medsci-skills 4.1.0

package/skills/analyze-stats/references/style/theme_publication.R

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+# theme_publication.R
+# Publication-ready ggplot2 theme for medical research figures
+# Standards: Arial 8-10pt, 300 DPI, colorblind-safe (Wong 2011) palette
+#
+# Usage:
+#   source("theme_publication.R")
+#   ggplot(data, aes(x, y)) + geom_point() + theme_publication()
+
+# ── Wong (2011) colorblind-safe palette (8 colors) ──────────────────────────
+WONG_COLORS <- c(
+  "#E69F00",  # orange
+  "#56B4E9",  # sky blue
+  "#009E73",  # bluish green
+  "#F0E442",  # yellow
+  "#0072B2",  # blue
+  "#D55E00",  # vermillion
+  "#CC79A7",  # reddish purple
+  "#000000"   # black
+)
+
+# Primary 2-color pair (high contrast, colorblind-safe)
+WONG_2 <- c("#0072B2", "#D55E00")  # blue + vermillion
+
+# ── Publication theme ────────────────────────────────────────────────────────
+theme_publication <- function(base_size = 9,
+                               base_family = "Arial",
+                               border = TRUE) {
+  require(ggplot2)
+  require(ggthemes)
+
+  t <- theme_foundation(base_size = base_size, base_family = base_family) +
+    theme(
+      # Panel
+      panel.background  = element_rect(fill = "white", colour = NA),
+      panel.grid.major  = element_line(colour = "grey85", linewidth = 0.3),
+      panel.grid.minor  = element_blank(),
+      panel.border      = if (border) element_rect(colour = "black", fill = NA,
+                                                    linewidth = 0.5)
+                          else element_blank(),
+
+      # Axes
+      axis.line         = if (!border) element_line(colour = "black",
+                                                     linewidth = 0.5)
+                          else element_blank(),
+      axis.text         = element_text(size = base_size - 1, colour = "black"),
+      axis.title        = element_text(size = base_size, face = "plain",
+                                       colour = "black"),
+      axis.ticks        = element_line(colour = "black", linewidth = 0.3),
+      axis.ticks.length = unit(2, "pt"),
+
+      # Legend
+      legend.background = element_rect(fill = "white", colour = NA),
+      legend.key        = element_rect(fill = "white", colour = NA),
+      legend.key.size   = unit(0.9, "lines"),
+      legend.text       = element_text(size = base_size - 1),
+      legend.title      = element_text(size = base_size - 1, face = "bold"),
+      legend.margin     = margin(2, 2, 2, 2),
+      legend.position   = "bottom",
+
+      # Strip (facet labels)
+      strip.background  = element_rect(fill = "grey92", colour = "black",
+                                       linewidth = 0.4),
+      strip.text        = element_text(size = base_size - 1, face = "bold"),
+
+      # Plot labels
+      plot.title        = element_text(size = base_size + 1, face = "bold",
+                                       hjust = 0),
+      plot.subtitle     = element_text(size = base_size, colour = "grey30",
+                                       hjust = 0),
+      plot.caption      = element_text(size = base_size - 2, colour = "grey50",
+                                       hjust = 1),
+      plot.margin       = margin(4, 4, 4, 4, "pt"),
+
+      # Complete theme
+      complete = TRUE
+    )
+
+  return(t)
+}
+
+# ── Color scales ─────────────────────────────────────────────────────────────
+scale_colour_wong <- function(...) {
+  scale_colour_manual(values = WONG_COLORS, ...)
+}
+
+scale_fill_wong <- function(...) {
+  scale_fill_manual(values = WONG_COLORS, ...)
+}
+
+# ── Figure dimension helpers ─────────────────────────────────────────────────
+# Single column: 3.5 inches wide
+# Double column: 7.0 inches wide
+# Height: typically 2.5–4 inches
+
+save_figure <- function(plot, filename, width = 7.0, height = 3.5,
+                        dpi = 300, device = c("pdf", "png")) {
+  require(ggplot2)
+
+  device <- match.arg(device, several.ok = TRUE)
+  base_name <- tools::file_path_sans_ext(filename)
+
+  for (dev in device) {
+    out_file <- paste0(base_name, ".", dev)
+    ggsave(out_file, plot = plot, width = width, height = height,
+           dpi = dpi, device = dev, bg = "white")
+    message("Saved: ", out_file)
+  }
+
+  invisible(plot)
+}
+
+# ── Reproducibility helper ───────────────────────────────────────────────────
+print_session_info <- function() {
+  cat("─── Reproducibility Info ───────────────────────────────────────\n")
+  cat("Date:", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "\n")
+  cat("R version:", R.version$version.string, "\n")
+  pkgs <- c("ggplot2", "ggthemes", "dplyr", "tidyr")
+  for (pkg in pkgs) {
+    if (requireNamespace(pkg, quietly = TRUE)) {
+      cat(sprintf("  %-12s %s\n", pkg,
+                  as.character(packageVersion(pkg))))
+    }
+  }
+  cat("────────────────────────────────────────────────────────────────\n")
+}
+
+# ── Example usage (run interactively) ────────────────────────────────────────
+if (FALSE) {
+  library(ggplot2)
+  library(ggthemes)
+
+  # Basic scatter plot with theme
+  p <- ggplot(mtcars, aes(x = wt, y = mpg, colour = factor(cyl))) +
+    geom_point(size = 2) +
+    scale_colour_wong() +
+    labs(title = "Example Plot",
+         x = "Weight (1000 lbs)",
+         y = "Miles per Gallon",
+         colour = "Cylinders") +
+    theme_publication()
+
+  # Save in both formats
+  save_figure(p, "example_figure", width = 7.0, height = 3.5,
+              device = c("pdf", "png"))
+
+  print_session_info()
+}

package/skills/analyze-stats/references/table-standards/journal-profiles/ajr.yaml

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+# AJR — Table Style Profile
+journal: American Journal of Roentgenology
+publisher: ARRS
+style_base: AMA (with AJR-specific overrides)
+
+format:
+  allowed: Word table (editable)
+  rejected: [Excel, image, links]
+  placement: "end of MS Word file, after References"
+
+limits:
+  max_tables: 5
+  word_limit: 4500
+  min_size: "4 rows x 2 columns"
+  max_pages_per_table: 2
+
+lines:
+  vertical: false
+  horizontal: AMA_style
+
+font:
+  size: 12pt
+  spacing: double
+
+title:
+  format: "Table N — Title text"
+  all_columns_must_have_headings: true
+
+footnotes:
+  marker_system: superscript_lowercase_letters  # AMA style
+  abbreviation_list: "ajronline.org/abbreviationlist"
+  note: "Abbreviations on AJR list need no definition"
+
+p_value:
+  case: lowercase  # AJR override: lowercase italic p
+  italic: true
+  symbol: "*p*"
+  leading_zero: false
+  examples: ["*p* = .03", "*p* < .001"]
+
+numbering:
+  sub_parts: false  # Table 1A, 1B forbidden
+  rule: "each table gets independent number"
+
+gtsummary_theme: null  # no built-in theme, use "jama" as base
+
+notes:
+  - "AJR has its own approved abbreviation list"
+  - "Lowercase italic p (differs from Radiology's uppercase P)"
+  - "No 1A/1B sub-numbering — separate tables"
+  - "Minimum 4 rows x 2 columns"

package/skills/analyze-stats/references/table-standards/journal-profiles/european_radiology.yaml

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+# European Radiology — Table Style Profile
+journal: European Radiology
+publisher: Springer Nature
+style_base: Springer house style
+
+format:
+  allowed: Word table (Table object function), separate file
+  rejected: [spreadsheet, image]
+
+limits:
+  max_tables: 5
+  max_figures: 6
+  word_limit: 3000
+
+lines:
+  vertical: false
+  color_shading: false  # no colors/shading in tables
+  emphasis: [superscript, numbers, symbols, bold]
+
+font:
+  size: null
+
+title:
+  format: "Table N Title text"
+  numbering: arabic
+  placement: above
+  legends_placement: "after References, grouped"
+
+footnotes:
+  marker_system: superscript_lowercase_letters
+  significance_markers: asterisks  # * for significance (Springer convention)
+  placement: below_table_body
+
+p_value:
+  case: lowercase
+  italic: false
+  symbol: "p"
+  leading_zero: varies
+  significance_asterisks: true  # * allowed for p<.05
+
+ci_format:
+  separator: varies
+  example: null
+
+data_conventions:
+  no_comma_as_decimal: true  # avoid European decimal comma confusion
+  oversized_tables: "place at end of document if > 1 A4 page"
+
+abbreviations:
+  define_in: [title, first_use, footnote]  # any of these locations
+
+notes:
+  - "No color or shading in tables"
+  - "Abbreviations can be defined in title, first use, OR footnote"
+  - "Comma must not be used as numeric value (decimal confusion)"

package/skills/analyze-stats/references/table-standards/journal-profiles/jama.yaml

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+# JAMA — Table Style Profile
+journal: JAMA
+publisher: AMA (American Medical Association)
+style_base: AMA 11th Edition
+
+format:
+  allowed: Word table (table function)
+  rejected: [Excel, PDF, image]
+
+limits:
+  max_display_items: 5  # tables + figures combined
+  word_limit: null
+
+lines:
+  vertical: false
+  horizontal: minimal  # cell gridlines serve as outlines
+  note: "Do not draw extra lines/rules"
+
+font:
+  size: "10pt or 12pt"
+  shrink: false  # never reduce font to fit
+
+spacing: single
+
+title:
+  format: "**Table N.** Title text"
+  placement: above
+  bold_prefix: true
+  separator: period
+
+footnotes:
+  marker_system: superscript_lowercase_letters
+  assignment_order: top_to_bottom_left_to_right
+  each_on_separate_line: true
+  abbreviation_order: alphabetical  # JAMA prefers alphabetical
+  abbreviation_format: "BMI, body mass index; CI, confidence interval"
+  abbreviation_separator: "; "
+
+p_value:
+  case: uppercase
+  italic: true
+  symbol: "*P*"
+  leading_zero: false
+  examples: ["*P* = .04", "*P* = .003", "*P* < .001"]
+  decimals_above_01: 2
+  decimals_01_to_001: 3
+  floor: "*P* < .001"
+  asterisk_significance: false  # never use *, **, ***
+
+ci_format:
+  separator: "to"
+  brackets: null
+  example: "1.23 (95% CI, 0.89 to 1.70)"
+
+data_conventions:
+  si_units: "Provide conversion factor in footnote"
+  vertical_cell_merge: false  # forbidden
+  percentages: "n (%) with denominator clear"
+  summary_stats: "mean [SD] or median [IQR]"
+
+gtsummary_theme: "jama"
+
+notes:
+  - "Original Investigation: max 5 display items"
+  - "Empty cells must be explained in footnotes"
+  - "Abbreviation: semicolon-separated, alphabetical"

package/skills/analyze-stats/references/table-standards/journal-profiles/lancet.yaml

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+# The Lancet — Table Style Profile
+journal: The Lancet
+publisher: Elsevier
+style_base: Lancet house style (Vancouver-influenced)
+
+format:
+  allowed: Word table (table function), separate Word file
+  rejected: [Excel, PDF, image]
+
+limits:
+  max_display_items: 5  # tables + figures combined (approximate)
+
+lines:
+  vertical: false
+  horizontal: [top, below_header, bottom]  # exactly 3
+
+font:
+  size: null
+
+title:
+  format: "Table N: Title text"
+  placement: above
+  separator: colon  # different from AMA period
+  keep_minimal: true
+
+footnotes:
+  marker_system: symbols
+  symbol_order: ["*", "†", "‡", "§", "¶", "‖", "**", "††"]
+  note: "¶ and ‖ swapped compared to NEJM order"
+
+p_value:
+  case: lowercase
+  italic: false
+  symbol: "p"
+  leading_zero: true  # KEY DIFFERENCE from AMA
+  examples: ["p=0.03", "p=0.0023", "p<0.0001"]
+  significant_figures: 2
+  max_decimals: 4
+  floor: "p<0.0001"
+
+ci_format:
+  separator: "to"
+  example: "1.23 (0.89 to 1.70)"
+
+data_conventions:
+  format_patterns:
+    continuous: "mean (SD) or median (IQR)"
+    categorical: "n (%) — percent sign required"
+    proportion: "n/N (%)"
+  references_in_tables: "numbered per main text citation order"
+
+gtsummary_theme: "lancet"
+
+notes:
+  - "Caption must NOT repeat Methods details"
+  - "Leading zero on p-values (0.05, not .05)"
+  - "Lowercase p, not italic"

package/skills/analyze-stats/references/table-standards/journal-profiles/nejm.yaml

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+# NEJM — Table Style Profile
+journal: New England Journal of Medicine
+publisher: NEJM Group
+style_base: Custom (AMA-influenced)
+
+format:
+  allowed: Word table
+  rejected: [Excel, PDF, image]
+
+limits:
+  max_display_items: 5  # tables + figures combined (4-5)
+  word_limit: 2700
+
+lines:
+  vertical: false
+  horizontal_internal: false  # "Do not use internal horizontal and vertical rules"
+  horizontal: [top, below_header, bottom]
+
+font:
+  size: null
+
+title:
+  format: "Table N. Title text"
+  placement: above
+  separator: period
+
+footnotes:
+  marker_system: symbols
+  symbol_order: ["*", "†", "‡", "§", "‖", "¶", "**", "††"]
+  assignment_order: top_to_bottom_left_to_right
+  explanatory_content: footnotes_not_headings
+
+p_value:
+  case: uppercase
+  italic: true
+  symbol: "*P*"
+  leading_zero: false
+  decimals_above_01: 2
+  decimals_01_to_001: 3
+  floor: "*P* < .001"
+
+ci_format:
+  separator: "to"
+  example: "1.23 (95% CI, 0.89 to 1.70)"
+
+gtsummary_theme: "nejm"
+
+notes:
+  - "Original Article: ~4-5 display items"
+  - "Non-standard abbreviations defined per table"
+  - "Symbol footnotes (not letters) — different from AMA 11th"

package/skills/analyze-stats/references/table-standards/journal-profiles/radiology.yaml

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+# Radiology (RSNA) — Table Style Profile
+journal: Radiology
+publisher: RSNA
+style_base: AMA 11th Edition
+
+format:
+  allowed: Word table (editable)
+  rejected: [Excel, PDF, image]
+
+limits:
+  max_tables: null  # no explicit limit for Original Research
+  max_display_items: null
+  max_rows: 40
+  max_columns: 8
+  max_pages_per_table: 1
+  word_limit: 3000  # Introduction through Discussion
+
+lines:
+  vertical: false
+  horizontal: [top, below_header, bottom]
+  additional_horizontal: sparingly
+
+font:
+  body: null  # not specified
+  size: null
+
+spacing: null
+
+title:
+  format: "**Table N.** Title text"
+  placement: above
+  bold_prefix: true
+  separator: period
+
+footnotes:
+  marker_system: superscript_lowercase_letters  # a, b, c...
+  assignment_order: top_to_bottom_left_to_right
+  abbreviation_order: appearance_in_table  # not alphabetical
+  abbreviation_format: "BMI = body mass index, OR = odds ratio"
+  abbreviation_separator: ", "
+  max_abbreviations_per_manuscript: 10
+
+p_value:
+  case: uppercase
+  italic: true
+  symbol: "*P*"
+  leading_zero: false
+  examples: ["*P* = .03", "*P* < .001"]
+  decimals_above_01: 2
+  decimals_01_to_001: 3
+  floor: "*P* < .001"
+  never_report_p_equals_1: true  # use > .99
+
+ci_format:
+  separator: comma
+  brackets: parentheses
+  example: "(0.82, 0.95)"
+
+data_conventions:
+  parentheses_default: percentage  # unspecified parenthetical data = %
+  decking_max_levels: 3
+
+notes:
+  - "RSNA Scientific Style Guide is authoritative"
+  - "Review articles: max 4 tables"
+  - "Radiology:AI follows same RSNA style"