Fix filter_linkages example error and drop oldrel-1 from CI

Use .data$ pronoun for NSE bindings in filter_linkages() to fix
R CMD check NOTE. Regenerate docs to sync stale man page (p_value →
p_adjusted). Drop oldrel-1 from CI matrix since ggrepel now requires
R >= 4.5.0.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: jayhesselberth

.github/workflows/R-CMD-check.yaml

@@ -22,7 +22,6 @@ jobs:
         config:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

R/odds-ratios.R

@@ -81,11 +81,15 @@ clean_odds_ratios <- function(data, cap_inf = 2) {
 filter_linkages <- function(data, max_p = 0.01, min_obs = 100, min_lor = 1.0) {
   data |>
     dplyr::filter(
-      p_adjusted < max_p,
-      total_obs >= min_obs,
-      abs(log_odds_ratio) >= min_lor
+      .data$p_adjusted < max_p,
+      .data$total_obs >= min_obs,
+      abs(.data$log_odds_ratio) >= min_lor
     ) |>
-    dplyr::transmute(pos1, pos2, value = log_odds_ratio)
+    dplyr::transmute(
+      pos1 = .data$pos1,
+      pos2 = .data$pos2,
+      value = .data$log_odds_ratio
+    )
 }
 
 #' Aggregate odds ratios to isodecoder level.