Table Export

In summata: Publication-Ready Summary Tables and Forest Plots

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  message = FALSE,
  warning = FALSE,
  eval = FALSE
)
old_opts <- options(width = 180)

Publication requires tables in specific formats: PDF for static outputs, Word documents for collaborative drafting, LaTeX for manuscript preparation, HTML for web supplements, PowerPoint for presentations, and RTF for broad compatability. The summata package provides export functions for each format, with consistent parameters across formats and format-specific options where needed.

| Function | Format | Dependencies | |:---------|:-------|:-------------| | data.table::fwrite() | CSV / TSV | data.table | | table2pdf() | PDF | xtable, LaTeX distribution | | table2docx() | Microsoft Word (.docx) | flextable, officer | | table2html() | HTML | xtable | | table2pptx() | PowerPoint (.pptx) | flextable, officer | | table2tex() | LaTeX source (.tex) | xtable | | table2rtf() | Rich Text Format (.rtf) | flextable | | autotable() | Auto-detect from extension | Varies |

For delimited text formats (CSV, TSV), tables can be written directly with data.table::fwrite() since all summata output tables are data.table objects. For formatted document output, these functions follow a standard syntax when called:

result <- autotable(data, "output.pdf", ...)

where data is the dataset, and "output.pdf" is the name of the destination file. This vignette demonstrates the various capabilities of these functions using the included sample dataset.

---

Preliminaries

The examples in this vignette create sample tables using summata functions:

library(summata)

data(clintrial)
data(clintrial_labels)

# Create sample tables for export
table1 <- desctable(
  data = clintrial,
  by = "treatment",
  variables = c("age", "sex", "bmi", "smoking", "stage", "ecog"),
  labels = clintrial_labels
)

table2 <- fullfit(
  data = clintrial,
  outcome = "surgery",
  predictors = c("age", "sex", "stage", "treatment", "ecog"),
  model_type = "glm",
  labels = clintrial_labels
)

table3 <- fullfit(
  data = clintrial,
  outcome = "Surv(os_months, os_status)",
  predictors = c("age", "sex", "stage", "treatment", "ecog"),
  model_type = "coxph",
  labels = clintrial_labels
)

table4 <- compfit(
  data = clintrial,
  outcome = "surgery",
  model_list = list(
    "Demographics" = c("age", "sex"),
    "Clinical" = c("age", "sex", "stage", "ecog"),
    "Full" = c("age", "sex", "stage", "ecog", "treatment")
  ),
  model_type = "glm"
)

---

CSV / TSV Export

All summata output tables are data.table objects, so they can be written to delimited text files directly with data.table::fwrite(). This is the simplest export path and requires no additional dependencies beyond data.table, which summata already imports.

Example 1: CSV Export

data.table::fwrite(table1, file.path(tempdir(), "Table1.csv"))

Example 2: TSV Export

Specify a tab delimiter for TSV output:

data.table::fwrite(table1, file.path(tempdir(), "Table1.tsv"), sep = "\t")

Example 3: Semicolon-Delimited (European Locale)

Use a semicolon delimiter for compatibility with locales where the comma is the decimal separator:

data.table::fwrite(table1, file.path(tempdir(), "Table1.csv"), sep = ";")

CSV and TSV files are useful for archiving raw table output, importing into spreadsheet software, or downstream processing in other statistical environments. For formatted, publication-ready output, use the export functions described in the sections that follow.

---

PDF Export

The table2pdf() function creates PDF documents using LaTeX typesetting via the xtable package. A LaTeX distribution (TinyTeX, TeX Live, MiKTeX, or MacTeX) is required.

Example 4: Basic Export

The simplest usage requires only a table and filename:

table2pdf(
  table = table1,
  file = file.path(tempdir(), "Table1.pdf")
)

Example 5: With Caption

Add a caption using the caption parameter:

table2pdf(
  table = table1,
  file = file.path(tempdir(), "Table1.pdf"),
  caption = "Table 1. Baseline Characteristics by Group"
)

Example 6: With Formatting Options

Multiple formatting options can be combined:

table2pdf(
  table = table2,
  file = file.path(tempdir(), "Table2.pdf"),
  caption = "Table 2. Regression Analysis",
  font_size = 8,
  bold_significant = TRUE,
  p_threshold = 0.05,
  indent_groups = TRUE,
  variable_padding = TRUE,
  zebra_stripes = TRUE
)

Example 7: Page Layout

Control page size and orientation:

table2pdf(
  table = table2,
  file = file.path(tempdir(), "Table2_Landscape.pdf"),
  caption = "Table 2. Regression Results",
  paper = "letter",
  orientation = "landscape"
)

Example 8: Custom Margins

Adjust page margins (in inches):

table2pdf(
  table = table2,
  file = file.path(tempdir(), "Table2_Margins.pdf"),
  margins = c(0.5, 0.5, 0.5, 0.5)  # top, right, bottom, left
)

Example 9: Fit to Page Width

Scale tables to fit the page width:

table2pdf(
  table = table2,
  file = file.path(tempdir(), "Table2_Fitted.pdf"),
  fit_to_page = TRUE
)

Example 10: Standalone Table

Standalone settings are useful for embedding tables in larger documents:

table2pdf(
  table = table2,
  file = file.path(tempdir(), "Table2_Auto.pdf"),
  paper = "auto"
)

---

Microsoft Word Export

The table2docx() function creates editable Word documents using the flextable and officer packages.

Example 11: Basic Export

The simplest usage requires only a table and filename:

table2docx(
  table = table1,
  file = file.path(tempdir(), "Table1.docx")
)

Example 12: With Caption

Add a caption using the caption parameter:

table2docx(
  table = table1,
  file = file.path(tempdir(), "Table1.docx"),
  caption = "Table 1. Baseline Characteristics by Group"
)

Example 13: With Formatting Options

Multiple formatting options can be combined:

table2docx(
  table = table2,
  file = file.path(tempdir(), "Table2.docx"),
  caption = "Table 2. Regression Analysis",
  font_size = 9,
  font_family = "Times New Roman",
  bold_significant = TRUE,
  p_threshold = 0.05,
  indent_groups = TRUE,
  zebra_stripes = TRUE
)

Example 14: Page Layout

Control page size and orientation for wide tables:

table2docx(
  table = table2,
  file = file.path(tempdir(), "Table2_Landscape.docx"),
  caption = "Table 2. Regression Results",
  paper = "letter",
  orientation = "landscape"
)

Example 15: Dark Header Style

Use a dark header background for visual emphasis:

table2docx(
  table = table1,
  file = file.path(tempdir(), "Table1_DarkHeader.docx"),
  caption = "Table 1. Baseline Characteristics",
  dark_header = TRUE,
  zebra_stripes = TRUE
)

---

HTML Export

The table2html() function exports tables to HTML file output for web use via the xtable package.

Example 16: Basic Export

The simplest usage requires only a table and filename:

table2html(
  table = table1,
  file = file.path(tempdir(), "Table1.html")
)

Example 17: With Caption

Add a caption using the caption parameter:

table2html(
  table = table1,
  file = file.path(tempdir(), "Table1.html"),
  caption = "Table 1. Baseline Characteristics"
)

Example 18: With Formatting Options

Multiple formatting options can be combined:

table2html(
  table = table2,
  file = file.path(tempdir(), "Table2.html"),
  caption = "Table 2. Regression Analysis",
  bold_significant = TRUE,
  indent_groups = TRUE,
  zebra_stripes = TRUE,
  stripe_color = "#f5f5f5"
)

---

PowerPoint Export

The table2pptx() function creates PowerPoint presentations with tables using the flextable and officer packages.

Example 19: Basic Export

The simplest usage creates a single-slide presentation:

table2pptx(
  table = table1,
  file = file.path(tempdir(), "Table1.pptx")
)

Example 20: With Slide Title

Add a slide title using the slide_title parameter:

table2pptx(
  table = table1,
  file = file.path(tempdir(), "Table1.pptx"),
  slide_title = "Baseline Characteristics"
)

Example 21: With Formatting Options

Multiple formatting options can be combined:

table2pptx(
  table = table2,
  file = file.path(tempdir(), "Table2.pptx"),
  slide_title = "Regression Analysis",
  font_size = 10,
  font_family = "Arial",
  bold_significant = TRUE,
  indent_groups = TRUE,
  zebra_stripes = TRUE
)

Example 22: Custom Template

Use an existing PowerPoint template:

table2pptx(
  table = table1,
  file = file.path(tempdir(), "Table1_Custom.pptx"),
  template = "my_template.pptx",
  layout = "Title and Content",
  master = "Office Theme"
)

---

LaTeX Export

The table2tex() function creates LaTeX source files for inclusion in manuscripts via the xtable package.

Example 23: Basic Export

The simplest usage requires only a table and filename:

table2tex(
  table = table1,
  file = file.path(tempdir(), "Table1.tex")
)

Example 24: With Caption and Label

Add caption and cross-reference label:

table2tex(
  table = table1,
  file = file.path(tempdir(), "Table1.tex"),
  caption = "Baseline Characteristics by Group",
  label = "tab:demographics"
)

Example 25: With Booktabs Styling

Use the booktabs package for professional formatting:

table2tex(
  table = table2,
  file = file.path(tempdir(), "Table2.tex"),
  caption = "Regression Analysis",
  label = "tab:regression",
  booktabs = TRUE,
  bold_significant = TRUE,
  indent_groups = TRUE
)

---

RTF Export

The table2rtf() function creates Rich Text Format files using the flextable and officer packages.

Example 26: Basic Export

The simplest usage requires only a table and filename:

table2rtf(
  table = table1,
  file = file.path(tempdir(), "Table1.rtf")
)

Example 27: With Formatting Options

Multiple formatting options can be combined:

table2rtf(
  table = table2,
  file = file.path(tempdir(), "Table2.rtf"),
  caption = "Table 2. Regression Analysis",
  font_size = 9,
  font_family = "Times New Roman",
  bold_significant = TRUE,
  indent_groups = TRUE,
  zebra_stripes = TRUE
)

Example 28: Page Layout

Control page size and orientation:

table2rtf(
  table = table2,
  file = file.path(tempdir(), "Table2_Landscape.rtf"),
  paper = "letter",
  orientation = "landscape"
)

---

Automatic Format Detection

The autotable() function detects the output format from the file extension, simplifying the export workflow:

autotable(table1, file.path(tempdir(), "Table1.csv"))   # CSV output
autotable(table1, file.path(tempdir(), "Table1.tsv"))   # TSV output
autotable(table1, file.path(tempdir(), "Table1.pdf"))   # PDF output
autotable(table1, file.path(tempdir(), "Table1.docx"))  # DOCX output
autotable(table1, file.path(tempdir(), "Table1.html"))  # HTML output
autotable(table1, file.path(tempdir(), "Table1.pptx"))  # PPTX output
autotable(table1, file.path(tempdir(), "Table1.tex"))   # TeX output
autotable(table1, file.path(tempdir(), "Table1.rtf"))   # RTF output

Format-specific parameters pass through to the underlying function:

autotable(
  table = table2,
  file = file.path(tempdir(), "Table2.pdf"),
  caption = "Table 2. Regression Analysis",
  orientation = "landscape",
  font_size = 8,
  bold_significant = TRUE,
  indent_groups = TRUE,
  zebra_stripes = TRUE
)

---

Common Formatting Parameters

All export functions share common parameters for consistent results:

| Parameter | Description | Default | |:----------|:------------|:--------| | caption | Table caption/title | NULL | | font_size | Base font size (points) | 8–10 | | format_headers | Auto-format column headers | TRUE | | bold_significant | Bold significant p-values | TRUE | | p_threshold | Significance threshold | 0.05 | | indent_groups | Indent factor levels | FALSE | | condense_table | Show essential rows only | FALSE | | condense_quantitative | Condense continuous/survival only (desctable() only) | FALSE | | zebra_stripes | Alternating row shading | FALSE | | dark_header | Dark header background | FALSE |

Condensing Options

The condense_table and condense_quantitative parameters reduce table height:

• condense_table = TRUE: Condenses continuous, survival, and binary categorical variables
• condense_quantitative = TRUE: Condenses only continuous and survival variables (desctable() outputs only)

# Full display
table2docx(table1, file.path(tempdir(), "Table1_Full.docx"))

# Condense all variable types
table2docx(
  table = table1,
  file = file.path(tempdir(), "Table1_Condensed.docx"),
  condense_table = TRUE,
  zebra_stripes = TRUE
)

# Condense only continuous/survival (descriptive tables only)
table2docx(
  table = table1,
  file = file.path(tempdir(), "Table1_CondenseQuant.docx"),
  condense_quantitative = TRUE,
  zebra_stripes = TRUE
)

---

Format-Specific Parameters

PDF

| Parameter | Description | Default | |:----------|:------------|:--------| | margins | Page margins c(top, right, bottom, left) | c(1, 1, 1, 1) | | fit_to_page | Scale table to fit page width | TRUE | | cell_padding | Vertical padding ("none", "normal", "relaxed", "loose") | "normal" | | variable_padding | Add spacing between variables | FALSE | | show_logs | Keep LaTeX log files | FALSE |

Word/RTF/PowerPoint

| Parameter | Description | Default | |:----------|:------------|:--------| | font_family | Font name | Arial | | width | Table width (inches) | NULL | | align | Column alignment vector | NULL | | return_ft | Return flextable object | FALSE |

HTML

| Parameter | Description | Default | |:----------|:------------|:--------| | include_css | Include embedded CSS styling | FALSE | | stripe_color | Zebra stripe color (hex or name) | "#EEEEEE" |

LaTeX

| Parameter | Description | Default | |:----------|:------------|:--------| | booktabs | Use booktabs package styling | FALSE | | label | LaTeX cross-reference label | NULL | | cell_padding | Arraystretch value | "normal" |

PowerPoint (additional)

| Parameter | Description | Default | |:----------|:------------|:--------| | template | Custom PPTX template file | NULL | | layout | Slide layout name | "Title and Content" | | master | Slide master name | "Office Theme" | | left, top | Table position (inches) | 0.5, 1.5 |

---

Best Practices

Format Selection

| Use-Case | Recommended Format | |:---------|:-------------------| | Data archival, further processing | CSV (.csv) or TSV (.tsv) | | Journal submission | PDF (.pdf) or LaTeX (.tex) | | Manuscript drafts, collaboration | Word (.docx) | | Web/R Markdown | HTML (.html) | | Presentations | PowerPoint (.pptx) | | Maximum compatibility | RTF (.rtf) |

Page Layout Guidelines

1. Portrait: Tables with ≤ 6 columns
2. Landscape: Tables with > 6 columns
3. Auto-sizing: Use paper = "auto" for embedding

Consistent Multi-Format Export

Export to multiple formats with consistent formatting:

common_opts <- list(
  caption = "Table 2. Regression Analysis",
  bold_significant = TRUE,
  indent_groups = TRUE,
  zebra_stripes = TRUE
)

formats <- c("csv", "pdf", "docx", "html", "pptx", "rtf", "tex")

for (fmt in formats) {
  autotable(
    table = table2,
    file = file.path(tempdir(), paste0("Table2.", fmt)),
    caption = common_opts$caption,
    bold_significant = common_opts$bold_significant,
    indent_groups = common_opts$indent_groups,
    zebra_stripes = common_opts$zebra_stripes
  )
}

---

Troubleshooting

PDF Compilation Fails

Verify LaTeX installation and consider keeping log files for debugging:

# Check LaTeX installation
Sys.which("pdflatex")

# Install TinyTeX if needed
# tinytex::install_tinytex()

# Keep log files for debugging
table2pdf(table, file.path(tempdir(), "debug.pdf"), show_logs = TRUE)

See Installation and Setup for LaTeX configuration details.

Table Too Wide

Several options address wide tables:

# Use landscape orientation
table2pdf(table, file.path(tempdir(), "wide.pdf"), orientation = "landscape")

# Enable fit-to-page scaling
table2pdf(table, file.path(tempdir(), "wide.pdf"), fit_to_page = TRUE)

# Reduce font size
table2pdf(table, file.path(tempdir(), "wide.pdf"), font_size = 7)

Customizing flextable Output

Get the flextable object for further customization:

ft <- table2docx(table1, file.path(tempdir(), "Table1.docx"), return_ft = TRUE)

library(flextable)
ft <- ft %>%
  bold(i = 1, part = "header") %>%
  color(i = 1, color = "navy", part = "header")

save_as_docx(ft, path = file.path(tempdir(), "Table1_Custom.docx"))

options(old_opts)

---

Further Reading

• Descriptive Tables: desctable() for baseline characteristics
• Regression Modeling: fit(), uniscreen(), and fullfit()
• Model Comparison: compfit() for comparing models
• Forest Plots: Visualization of regression results
• Multivariate Regression: multifit() for multi-outcome analysis
• Advanced Workflows: Interactions and mixed-effects models

summata documentation built on May 7, 2026, 5:07 p.m.