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:
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 colortblMicrosoft 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:
Package Installation Failures
Ensure repository access is configured:
For packages requiring system libraries (Linux):
Write Permission Errors
Verify write access to the target directory:
getwd()
file.access(getwd(), mode = 2) # Returns 0 if writable