For PDFs generated from Sweave projects with multiple files, for quality checking and proofreading of the following tips are recommended:

Check the Compilation Process: Make sure all the.Rnw files knit properly without any compilation error. Compilers in a single file have a tendency to impact the document as a whole.

Syntax Check Automation: Utilize tools like lintr in R code to identify syntax errors early on and thereby save time while reviewing.

Proofread R Code and Outputs: Read through every block of R code and outputs that they generate (figures, tables, etc.) thoroughly to ensure that they are accurate and properly referenced.

Cross-Referencing Figures and Tables: Make sure cross-references to tables and figures are accurate and refer to the corresponding labels and numbers of the document.

Consistent Formatting: Establish a plain LaTeX template for captions, table format, and headings such that the document is uniform.

Check for Missing Files: Verify all links to external files (e.g., images, data files) are correctly referenced and not missing from the project.

Spell Check and Grammar: Utilize LaTeX-compatible spell check programs or applications such as languageTool to check for spelling and grammar mistakes in text.

Version Control: In case of team work, utilize Git or some other version control package to monitor changes and avoid overwriting one's own files.

Pre-Export Review: Editing the document using an editor like Overleaf or TeXShop is a good practice in advance to find out any layout or formatting issues prior to exporting the final PDF as they might not show up inside RStudio.

Final Read-Through: Either if automated tools have been used or not, always provide a final read-through to detect any last-minute mistake or inconsistencies.

Cross-Device Testing: Make sure the end PDF will look fine on different devices and PDF readers to ensure compatibility.