capybara

About

tldr; If you have a 2-4GB dataset and you need to estimate a (generalized) linear model with a large number of fixed effects, this package is for you. It works with larger datasets as well and facilites computing clustered standard errors.

‘capybara’ is a fast and small footprint software that provides efficient functions for demeaning variables before conducting a GLM estimation. This technique is particularly useful when estimating linear models with multiple group fixed effects. It is a fork of the excellent Alpaca package created and maintained by Dr. Amrei Stammann. The software can estimate Exponential Family models (e.g., Poisson) and Negative Binomial models.

Traditional QR estimation can be unfeasible due to additional memory requirements. The method, which is based on Halperin (1962) vector projections offers important time and memory savings without compromising numerical stability in the estimation process.

The software heavily borrows from Gaure (2013) and Stammann (2018) works on OLS and GLM estimation with large fixed effects implemented in the ‘lfe’ and ‘alpaca’ packages. The differences are that ‘capybara’ does not use C nor Rcpp code, instead it uses cpp11 and cpp11armadillo.

The summary tables borrow from Stata outputs. I have also provided integrations with ‘broom’ to facilitate the inclusion of statistical tables in Quarto/Jupyter notebooks.

If this software is useful to you, please consider donating on Buy Me A Coffee. All donations will be used to continue improving capybara.

Installation

You can install the development version of capybara like so:

remotes::install_github("pachadotdev/capybara")

Examples

See the documentation in progress: https://pacha.dev/capybara.

Design choices

Capybara uses C++ and vectorized R operations to address bottlenecks where possible. Some parts of the code use ‘dplyr’, which allows me to write code that is easier to understand and it works well to performed grouped operations. The intensive computations are done on C++ side. I tried to implement this idea from v0.2 and onwards: “He who gives up code safety for code speed deserves neither.” (Wickham, 2014).

I know some parts of the code are not particularly easy to understand. For example, such as my implementation of Kendall’s Tau (or Kendall’s correlation) with a time complexity of O(n * log(n)) instead of O(n^2). I still did my best to write a straightforward code.

Capybara is full of trade-offs. I have a branch where I used ‘dplyr’ and ‘dtplyr’ to help myself with the ‘data.table’ syntax, otherwise there is no way to use in-place modification of data. Because ‘data.table’ modifies the original data (e.g., it converts ‘data.frame’ and ‘tibble’ structures into ‘data.table’ structures), the main branch uses ‘dplyr’ to avoid side effects.

In my research I use ‘SQL’ because I have over 200 GB of international trade data, where ‘dplyr’ helps a lot because it allows me to query ‘SQL’ directly from R mand just using ‘dplyr’ syntax, something impossible with ‘data.table’, which requires me to go to the ‘SQL’ editor en export my queries in CSV format and then import them in R. The downside is that ‘dplyr’ is slower than ‘data.table’ and uses more memory.

I think with my design choices I accomplished my goal of fitting models in my laptop instead of relying on UofT’s servers.

Future plans

I will add a RESET test.

There are a few tests but these have to be expanded.

Benchmarks

Median time for the different models in the book An Advanced Guide to Trade Policy Analysis.

Memory allocation for the same models

Changing the number of cores

Note that you can edit the Makevars file to change the number of cores that capybara uses, here is an example of how it affects the performance

Testing and debugging

Testing

I use testthat (e.g., devtools::test()) to compare the results with base R. These tests are about the correctness of the results.

Debuging

I run r_valgrind "dev/valgrind-kendall-correlation.r" or the corresponding test from the project’s root in a new terminal (bash) after running devtools::install(). These tests are about memory leaks (e.g., I use repeteated computations and sometimes things such as “pi = 3”).

This works because I previously defined this in .bashrc, to make it work you need to run source ~/.bashrc or reboot your computer.

function r_debug_symbols () {
    # if src/Makevars does not exist, exit
    if [ ! -f src/Makevars ]; then
        echo "File src/Makevars does not exist"
        return 1
    fi

    # if src/Makevars contains a line that says "PKG_CPPFLAGS"
    # but there is no "-UDEBUG -g" on it
    # then add "PKG_CPPFLAGS += -UDEBUG -g" at the end
    if grep -q "PKG_CPPFLAGS" src/Makevars; then
        if ! grep -q "PKG_CPPFLAGS.*-UDEBUG.*-g" src/Makevars; then
            echo "PKG_CPPFLAGS += -UDEBUG -g" >> src/Makevars
        fi
    fi

    # if src/Makevars does not contain a line that reads
    # PKG_CPPFLAGS ...something... -UDEBUG -g ...something...
    # then add PKG_CPPFLAGS = -UDEBUG -g to it
    if ! grep -q "PKG_CPPFLAGS.*-UDEBUG.*-g" src/Makevars; then
        echo "PKG_CPPFLAGS = -UDEBUG -g" >> src/Makevars
    fi
}

function r_valgrind () {
    # if no argument is provided, ask for a file
    if [ -z "$1" ]; then
        read -p "Enter the script to debug: " script
    else
        script=$1
    fi

    # if no output file is provided, use the same filename but ended in txt
    if [ -z "$2" ]; then
        output="${script%.*}.txt"
    else
        output=$2
    fi

    # if the file does not exist, exit
    if [ ! -f "$script" ]; then
        echo "File $script does not exist"
        return 1
    fi

    # if the file does not end in .R/.r, exit
    shopt -s nocasematch
    if [[ "$script" != *.R ]]; then
        echo "File $script does not end in .R or .r"
        return 1
    fi
    shopt -u nocasematch

    # run R in debug mode, but after that we compiled with debug symbols
    # see https://reside-ic.github.io/blog/debugging-memory-errors-with-valgrind-and-gdb/
    # R -d 'valgrind -s --leak-check=full --show-leak-kinds=all --track-origins=yes' -f $script 2>&1 | tee valgrind.txt
    R --vanilla -d 'valgrind -s --track-origins=yes' -f $script 2>&1 | tee $output
}

# create an alias for R
alias r="R"
alias rvalgrind="R --vanilla -d 'valgrind -s --track-origins=yes'"

r_debug_symbols makes everything slower, but makes sure that all compiler optimizations are disabled and then valgrind will point us to the lines that create memory leaks.

r_valgrind will run an R script and use Linux system tools to test for initialized values and all kinds of problems that result in memory leaks.

When you are ready testing, you need to remove -UDEBUG from src/Makevars.

Code of Conduct

Please note that the capybara project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.