diff --git a/OUTPUTS/figures/theoph-pk-exposure_png_metadata.json b/OUTPUTS/figures/theoph-pk-exposure_png_metadata.json index 9a58ff8..c24abdd 100644 --- a/OUTPUTS/figures/theoph-pk-exposure_png_metadata.json +++ b/OUTPUTS/figures/theoph-pk-exposure_png_metadata.json @@ -35,7 +35,6 @@ "cli.version": "3.6.3", "rlang.version": "1.1.4", "fontquiver.version": "0.2.1", - "pak.version": "0.8.0", "splines.version": "4.4.1", "munsell.version": "0.5.1", "withr.version": "3.0.1", @@ -83,16 +82,16 @@ } }, "source_meta": { - "creation_author": "COULD NOT ACCESS GIT", - "latest_author": "COULD NOT ACCESS GIT", + "creation_author": "jacobdum ", + "latest_author": "jacobdum ", "path": "/cluster-data/user-homes/jacob/projects_internal/reportifyr_examples/scripts/01_analysis/analysis.R", - "creation_time": "COULD NOT ACCESS GIT", - "latest_time": "COULD NOT ACCESS GIT" + "creation_time": "2025-01-08 18:30:22", + "latest_time": "2025-01-08 18:30:22" }, "object_meta": { "author": "jacobdum ", "path": "/cluster-data/user-homes/jacob/projects_internal/reportifyr_examples/OUTPUTS/figures/theoph-pk-exposure.png", - "creation_time": "2025-01-08 18:19:55", + "creation_time": "2025-01-15 15:41:53", "file_type": "png", "meta_type": "linear-regression-plot", "hash": "b596d0f1ebed494e600b43d71c71dadd7ed34cdaee9a78ac5d580b3ad5ac242e", diff --git a/OUTPUTS/tables/theoph-pk-parameters_csv_metadata.json b/OUTPUTS/tables/theoph-pk-parameters_csv_metadata.json index 253740c..66eeca0 100644 --- a/OUTPUTS/tables/theoph-pk-parameters_csv_metadata.json +++ b/OUTPUTS/tables/theoph-pk-parameters_csv_metadata.json @@ -25,7 +25,6 @@ "here.version": "1.0.1", "base.version": "4.4.1", "R6.version": "2.5.1", - "pak.version": "0.8.0", "gdtools.version": "0.4.0", "generics.version": "0.1.3", "knitr.version": "1.48", @@ -33,8 +32,8 @@ "methods.version": "4.4.1", "tibble.version": "3.2.1", "rprojroot.version": "2.0.4", - "munsell.version": "0.5.1", "openssl.version": "2.2.2", + "munsell.version": "0.5.1", "pillar.version": "1.9.0", "rlang.version": "1.1.4", "utf8.version": "1.2.4", @@ -71,16 +70,16 @@ } }, "source_meta": { - "creation_author": "COULD NOT ACCESS GIT", - "latest_author": "COULD NOT ACCESS GIT", + "creation_author": "jacobdum ", + "latest_author": "jacobdum ", "path": "/cluster-data/user-homes/jacob/projects_internal/reportifyr_examples/scripts/01_analysis/analysis.R", - "creation_time": "COULD NOT ACCESS GIT", - "latest_time": "COULD NOT ACCESS GIT" + "creation_time": "2025-01-08 18:30:22", + "latest_time": "2025-01-08 18:30:22" }, "object_meta": { "author": "jacobdum ", "path": "/cluster-data/user-homes/jacob/projects_internal/reportifyr_examples/OUTPUTS/tables/theoph-pk-parameters.csv", - "creation_time": "2025-01-08 18:19:53", + "creation_time": "2025-01-15 15:41:51", "file_type": "csv", "meta_type": "parameter-summary", "hash": "40cda63faf15ecb14f7768a3547039db67998d6e746779ad6403ef3bbcc2c116", diff --git a/README.md b/README.md new file mode 100644 index 0000000..7256c03 --- /dev/null +++ b/README.md @@ -0,0 +1,29 @@ +# reportifyr_examples + +This repository contains example scripts showcasing the features of the `reportifyr` +R package and is designed to complement the `reportifyr` pkgdown site and `reportifyr` +analysis repository. + +## Repository Structure + +`OUTPUTS`: Directory containing pre-generated artifacts (tables, figures, and footnotes) +from example script: `01_analysis`. These artifacts are provided for use in other +example scripts, but users are encouraged to generate them independently. Typically, +this directory is created using `reportifyr`'s `initialize_report_project()` function. + +`report`: Directory containing report scripts, along with shell, draft, and final +directories, as well as a `standard_footnotes.yaml` file. Again, this setup is provided +to pre-generate artifacts and inputs for the example scripts but is typically created using +`reportifyr`'s `initialize_report_project()` function. + +`scripts`: Directory containing standalone example scripts. This repository is +structured so users can run each script independently. + +## Getting Started + +To get started, please clone down this repository and navigate to an example script +of your choice. + +At the beginning of each R script, you will find package installation lines. +If your R packages are managed by external enterprise solutions, please disregard +or comment out these lines. diff --git a/report/draft/intermediate_files/template-clean.docx b/report/draft/intermediate_files/template-clean.docx index 847e509..a442c20 100644 Binary files a/report/draft/intermediate_files/template-clean.docx and b/report/draft/intermediate_files/template-clean.docx differ diff --git a/report/draft/intermediate_files/template-tabs.docx b/report/draft/intermediate_files/template-tabs.docx index c945933..8621177 100644 Binary files a/report/draft/intermediate_files/template-tabs.docx and b/report/draft/intermediate_files/template-tabs.docx differ diff --git a/report/draft/intermediate_files/template-tabsfigs.docx b/report/draft/intermediate_files/template-tabsfigs.docx index 07b00e1..39dd1f7 100644 Binary files a/report/draft/intermediate_files/template-tabsfigs.docx and b/report/draft/intermediate_files/template-tabsfigs.docx differ diff --git a/report/draft/template-draft.docx b/report/draft/template-draft.docx index 7c4917c..12933e8 100644 Binary files a/report/draft/template-draft.docx and b/report/draft/template-draft.docx differ diff --git a/report/final/template-final.docx b/report/final/template-final.docx index 46c303a..fc68228 100644 Binary files a/report/final/template-final.docx and b/report/final/template-final.docx differ diff --git a/report/final/template-final_docx_metadata.json b/report/final/template-final_docx_metadata.json index 45d6d88..3c95718 100644 --- a/report/final/template-final_docx_metadata.json +++ b/report/final/template-final_docx_metadata.json @@ -8,95 +8,94 @@ "dplyr.version": "1.1.4", "ggplot2.version": "3.5.1", "reportifyr.version": "0.2.5", - "gtable.version": "0.3.5", - "xfun.version": "0.48", - "processx.version": "3.8.4", + "methods.version": "4.4.1", + "graphics.version": "4.4.1", + "utf8.version": "1.2.4", + "generics.version": "0.1.3", + "fontLiberation.version": "0.1.0", + "xml2.version": "1.3.6", "lattice.version": "0.22.6", - "vctrs.version": "0.6.5", - "tools.version": "4.4.1", - "pak.version": "0.8.0", + "digest.version": "0.6.37", + "magrittr.version": "2.0.3", + "evaluate.version": "1.0.0", + "grid.version": "4.4.1", + "grDevices.version": "4.4.1", + "fastmap.version": "1.2.0", + "Matrix.version": "1.7.0", + "jsonlite.version": "1.8.9", + "rprojroot.version": "2.0.4", + "processx.version": "3.8.4", + "zip.version": "2.3.1", "ps.version": "1.8.0", - "generics.version": "0.1.3", - "tibble.version": "3.2.1", + "mgcv.version": "1.9.1", "fansi.version": "1.0.6", - "pkgconfig.version": "2.0.3", - "methods.version": "4.4.1", - "Matrix.version": "1.7.0", - "data.table.version": "1.16.0", - "assertthat.version": "0.2.1", - "uuid.version": "1.2.1", - "lifecycle.version": "1.0.4", - "compiler.version": "4.4.1", - "farver.version": "2.1.2", - "tictoc.version": "1.2.1", - "credentials.version": "2.0.2", + "scales.version": "1.3.0", + "fontBitstreamVera.version": "0.1.1", "textshaping.version": "0.4.0", - "munsell.version": "0.5.1", + "cli.version": "3.6.3", + "rlang.version": "1.1.4", "fontquiver.version": "0.2.1", - "fontLiberation.version": "0.1.0", - "htmltools.version": "0.5.8.1", - "sys.version": "3.4.3", - "yaml.version": "2.3.10", - "pillar.version": "1.9.0", - "openssl.version": "2.2.2", - "nlme.version": "3.1.164", - "fontBitstreamVera.version": "0.1.1", - "tidyselect.version": "1.2.1", - "zip.version": "2.3.1", - "digest.version": "0.6.37", - "labeling.version": "0.4.3", "splines.version": "4.4.1", - "rprojroot.version": "2.0.4", - "fastmap.version": "1.2.0", - "grid.version": "4.4.1", - "here.version": "1.0.1", - "colorspace.version": "2.1.1", - "cli.version": "3.6.3", - "magrittr.version": "2.0.3", - "grDevices.version": "4.4.1", - "utf8.version": "1.2.4", + "munsell.version": "0.5.1", "withr.version": "3.0.1", - "gdtools.version": "0.4.0", "utils.version": "4.4.1", - "scales.version": "1.3.0", - "rmarkdown.version": "2.28", - "officer.version": "0.6.6", - "askpass.version": "1.2.1", - "datasets.version": "4.4.1", - "ragg.version": "1.3.3", + "yaml.version": "2.3.10", + "gdtools.version": "0.4.0", "stats.version": "4.4.1", - "graphics.version": "4.4.1", - "evaluate.version": "1.0.0", - "knitr.version": "1.48", + "tools.version": "4.4.1", + "officer.version": "0.6.6", + "base.version": "4.4.1", + "uuid.version": "1.2.1", + "colorspace.version": "2.1.1", + "here.version": "1.0.1", + "credentials.version": "2.0.2", + "assertthat.version": "0.2.1", + "vctrs.version": "0.6.5", + "R6.version": "2.5.1", + "lifecycle.version": "1.0.4", + "tictoc.version": "1.2.1", "log4r.version": "0.4.3", - "mgcv.version": "1.9.1", - "rlang.version": "1.1.4", - "gert.version": "2.1.2", - "Rcpp.version": "1.0.13", + "ragg.version": "1.3.3", + "pkgconfig.version": "2.0.3", + "pillar.version": "1.9.0", + "gtable.version": "0.3.5", + "data.table.version": "1.16.0", "glue.version": "1.8.0", - "xml2.version": "1.3.6", + "Rcpp.version": "1.0.13", + "systemfonts.version": "1.1.0", + "gert.version": "2.1.2", + "xfun.version": "0.48", + "tibble.version": "3.2.1", + "tidyselect.version": "1.2.1", + "sys.version": "3.4.3", "rstudioapi.version": "0.16.0", - "base.version": "4.4.1", - "jsonlite.version": "1.8.9", - "R6.version": "2.5.1", - "systemfonts.version": "1.1.0" + "knitr.version": "1.48", + "farver.version": "2.1.2", + "datasets.version": "4.4.1", + "nlme.version": "3.1.164", + "htmltools.version": "0.5.8.1", + "labeling.version": "0.4.3", + "rmarkdown.version": "2.28", + "compiler.version": "4.4.1", + "askpass.version": "1.2.1", + "openssl.version": "2.2.2" } } }, "source_meta": { - "creation_author": "COULD NOT ACCESS GIT", - "latest_author": "COULD NOT ACCESS GIT", + "creation_author": "jacobdum ", + "latest_author": "jacobdum ", "path": "/cluster-data/user-homes/jacob/projects_internal/reportifyr_examples/scripts/07_finalize_document/finalize_document.R", - "creation_time": "COULD NOT ACCESS GIT", - 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