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)

    @@ -26,22 +27,26 @@ Imports:
  
        digest (>= 0.6.23.2),

        dplyr,

        fs,

        git2rdata (>= 0.5.0),

        MASS,

        methods,

        multimput (>= 0.2.13),

        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: 

    @@ -57,7 +62,7 @@ Config/checklist/keywords: analysis, reproducible research, natura 2000,
  
    Encoding: UTF-8

    Language: en-GB

    Roxygen: list(markdown = TRUE)

    RoxygenNote: 7.3.1

    RoxygenNote: 7.3.2

    Collate: 

        'n2k_parameter_class.R'

        'n2k_anomaly_class.R'

    @@ -71,31 +76,35 @@ Collate:
  
        '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'

        'n2k_aggregate_class.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'

        'n2k_inla_comparison_class.R'

        'fit_model_n2k_inla_comparison.R'

        'n2k_manifest_class.R'

        'fit_model_n2k_manifest.R'

        'n2k_model_imputed_class.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'

    @@ -120,8 +129,12 @@ Collate:
  
        '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'

    @@ -131,6 +144,7 @@ Collate:
  
        'n2k_inla_comparison.R'

        'n2k_manifest.R'

        'n2k_model_imputed.R'

        'n2k_spde.R'

        'parent_status.R'

        'read_manifest.R'

        'read_model.R'

    @@ -146,6 +160,9 @@ Collate:
  
        'select_observed_range.R'

        'session_package.R'

        'sha1.R'

        'spde.R'

        'spde2matern.R'

        'spde2mesh.R'

        'status.R'

        'store_manifest.R'

        'store_manifest_yaml.R'

LICENSE.md

-Original file line number
+Diff line change
@@ -1,4 +1,4 @@
-    ### GNU GENERAL PUBLIC LICENSE
+    # GNU GENERAL PUBLIC LICENSE
     Version 3, 29 June 2007
@@ Expand Down @@

NAMESPACE

-Original file line number
+Diff line change
@@ Expand Up / @@ -5,14 +5,21 @@ S3method(sha1,inla) @@
     S3method(sha1,rawImputed)
     export(display)
     export(fit_every_model)
+    export(get_datafield_id)
     export(get_parents)
     export(inla_inverse)
     export(mark_obsolete_dataset)
+    export(moving_average)
+    export(moving_difference)
+    export(moving_trend)
+    export(order_manifest)
     export(select_factor_count_strictly_positive)
     export(select_factor_threshold)
     export(select_observed_range)
     export(sha1)
+    export(spde)
     export(union)
+    exportClasses(Spde)
     exportClasses(n2kAggregate)
     exportClasses(n2kAnalysisMetadata)
     exportClasses(n2kAnalysisVersion)
@@ Expand All / @@ -28,6 +35,7 @@ exportClasses(n2kModel) @@
     exportClasses(n2kModelImputed)
     exportClasses(n2kParameter)
     exportClasses(n2kResult)
+    exportClasses(n2kSpde)
     exportMethods("parent_status<-")
     exportMethods("status<-")
     exportMethods(combine)
@@ Expand All / @@ -49,6 +57,7 @@ exportMethods(get_scheme_id) @@
     exportMethods(get_seed)
     exportMethods(get_species_group_id)
     exportMethods(get_status_fingerprint)
+    exportMethods(make_a)
     exportMethods(manifest_yaml_to_bash)
     exportMethods(n2k_aggregate)
     exportMethods(n2k_composite)
@@ Expand All / @@ -58,13 +67,16 @@ exportMethods(n2k_inla) @@
     exportMethods(n2k_inla_comparison)
     exportMethods(n2k_manifest)
     exportMethods(n2k_model_imputed)
+    exportMethods(n2k_spde)
     exportMethods(parent_status)
     exportMethods(read_manifest)
     exportMethods(read_model)
     exportMethods(read_result)
     exportMethods(result_estimate)
     exportMethods(result_metadata)
     exportMethods(session_package)
+    exportMethods(spde2matern)
+    exportMethods(spde2mesh)
     exportMethods(status)
     exportMethods(store_manifest)
     exportMethods(store_manifest_yaml)
@@ Expand Down Expand Up / @@ -131,6 +143,10 @@ importFrom(fs,file_delete) @@
     importFrom(fs,file_exists)
     importFrom(fs,path)
     importFrom(fs,path_abs)
+    importFrom(git2rdata,is_git2rmeta)
+    importFrom(git2rdata,update_metadata)
+    importFrom(git2rdata,verify_vc)
+    importFrom(git2rdata,write_vc)
     importFrom(methods,new)
     importFrom(methods,setClass)
     importFrom(methods,setClassUnion)
@@ Expand Down Expand Up / @@ -160,6 +176,7 @@ importFrom(rlang,"!!") @@
     importFrom(rlang,.data)
     importFrom(stats,as.formula)
     importFrom(stats,coef)
+    importFrom(stats,median)
     importFrom(stats,na.fail)
     importFrom(stats,na.omit)
     importFrom(stats,qnorm)
@@ Expand All / @@ -169,6 +186,7 @@ importFrom(stats,terms) @@
     importFrom(tibble,rownames_to_column)
     importFrom(tibble,tibble)
     importFrom(tidyr,pivot_longer)
+    importFrom(tools,R_user_dir)
     importFrom(utils,file_test)
     importFrom(utils,flush.console)
     importFrom(utils,head)
@@ Expand Down @@

NEWS.md

-Original file line number
+Diff line change
@@ -1,3 +1,7 @@
+    # `n2kanalysis` 0.4.0
+    * Handle INLA models with an SPDE element.
     # `n2kanalysis` 0.3.2
     * Make `fit_model()` more efficient.
@@ Expand Down @@

R/extract.R

-Original file line number
+Diff line change
@@ Expand Up / @@ -63,3 +63,17 @@ @@
         extractor(object@Model)
       }
     )
+    #' @rdname extract
+    #' @aliases extract,n2kModelImputed-methods
+    #' @importFrom methods setMethod new
+    #' @include n2k_model_imputed_class.R
+    setMethod(
+      f = "extract",
+      signature = signature(object = "n2kModelImputed"),
+      definition = function(extractor, object, base = NULL, project = NULL) {
+        assert_that(inherits(extractor, "function"))
+        extractor(object)
+      }
+    )

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Spde #29

Uh oh!

Diff view

Diff view

There are no files selected for viewing

Codecov / codecov/patch

Uh oh!

Uh oh!