Do initial conversion to R package #1
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- Add RStudio project file (SPFFinalReport.Rproj) - Add R package structure (DESCRIPTION, R directory, .Rbuildignore, LICENSE) Note that the email currently specified for package maintainer is a placeholder - Add non-standard directories to .Rbuildignore - Add R project-specific entries to .gitignore - Move R scripts from Code/CaseStudy2/ to R/ - For now, remove Code/CaseStudy1/, Code/CaseStudy2/RTests/ and Report/ (some of which to add back later if needed)
- Create one function for each original R script - Strip whitespace off line endings (Note: Causes lines of identical-looking code to appear in a git diff) - Convert 'library()' statements into package dependencies - Remove occurrences of 'setwd()' and 'rm(list = ls())' as these requirements now addressed by converting to package - Where appropriate, parameterise functions with an 'msoa_lim' parameter to limit number of loops within functions (a temp aid to get initial code running)
- Change output locations to allow for comparing current results with historical data during initial testing - Add bare-bones vignette to describe data strategy - Replace occurrences of Data/ with Data_ref/ or Data_act/ as appropriate - Replace occurrences of Output/ with Output_ref/ or Output_act/ as appropriate (where '_ref' is for historical data and '_act' is for data produced by the current code) - Update paths in 4*_CollateResults_*.R to match current code
For 1a_DataPrep_StudyRegion.R: - Qualify occurrences of package functions - Save processed data as separate .rds files to facilitate testing - Derive parent_area_name instead of loading from Data_ref/Raw/Shapefiles/area_hierarchy.csv (which is not currently available) - Implement test to ensure (saved) data produced by running code matches reference data
For 1b_DataPrep_Population.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data Also: - Remove maptools package (as retired in Oct 2023 and does not seem to be used in the code) - Add 'Development' vignette
For 1c_DataPrep_TUS.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
For 1d_DataPrep_PM25_CAMS.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
…part of #42) - Implement system env vars (SPF_RUN_HLDT_1* or SPF_RUN_ALL_HLDT) which specify whether to run 'high-level' data tests - Add config vignette and update other vignettes
For 1e_DataPrep_PM25_EMEP.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
For 1f_DataPrep_PM25_GM.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
For 2_Activities_2021.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
For 3a_Exposures_July_2021.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
For 3b_Exposures_Q1_2021.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
For 4a_CollateResults_July_2021.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
For 4b_CollateResults_Q1_2021.R: - Qualify occurrences of package functions - Save processed data as separate .rds file to facilitate testing - Implement test to ensure (saved) data produced by running code matches reference data
For 5a_PlotResults_July_2021.R: - Qualify occurrences of package functions - Substitute gridExtra::arrangeGrob for deprecated multiplot - Use ggplot2::ggsave to save graphs
For 5b_PlotResults_Q1_2021.R: - Qualify occurrences of package functions - Substitute gridExtra::arrangeGrob for deprecated multiplot - Use ggplot2::ggsave to save graphs Also: - Update man pages - Move test-helpers.R to testthat/helper-run-test-check.R as it should be in the testthat directory
Add option to specify whether to import the openair AURN data or use a cached version
Note: These parameters will provide a mechanism for parameterising a run, though they do not serve any purpose yet.
Add utilities for managing file system paths, e.g. to split a path into its sub-directory components and reconstruct a path from a vector of components.
Setup code: - Create test fixtures - Silence cli output in tests Teardown code: - Ensure cli output is restored after tests
Note: The 'Browse source code' link on the website's front page is currently not being rendered so this is to provide a link for it.
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These commits fulfil #40 and #42, initial conversion to an R package (with automated testing which will facilitate refactoring the code into smaller units). They involve large changes to the original R codebase as there is restructuring required for this task. Note that this is a minimal conversion which does not include the configuration system with support for (inter alia) eliminating hard-coded paths.