bcgwcat - Groundwater Chemistry Analysis Tool

Previously known as rems2aquachem, as the scope of this tool has expanded, we have renamed it to better reflect what it does

The goal of bcgwcat is to provide easy access to EMS data as well as tools specific to those working with groundwater through R functions but also through a Shiny user-interface. This tool can help with:

• Downloading EMS data via the rems package
• Calculating charge balances
• Calculating water types
• Converting data to a format for importing into AquaChem
• Providing water quality summaries
• Piperplots and Stiff plots

Quick Start

• Install/Update R and RStudio
• Install pak - install.packages("pak", dependencies = TRUE)
• Install bcgwcat - pak::pkg_install("bcgov/bcgwcat") [Update All if asked]
• Launch the Shiny App - gw_app()

In Detail

1. Install/Update RStudio (if it’s been a while)

2. Install/Update R (if it’s been a while)

3. Open RStudio

4. Install pak In the console type the following and hit enter

   install.packages("pak", dependencies = TRUE)

5. Check that your system is ready Install build tools if prompted

   pkgbuild::check_build_tools()

6. Install bcgwcat In the console type the following and hit enter (be sure to install all updates if prompted!)

   pak::pkg_install("bcgov/bcgwcat")

Troubleshooting

1. Update rems In the console type the following and hit enter

   pak::pkg_install("bcgov/rems")

   Note: If you run into errors during the rems data updates, this might be due to old rems caches.

   Try the following:

   1. Uninstall rems - RStudio, go to the lower right hand window, click on the “Packages” tab, in the search bar, search for “rems”, then click on the “X” in a circle to the right of it’s name.

   2. Remove the rems cache - Delete the cache folders by going to C:\Users\YOUR_USER\AppData\Local (windows) or ~/Library/Application Support (mac) and delete the “rems” folder

   3. Re-install rems pak::pkg_install("bcgov/rems") and then try again

2. Update all packages If you run into errors right at the start, consider updating your packages.

   pak::pkg_install("bcgov/bcgwcat", upgrade = TRUE)

Using bcgwcat

Shiny User-Interface

Type this line into the R console at the prompt (in the screen with >) and hit ‘Enter’.

bcgwcat::gw_app() # Launch the app

See the tutorial for a more in-depth look at how to use the User Interface

Screenshot

R command line

bcgwcat can also be used directly from R.

To extract EMS data, and convert for use in AquaChem… (by default saved as CSV)

library(bcgwcat)
r <- rems_to_aquachem(ems_ids = c("1401030", "1401377", "E292373"))

#> Checking for locally stored historical data...

#> Last download was 5 days ago

#> If you would like to update historical data, run 'rems::download_historic_data()'

#> Checking for locally stored recent data...

#> Fetching data from cache...

#> For consistency EMS charge balances, anion sums, and cation sums have been replaced with recalculated values.
#> See `?charge_balance` for more details.

r

#> # A tibble: 16 × 178
#>    Sample_Date  SampleID    Coord_Lat Project     Coord_Long StationID Watertype
#>    <chr>        <chr>       <chr>     <chr>       <chr>      <chr>     <chr>    
#>  1 ""           ""          °         ""          °          ""        ""       
#>  2 "1987-07-07" "1401030-1" 49.20635  "BACKGROUN… -119.82532 "075"     "Fresh W…
#>  3 "1991-08-07" "1401030-2" 49.20635  "BACKGROUN… -119.82532 "075"     "Fresh W…
#>  4 "1994-06-08" "1401030-3" 49.20635  "BACKGROUN… -119.82532 "075"     "Fresh W…
#>  5 "2001-09-09" "1401030-4" 49.20635  "BACKGROUN… -119.82532 "075"     "Fresh W…
#>  6 "2009-11-11" "1401030-5" 49.20635  "BACKGROUN… -119.82532 "075"     "Fresh W…
#>  7 "2010-08-09" "1401030-6" 49.20635  "BACKGROUN… -119.82532 "075"     "Fresh W…
#>  8 "2016-11-02" "1401030-7" 49.20635  "BACKGROUN… -119.82532 "075"     "Fresh W…
#>  9 "2018-06-14" "1401030-8" 49.20635  "BACKGROUN… -119.82532 "075"     "Ground …
#> 10 "1987-07-07" "1401377-1" 49.175    "BACKGROUN… -119.7353  "203"     "Fresh W…
#> 11 "1989-10-11" "1401377-2" 49.175    "BACKGROUN… -119.7353  "203"     "Fresh W…
#> 12 "1994-03-24" "1401377-3" 49.175    "BACKGROUN… -119.7353  "203"     "Fresh W…
#> 13 "2016-11-02" "1401377-4" 49.175    "BACKGROUN… -119.7353  "203"     "Fresh W…
#> 14 "2020-06-29" "1401377-5" 49.175    "BACKGROUN… -119.7353  "203"     "Ground …
#> 15 "2015-03-06" "E292373-1" 49.364604 "GROUNDWAT… -124.6141… "426"     "Fresh W…
#> 16 "2017-10-11" "E292373-2" 49.364604 "GROUNDWAT… -124.6141… "426"     "Fresh W…
#> # ℹ 171 more variables: Analysis_Date <chr>, shortWatertype <chr>,
#> #   Comment <chr>, Reference <chr>, Quality_control <chr>, Duplicate_ID <chr>,
#> #   Labcode <chr>, Location <chr>, Geology <chr>, X <chr>, Y <chr>,
#> #   Elevation <chr>, Well_Depth <chr>, Screen_Top <chr>, Screen_Mid <chr>,
#> #   Screen_Bottom <chr>, Gradient <chr>, Station_Comment <chr>,
#> #   Sample_Depth <chr>, Temp <chr>, `14C` <chr>, `18O` <chr>, `2H` <chr>,
#> #   Ag_diss <chr>, Ag_tot <chr>, Al_diss <chr>, Al_tot <chr>, As_diss <chr>, …

To create plots…

piper_plot(r, ems_id = "1401030")

stiff_plot(r, ems_id = "1401030")

Vignette/Tutorials

See the bcgwcat website

License

Copyright 2024 Province of British Columbia

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.