Replace global variable defaults with getOption() pattern

[NewGraphEnvironment]

Problem

Many fpr functions use global variables as default arguments:

fpr_kable <- function(dat, font = font_set, ...) {

This works in RStudio (persistent global env) but fails in scripted/CI contexts like GitHub Actions builds where environment scoping is stricter.

Error example:

Error in `fpr::fpr_kable()`:
! object 'font_set' not found

Proposed Solution

Replace global variable defaults with getOption() pattern:

fpr_kable <- function(dat, font = getOption("fpr.font_set", 11), ...) {

Implementation

1. Audit functions for global variable dependencies
2. Create options list with defaults:

# In zzz.R or similar
.onLoad <- function(libname, pkgname) {
  options(
    fpr.font_set = 11,
    fpr.photo_width = "100%"
    # ... other defaults
  )
}

3. Update function signatures to use getOption()
4. Document available options in package docs

Benefits

• Works in interactive AND scripted contexts
• Users can override via options(fpr.font_set = 14)
• Enables GitHub Actions builds for bookdown reports
• Cleaner, more explicit design

Known Global Variables to Audit

• font_set
• photo_width
• (need full audit)

Related

• Blocks NewGraphEnvironment/mybookdown-template#75 (GitHub Actions builds)
• Part of https://github.com/NewGraphEnvironment/sred-2025-2026/issues/3

[NewGraphEnvironment]

Implementation Guide for Claude

R CMD check output - global variable errors

fpr_appendix_title: no visible binding for global variable 'my_site'
fpr_kable: no visible binding for global variable 'font_set'
fpr_my_bcfishpass: no visible binding for global variable 'bcfishpass'
fpr_my_bcfishpass: no visible binding for global variable 'my_site'
fpr_my_cost_estimate: no visible binding for global variable 'my_site'
fpr_my_cost_estimate: no visible binding for global variable 'cost_est'
fpr_my_cover_sentence: no visible binding for global variable 'my_site'
fpr_my_habitat_cover: no visible binding for global variable 'hab_site'
fpr_my_habitat_cover: no visible binding for global variable 'my_site'
fpr_my_habitat_info: no visible binding for global variable 'hab_site'
fpr_my_habitat_info: no visible binding for global variable 'my_site'
fpr_my_priority_info: no visible binding for global variable 'my_site'
fpr_my_pscis_info: no visible binding for global variable 'my_site'
fpr_my_survey_dist: no visible binding for global variable 'my_site'
fpr_my_wshd: no visible binding for global variable 'my_site'
fpr_my_wshd: no visible binding for global variable 'wshds'
fpr_photo_pull_by_str: no visible binding for global variable 'my_site'
fpr_photo_qa: no visible binding for global variable 'pscis_all'
fpr_photo_qa2: no visible binding for global variable 'pscis_all'

Note: Many other "no visible binding" errors are NSE column references (tidyverse) - those are handled differently with .data$col or utils::globalVariables(). Focus on the function argument defaults above.

Key global variables to convert to getOption():

Variable	Used in	Suggested default
font_set	fpr_kable	11
my_site	many functions	NULL (required)
bcfishpass	fpr_my_bcfishpass	NULL (required)
hab_site	fpr_my_habitat_*	NULL (required)
cost_est	fpr_my_cost_estimate	NULL (required)
wshds	fpr_my_wshd	NULL (required)
pscis_all	fpr_photo_qa*	NULL (required)

Step-by-step implementation

1. Replace default args with getOption():

# Before:
fpr_kable <- function(dat, font = font_set, ...) {

# After:
fpr_kable <- function(dat, font = getOption("fpr.font_set", 11), ...) {

For required variables (no sensible default):

# Before:
fpr_my_pscis_info <- function(dat, site = my_site, ...) {

# After:
fpr_my_pscis_info <- function(dat, site = getOption("fpr.my_site"), ...) {
  if (is.null(site)) stop("site is required. Set options(fpr.my_site = ...) or pass site argument.")

2. Create/update R/zzz.R with defaults:

.onLoad <- function(libname, pkgname) {
  op <- options()
  op.fpr <- list(
    fpr.font_set = 11,
    fpr.my_site = NULL,
    fpr.bcfishpass = NULL,
    fpr.hab_site = NULL,
    fpr.cost_est = NULL,
    fpr.wshds = NULL,
    fpr.pscis_all = NULL
  )
  toset <- !(names(op.fpr) %in% names(op))
  if (any(toset)) options(op.fpr[toset])
  invisible()
}

3. Document options in fpr-package.R or README

Testing the fix

After changes, R CMD check should no longer show "no visible binding" for these variables in function defaults.

Users set options in their scripts:

options(
  fpr.my_site = 123456,
  fpr.bcfishpass = my_bcfishpass_data
)