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Installation and Setup

This document provides instructions for installing the summata package and configuring the dependencies required for complete functionality. The package requires R ≥ 4.2.0 and several additional components for document generation.

Package Installation

From Repository

Install the stable release from CRAN:

install.packages("summata")

Alternatively, the latest development version may be installed from GitHub:

install.packages("remotes")
remotes::install_github("phmcc/summata")

The development version is available from Codeberg:

remotes::install_git("https://codeberg.org/phmcc/summata.git")

Verification

Confirm successful installation by loading the package:

library(summata)
packageVersion("summata")

Dependencies

Required Dependencies

The following packages are installed automatically as dependencies:

Package	Purpose
`data.table`	High-performance data manipulation and core data operations
`survival`	Survival and time-to-event analysis
`ggplot2`	Visualization system for forest plots and graphics
`stats`	Statistical functions and model fitting
`grDevices`	Graphics devices and color palettes

Optional Dependencies

Additional packages extend functionality for specific use-cases:

Package	Purpose	Required For
`lme4`	Linear mixed-effects models	`lmer()`, `glmer()` model types
`coxme`	Mixed-effects Cox models	`coxme()` model type
`xtable`	LaTeX table generation	`table2pdf()`, `table2tex()`, `table2html()`
`flextable`	Office document tables	`table2docx()`, `table2pptx()`, `table2rtf()`
`officer`	Office document creation	`table2docx()`, `table2pptx()`
`knitr`	Dynamic document generation	R Markdown integration, vignettes
`rmarkdown`	R Markdown documents	Vignette rendering
`ragg`	High-quality graphics	Enhanced PNG rendering with better fonts
`systemfonts`	Font management	Font detection for graphics
`tinytex`	R-integrated LaTeX distribution	PDF table export via `table2pdf()`
`MASS`	Statistical methods	Model diagnostics and testing
`MuMIn`	Multi-model inference	Model selection and averaging
`pROC`	ROC curve analysis	Diagnostic performance evaluation
`ResourceSelection`	Goodness-of-fit tests	Hosmer-Lemeshow tests for logistic models
`stringr`	String manipulation	Text processing utilities
`utils`	Utility functions	Data import/export helpers
`withr`	Temporary state changes	Testing and safe state modifications

Install optional dependencies as needed:

# For mixed-effects models
install.packages(c("lme4", "coxme"))

# For table export (all formats)
install.packages(c("xtable", "flextable", "officer", "knitr", "tinytex"))

# For enhanced graphics
install.packages(c("ragg", "systemfonts"))

# For model diagnostics and selection
install.packages(c("MASS", "MuMIn", "pROC", "ResourceSelection"))

Or install all suggested packages at once:

install.packages("summata", dependencies = TRUE)

LaTeX Configuration

PDF and LaTeX export through table2pdf() and table2tex() require a LaTeX distribution.

TinyTeX (Recommended)

TinyTeX provides a lightweight, R-integrated LaTeX distribution:

install.packages("tinytex")
tinytex::install_tinytex()

Verify the installation:

tinytex::is_tinytex()
tinytex::tlmgr_version()

TinyTeX installs required LaTeX packages automatically on first use.

Alternative LaTeX Distributions

Full LaTeX distributions may be installed system-wide:

Distribution	Platform	URL
TeX Live	Cross-platform	https://www.tug.org/texlive/
MiKTeX	Windows	https://miktex.org/
MacTeX	macOS	https://www.tug.org/mactex/

For Debian/Ubuntu systems:

sudo apt install texlive-latex-base texlive-latex-extra texlive-fonts-recommended

Required LaTeX Packages

The export functions utilize the following LaTeX packages:

Category	Packages
Typography	fontenc, inputenc, helvet
Tables	array, booktabs, longtable, colortbl
Layout	geometry, pdflscape, lscape
Graphics	graphicx, xcolor
Specialized	standalone, varwidth, float, caption

With TinyTeX, these packages install automatically. For standard distributions:

tlmgr install fontenc inputenc array booktabs longtable graphicx geometry \
  pdflscape lscape helvet standalone varwidth float caption xcolor colortbl

Microsoft Office Export

Export to Word, PowerPoint, and RTF formats requires:

install.packages(c("flextable", "officer"))

These packages enable creation of .docx, .pptx, and .rtf files that can be opened and edited in Microsoft Office or compatible applications.

Export Verification Procedure

Execute the following to verify complete functionality:

library(summata)

# Create test data
test_data <- data.frame(
  Variable = c("Sample Size", "Mean", "Standard Deviation"),
  Value = c("150", "45.3", "12.1")
)

# Test Word export (requires flextable, officer)
table2docx(test_data, file = file.path(tempdir(), "verification_test.docx"))

# Test PDF export (requires xtable, LaTeX)
table2pdf(test_data, file = file.path(tempdir(), "verification_test.pdf"))

# Clean up
file.remove(
  file.path(tempdir(), "verification_test.docx"),
  file.path(tempdir(), "verification_test.pdf")
)

Successful execution confirms proper configuration of all export-related dependencies.

Troubleshooting

LaTeX Not Found

If PDF generation fails, verify LaTeX accessibility:

Sys.which("pdflatex")

An empty return value indicates LaTeX is not in the system PATH. Solutions include:

Restart the R session after LaTeX installation
Add the LaTeX binary directory to PATH manually
Reinstall TinyTeX: tinytex::reinstall_tinytex()

Missing LaTeX Packages

For TinyTeX, install missing packages directly:

tinytex::tlmgr_install("package_name")

For compilation errors, examine the log file:

table2pdf(test_data, file = file.path(tempdir(), "debug.pdf"), show_logs = TRUE)

Package Installation Failures

Ensure repository access is configured:

options(repos = c(CRAN = "https://cloud.r-project.org"))

For packages requiring system libraries (Linux):

sudo apt install r-base-dev libcurl4-openssl-dev libssl-dev libxml2-dev

Write Permission Errors

Verify write access to the target directory:

getwd()
file.access(getwd(), mode = 2)  # Returns 0 if writable

System Requirements

Component	Requirement
R	≥ 4.2.0
Operating System	Windows, macOS, or Linux
RAM	4 GB minimum; 8 GB recommended
Disk Space	Base package (< 5 MB) TinyTeX (~150 MB) Full LaTeX distribution (2–6 GB)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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