Table Export

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
tablesave()	Any of the below, based on file extension	Varies
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

tablesave() writes any of these formats, choosing one from the file extension. The format-specific functions may also be called directly if preferred. The syntax for all functions follows the same paradigm:

result <- tablesave(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

Delimited text is the simplest export path and requires no dependencies beyond data.table, which summata already imports. Since all summata output tables are data.table objects, data.table::fwrite() may be used directly.

Example 1: CSV Export

Standard CSV export can be performed using data.table::fwrite():

data.table::fwrite(table1, "table1.csv")

Example 2: TSV Export

TSV export can be performed by using data.table::fwrite() with a specified tab delimiter:

data.table::fwrite(table1, "table1.tsv", sep = "\t")

Example 3: Semicolon-Delimited (European Locale)

Like data.table::fwrite(), tablesave() also accepts a custom delimiter:

data.table::fwrite(table1, "table1_semicolon.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 = "table1.pdf"
)

Example 5: With Caption

Add a caption using the caption parameter:

table2pdf(
  table = table1,
  file = "table1_caption.pdf",
  caption = "Table 1. Baseline Characteristics by Group"
)

Example 6: With Formatting Options

Multiple formatting options can be combined:

table2pdf(
  table = table2,
  file = "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 = "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 = "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 = "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 = "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 = "table1.docx"
)

Example 12: With Caption

Add a caption using the caption parameter:

table2docx(
  table = table1,
  file = "table1_caption.docx",
  caption = "Table 1. Baseline Characteristics by Group"
)

Example 13: With Formatting Options

Multiple formatting options can be combined:

table2docx(
  table = table2,
  file = "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 = "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 = "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 = "table1.html"
)

Example 17: With Caption

Add a caption using the caption parameter:

table2html(
  table = table1,
  file = "table1_caption.html",
  caption = "Table 1. Baseline Characteristics"
)

Example 18: With Formatting Options

Multiple formatting options can be combined:

table2html(
  table = table2,
  file = "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 = "table1.pptx"
)

Example 20: With Slide Title

Add a slide title using the slide_title parameter:

table2pptx(
  table = table1,
  file = "table1_slidetitle.pptx",
  slide_title = "Baseline Characteristics"
)

Example 21: With Formatting Options

Multiple formatting options can be combined:

table2pptx(
  table = table2,
  file = "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 = "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 = "table1.tex"
)

Example 24: With Caption and Label

Add caption and cross-reference label:

table2tex(
  table = table1,
  file = "table1_caption.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 = "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 = "table1.rtf"
)

Example 27: With Formatting Options

Multiple formatting options can be combined:

table2rtf(
  table = table2,
  file = "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 = "table2_landscape.rtf",
  paper = "letter",
  orientation = "landscape"
)

---

Saving to Any Format

The tablesave() function writes a table in the format indicated by the file extension, simplifying the export workflow:

tablesave(table1, "table1.csv")             # CSV output
tablesave(table1, "table1.tsv")             # TSV output
tablesave(table1, "table1.ssv", sep = " ")  # SSV output
tablesave(table1, "table1.pdf")             # PDF output
tablesave(table1, "table1.docx")            # DOCX output
tablesave(table1, "table1.html")            # HTML output
tablesave(table1, "table1.pptx")            # PPTX output
tablesave(table1, "table1.tex")             # TeX output
tablesave(table1, "table1.rtf")             # RTF output

Format-specific parameters pass through to the underlying function:

tablesave(
  table = table2,
  file = "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, "table1_full.docx")

# Condense all variable types
table2docx(
  table = table1,
  file = "table1_condensed.docx",
  condense_table = TRUE,
  zebra_stripes = TRUE
)

# Condense only continuous/survival (descriptive tables only)
table2docx(
  table = table1,
  file = "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) {
  tablesave(
    table = table2,
    file = 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, "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, "wide.pdf", orientation = "landscape")

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

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

Customizing flextable Output

Get the flextable object for further customization:

ft <- table2docx(table1, "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 = "table1_custom.docx")

---

Further Reading

• Descriptive Tables: desctable() for baseline characteristics
• Regression Modeling: uniscreen(), fit(), 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