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hillarymarler merged 1 commit into from
May 14, 2026
Merged

pkgdown workflow updates #55

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34 changes: 10 additions & 24 deletions .github/workflows/pkgdown.yaml
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Original file line number Diff line number Diff line change
@@ -1,28 +1,20 @@
# 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
name: pkgdown

on:
push:
branches: [develop]
pull_request:
branches: [develop]
#release:
#types: [published]
workflow_dispatch:

name: pkgdown
permissions:
contents: write

jobs:
pkgdown:
runs-on: ubuntu-latest
# Only restrict concurrency for non-PR jobs
concurrency:
group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
permissions:
contents: write
steps:
- uses: actions/checkout@v6
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

Expand All @@ -35,14 +27,8 @@ jobs:
extra-packages: any::pkgdown, local::.
needs: website

- name: Build site
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}

- name: Deploy to GitHub pages 🚀
if: github.event_name != 'pull_request'
uses: JamesIves/github-pages-deploy-action@v4.8.0
with:
clean: false
branch: gh-pages
folder: docs
- name: Build and deploy to gh-pages
run: |
git config --global user.name "github-actions[bot]"
git config --global user.email "github-actions[bot]@users.noreply.github.com"
Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
231 changes: 114 additions & 117 deletions docs/articles/CybertownTraining.html
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107 changes: 41 additions & 66 deletions docs/articles/CybertownTraining.md
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Expand Up @@ -59,18 +59,39 @@ remotes::install_github("USEPA/rExpertQuery", ref = "develop", dependencies = TR

## Downloading GitHub repo USEPA/rExpertQuery@develop

## sf (1.1-0 -> 1.1-1 ) [CRAN]
## cpp11 (0.5.4 -> 0.5.5 ) [CRAN]
## roxygen2 (7.3.3 -> 8.0.0 ) [CRAN]
## terra (1.9-11 -> 1.9-27) [CRAN]
## data.table (1.18.2.1 -> 1.18.4) [CRAN]

## Installing 5 packages: sf, cpp11, roxygen2, terra, data.table

## Installing packages into 'C:/Users/hmarler/AppData/Local/Temp/RtmpcdnLOt/temp_libpath2fa83ceb49fe'
## (as 'lib' is unspecified)

## package 'sf' successfully unpacked and MD5 sums checked
## package 'cpp11' successfully unpacked and MD5 sums checked
## package 'roxygen2' successfully unpacked and MD5 sums checked
## package 'terra' successfully unpacked and MD5 sums checked
## package 'data.table' successfully unpacked and MD5 sums checked
##
## The downloaded binary packages are in
## C:\Users\hmarler\AppData\Local\Temp\RtmpYnTxPW\downloaded_packages
## ── R CMD build ─────────────────────────────────────────────────────────────────
## checking for file 'C:\Users\hmarler\AppData\Local\Temp\RtmpywqNsa\remotes2b947e5159e5\USEPA-rExpertQuery-ce1ba15/DESCRIPTION' ... checking for file 'C:\Users\hmarler\AppData\Local\Temp\RtmpywqNsa\remotes2b947e5159e5\USEPA-rExpertQuery-ce1ba15/DESCRIPTION' ... ✔ checking for file 'C:\Users\hmarler\AppData\Local\Temp\RtmpywqNsa\remotes2b947e5159e5\USEPA-rExpertQuery-ce1ba15/DESCRIPTION' (601ms)
## ─ preparing 'rExpertQuery': (4.7s)
## checking for file 'C:\Users\hmarler\AppData\Local\Temp\RtmpYnTxPW\remotes59643c4c4d50\USEPA-rExpertQuery-96f363b/DESCRIPTION' ... checking for file 'C:\Users\hmarler\AppData\Local\Temp\RtmpYnTxPW\remotes59643c4c4d50\USEPA-rExpertQuery-96f363b/DESCRIPTION' ... ✔ checking for file 'C:\Users\hmarler\AppData\Local\Temp\RtmpYnTxPW\remotes59643c4c4d50\USEPA-rExpertQuery-96f363b/DESCRIPTION' (753ms)
## ─ preparing 'rExpertQuery': (33.7s)
## checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
## ─ checking for LF line-endings in source and make files and shell scripts (430ms)
## ─ checking for LF line-endings in source and make files and shell scripts (653ms)
## ─ checking for empty or unneeded directories
## Omitted 'LazyData' and 'LazyDataCompression' from DESCRIPTION
## ─ building 'rExpertQuery_0.1.0.tar.gz'
## ─ building 'rExpertQuery_0.1.0.tar.gz' (622ms)
##
##

## Installing package into 'C:/Users/hmarler/AppData/Local/Temp/RtmpcdnLOt/temp_libpath2fa83ceb49fe'
## (as 'lib' is unspecified)

``` r
library(rExpertQuery)
```
Expand All @@ -92,66 +113,19 @@ using the code chunk below:
# load additional packages for this vignette
library(datasets)
library(data.table)
```

## Warning: package 'data.table' was built under R version 4.4.3

``` r
library(dplyr)
```

## Warning: package 'dplyr' was built under R version 4.4.3

``` r
library(DT)
```

## Warning: package 'DT' was built under R version 4.4.3

``` r
library(ggplot2)
library(httr)
```

## Warning: package 'httr' was built under R version 4.4.3

``` r
library(leaflet)
```

## Warning: package 'leaflet' was built under R version 4.4.3

``` r
library(maps)
```

## Warning: package 'maps' was built under R version 4.4.3

``` r
library(plotly)
```

## Warning: package 'plotly' was built under R version 4.4.3

``` r
library(sf)
library(usdata)
```

## Warning: package 'usdata' was built under R version 4.4.3

``` r
library(usmap)
```

## Warning: package 'usmap' was built under R version 4.4.3

``` r
library(stringi)
```

## Warning: package 'stringi' was built under R version 4.4.3

As a final setup step, we will turn off scientific notation so that any
catchment id numbers from our queries are displayed correctly.

Expand Down Expand Up @@ -282,7 +256,7 @@ A screenshot of the Expert Query National Downloads web page
assessments.nat <- rExpertQuery::EQ_NationalExtract("assessments")
```

## [1] "EQ_NationalExtract: downloading Assessments Profile (Expert Query National Extract). It was last updated on November 07, 2025 at 08:50 PM EST."
## [1] "EQ_NationalExtract: downloading Assessments Profile (Expert Query National Extract). It was last updated on May 09, 2026 at 12:08 AM EDT."

``` r
# filter for latest assessments
Expand Down Expand Up @@ -452,7 +426,7 @@ A screenshot of the Expert Query National Downloads web page
dplyr::filter(epaIrCategory %in% c("4", "5"))
```

The resulting data frame is large, with 128,919 unique impaired
The resulting data frame is large, with 137,482 unique impaired
waters nationally. Due to its size, we’ll include a random subset of
250 results in a data table to review during the demo. You can view
the full results by viewing the imp.waters df.
Expand Down Expand Up @@ -531,8 +505,8 @@ A screenshot of the Expert Query National Downloads web page
dplyr::distinct()
```

There are 21 with monitoringLocationId data in ATTAINS. Of these
states, 3 also contain monitoringLocationDataLinks. We can create a
There are 22 with monitoringLocationId data in ATTAINS. Of these
states, 4 also contain monitoringLocationDataLinks. We can create a
data table to display this information and apply some conditional
formatting to highlight the states with
monitoringLocationIdentifiers in blue and those with
Expand Down Expand Up @@ -789,7 +763,7 @@ queries ATTAINS Assessment Units data. The default is to only return
)
```

## [1] "EQ_AssessmentUnits: The current query will return 35 rows."
## [1] "EQ_AssessmentUnits: The current query will return 0 rows."

``` r
# create data table
Expand Down Expand Up @@ -1011,7 +985,7 @@ ATTAINS Actions data by a variety of user supplied parameters.
n_act.fy.24 <- dplyr::n_distinct(act.fy.24$actionId)
```

There were 7 unique actions by actionId established in R3 in
There were 6 unique actions by actionId established in R3 in
FY 2024. We can create data table with counts for each actionType.

``` r
Expand Down Expand Up @@ -1053,7 +1027,7 @@ keyword.
)
```

This query yields 17,989 results. As well as providing the actionId
This query yields 16,962 results. As well as providing the actionId
and documentName for all results, *EQ_Actions()* also returns the
column “actionDocumentUrl” containing the URL to link to the
document. Because the query yields so many results, we’ll take a
Expand Down Expand Up @@ -1369,15 +1343,14 @@ value that should be used in queries.
domain.vals <- EQ_DomainValues()
```

## [1] "EQ_DomainValues: getting list of available domain names."
## [1] "EQ_DomainValues: getting list of available domain names. Values in the eq_param column can be used as inputs in EQ_DomainValues."

## EQ_DomainValues: domain list retrieved from ATTAINS web services.

EQ_DomainValues can provide values for the following query
parameters: act_agency, act_status, act_type, ad_param,
assess_basis, assess_methods, assess_types, au_status, cause,
delist_reason, doc_type, file_type, loc_type, org_id, org_name,
param_attain, param_group, param_name, param_state_ir_cat,
param_status, source_scale, source_type, statecode, use_name,
use_support and water_type .
parameters:

.

2. **How many different values for “water_type” can be used in
rExpertQuery functions?**
Expand All @@ -1390,7 +1363,9 @@ value that should be used in queries.
water.types <- rExpertQuery::EQ_DomainValues("water_type")
```

## [1] "EQ_DomainValues: For water_type the values in the name column of the function output are the allowable values for rExpert Query functions."
## [1] "EQ_DomainValues: For water_type the values in the 'name' column of the function output are the allowable values for rExpert Query functions."

## EQ_DomainValues: domain list retrieved from ATTAINS web services.

The printed message informs us that the “name” column contains the
values for use in water_type queries for rExpertQuery functions. For
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