Installation and Setup

In summata: Publication-Ready Summary Tables and Forest Plots

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

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.

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Package Installation

From Repository

Install the stable release from CRAN:

install.packages("summata")

Alternatively, install the stable release directly from GitHub:

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

For experimental builds, 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)

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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

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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.

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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.

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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:

1. Restart the R session after LaTeX installation
2. Add the LaTeX binary directory to PATH manually
3. 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

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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) |

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