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Merge branch 'master' of https://github.com/brandmaier/semtree # Conflicts: # DESCRIPTION
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| on: | ||
| workflow_dispatch | ||
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| name: Tests | ||
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| jobs: | ||
| document: | ||
| name: run tests | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| cache-version: 2 | ||
| extra-packages: | | ||
| any::testthat | ||
| any::devtools | ||
| # needs: pr-document | ||
| - name: install package | ||
| run: devtools::install_github("brandmaier/semtree") | ||
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| - name: run test | ||
| run: testthat::test_dir("tests/testthat/") | ||
| shell: Rscript {0} |
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [main, master] | ||
| pull_request: | ||
| branches: [main, master] | ||
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| name: test-coverage | ||
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| jobs: | ||
| test-coverage: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
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| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::covr | ||
| needs: coverage | ||
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| - name: Test coverage | ||
| run: | | ||
| covr::codecov( | ||
| quiet = FALSE, | ||
| clean = FALSE, | ||
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | ||
| ) | ||
| shell: Rscript {0} | ||
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| - name: Show testthat output | ||
| if: always() | ||
| run: | | ||
| ## -------------------------------------------------------------------- | ||
| find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash | ||
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| - name: Upload test results | ||
| if: failure() | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: coverage-test-failures | ||
| path: ${{ runner.temp }}/package |
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| @@ -1,42 +1,41 @@ | ||
| #' Wrapper function for computing the maxLR corrected p value | ||
| #' from strucchange | ||
| #' | ||
| #' | ||
| #' @param maxLR maximum of the LR test statistics | ||
| #' @param q number of free SEM parameters / degrees of freedom | ||
| #' @param covariate covariate under evaluation. This is important to get the level of | ||
| #' measurement from the covariate and the bin size for ordinal and | ||
| #' categorical covariates. | ||
| #' @param from numeric from interval (0, 1) specifying start of trimmed | ||
| #' sample period. With the default | ||
| #' sample period. With the default | ||
| #' from = 0.15 the first and last 15 percent of observations are | ||
| #' trimmed. This is only needed for continuous covariates. | ||
| #' @param to numeric from interval (0, 1) specifying end of trimmed | ||
| #' sample period. By default, to is 1. | ||
| #' @param nrep numeric. Number of replications used for simulating from the asymptotic | ||
| #' @param nrep numeric. Number of replications used for simulating from the asymptotic | ||
| #' distribution (passed to efpFunctional). Only needed for ordinal | ||
| #' covariates. | ||
| #' | ||
| # | ||
| #' @author Manuel Arnold | ||
| #' @return Numeric. p value for maximally selected LR statistic | ||
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| computePval_maxLR <- function(maxLR, q, covariate, from, to, nrep) { | ||
| # Level of measurement | ||
| if (!is.factor(covariate)) { # metric | ||
| pval <- strucchange::supLM(from = from, to = to)$computePval(x = maxLR, nproc = q) | ||
| } else { | ||
| covariate <- sort(covariate) # sort covariate | ||
| covariate <- droplevels(covariate) | ||
| if (is.ordered(covariate)) { # ordinal | ||
| pval <- strucchange::ordL2BB(freq = covariate, nproc = q, | ||
| nrep = nrep)$computePval(x = maxLR, nproc = q) | ||
| } else { # categorical | ||
| pval <- strucchange::catL2BB(covariate)$computePval(x = maxLR, nproc = q) | ||
| } | ||
| computePval_maxLR <- function(maxLR, q, covariate, from, to, nrep) { | ||
| # Level of measurement | ||
| if (!is.factor(covariate)) { # metric | ||
| pval <- strucchange::supLM(from = from, to = to)$computePval(x = maxLR, nproc = q) | ||
| } else { | ||
| covariate <- sort(covariate) # sort covariate | ||
| covariate <- droplevels(covariate) | ||
| if (is.ordered(covariate)) { # ordinal | ||
| pval <- strucchange::ordL2BB( | ||
| freq = covariate, nproc = q, | ||
| nrep = nrep | ||
| )$computePval(x = maxLR, nproc = q) | ||
| } else { # categorical | ||
| pval <- strucchange::catL2BB(covariate)$computePval(x = maxLR, nproc = q) | ||
| } | ||
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| pval | ||
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| } | ||
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| pval | ||
| } |
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