Roadmap: Workflow and Design Plan

This document compiles the ideas and their implementation discussed around this project. Here we describe the various steps, list how they are implemented in both the R code/functions as well as in the Shiny App (aq_app()).

Status and outstanding tasks/questions are listed below each item.

Here is a summary with links to the relevant sections

Downloading GWELLS - Complete
Standardize Lithology - Polishing
Defining area of interest - Complete
Fetching elevation data - Complete
Adding elevation data - Complete
Adding spatial data layers - Not implemented
Water flow analysis - Partially complete
Cross-sections - Partially complete
Flagging issues - Partially complete
R package development - Incomplete

Downloading GWELLS

[Code] Functions check for GWELLS data in cache and download as needed. User can use data_update() to download/update local cache. User can load data directly using data_read() (but not necessary as functions will do this automatically).
[App] First tab offers information on state of data in cache and options to download or clear cache

Standardize Lithology

As part of the GWELLS data download, lithology statements are processed into simplified categories
The steps of this process result in several new columns added
- Spelling mistakes are corrected, multiple terms are collapsed (lithology_clean)
- Remaining terms are established as primary, secondary, or tertiary (lith_primary, lith_secondary, lith_tertiary
- These are then categorized into lithology_category
- Special terms are listed in lithology_extra (e.g., “wet”)

Defining area of interest

[Code] User loads a shape file via the sf package (sf::st_read())
[App] User selects shape files or zip with shape files

Fetching elevation data

Sources - Lidar - https://catalogue.data.gov.bc.ca/dataset/lidarbc-open-lidar-data-portal - TRIM DEM - ~~https://catalogue.data.gov.bc.ca/dataset/1-20-000-georeferenced-topographic-base-maps-by-mapsheet~~ - https://catalogue.data.gov.bc.ca/dataset/digital-elevation-model-for-british-columbia-cded-1-250-000 - Custom DEM

Steps - Using area of interest, download relevant DEM data to the cache, load it, and trim it to the area of interest. - [Code] User passes area of interest to dem_region() function - [App] Automatically happens once area of interest is selected

Adding elevation data

Using region of interest, subset full GWELLS data to wells of interest
Join spatially with elevation data
Option to use combination of Lidar and TRIM
[Code] Subset with wells_subset(), add elevation with wells_elev()
- dem is the primary source, dem_extra is the optional secondary source
[App] Automatically happens once area of interest is selected
- toggle whether to use Lidar, TRIM, Lidar with Trim, or TRIM with Lidar

Adding spatial data layers

Bedrock geology: https://catalogue.data.gov.bc.ca/dataset/bedrock-geology
Faults: https://catalogue.data.gov.bc.ca/dataset/geology-faults
Quaternary Mapping: https://catalogue.data.gov.bc.ca/dataset/geology-quaternary-alluvium-and-cover
Aquifers: https://catalogue.data.gov.bc.ca/dataset/ground-water-aquifers
Freshwater Atlas lakes: https://catalogue.data.gov.bc.ca/dataset/freshwater-atlas-lakes
Freshwater Atlas wetlands: https://catalogue.data.gov.bc.ca/dataset/freshwater-atlas-wetlands
Freshwater Atlas streams: https://catalogue.data.gov.bc.ca/dataset/freshwater-atlas-stream-network

Steps

Add option to download spatial data layers (or as needed?)
Add option to export cropped spatial data

Water flow/yield

Extract water flow/yield details from lithology descriptions
Adds four columns: yield, yield units, depth, and depth units
Where there are multiple yields per record, corresponding to flow at multiple depths, extra records are created (currently duplicated)
Add a flow column with a flag (?) - Where ‘fracture’, any ‘wet’ term (e.g., ‘flow’, ‘seepage’, etc.), or ‘aquifer’, in lithology description [Not implemented]
[Code] User formats their data for water flow analysis using the wells_yield() function
[App] The hydrostratigraphy tab shows the data formated for water flow analysis.

Cross-sections

Export data in formats useful for Cross-section analyses
Strater
Voxler
ArcHydro
Leapfrog
[Code] Users can export the data to various formats with wells_export()
[App] The Exports tab previews the data in different formats with the option to save/download zipped copies of the files.

Flagging issues

Common problems with yield or lithology can be flagged (flag columns added)
[Code] flag_XXX columns are added to the data outputs. The flags data set includes a glossary explaining the flags
[App] flag_XXX columns are added to the data outputs. There is a dedicated ‘flags’ tab for exploring flags which includes a copy of the glossary in the flags data set.

R package development

Adding checks (give users informative feedback if they use a function incorrectly)
Adding tests (ensure that lithology categorizations are consistent, and that functions work as expected)
Adding documentation (help users use the app and/or functions)
- Function documentation
- Internal documentation
- pkgdown website