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propertee: Prognostic Regression Offsets with Propagation of ERrors, for Treatment Effect Estimation

propertee enables flexible direct adjustment with specification-informed standard errors and optional prior covariance adjustment.

Random trials often utilize units of assignment and blocking in assigning treatment status as a way to simplify implementation. This specification information must be utilized in future analyses. Using propertee, a user can generate a StudySpecification object which will keep track of the specification structure.

spec <- rct_spec(txt ~ unit_of_assignment(teacher) + block(school), data = teacherdata)

(Also supported are observational studies (obs_spec) and regression discontinuity specifications (rdd_spec which requires a forcing() variable as well.)

In order to pass the specification information into the model using the weights= argument, functions ett() and ate() will be used to convert the StudySpecification into a numeric vector with the StudySpecification object as an attribute.

lm(y ~ txt, data = studentdata, weights = ate(spec))

Note that the StudySpecification is created with teacher level data (teacherdata), but the analysis is carried out at the student level (studentdata); the ate() (and its alternative ett()) will expand the weights appropriately.

Optionally, we can also include a covariance adjustment model through the cov_adj() function.

covadjmod <- lm(y ~ x1 + x2 + ..., data = studentdata, subset = !txt)
lm(y ~ txt, studentdata, weights = ett(spec),
   offset = cov_adj(covadjmod, data = studentdata)
)

Contributing

You may use RStudio to develop for propertee, by opening the propertee.Rproj file. We suggest you ensure all required dependencies are installed by running

devtools::install_deps(dependencies = TRUE)

We prefer changes that include unit tests demonstrating the problem or showing how the new feature should be added. The test suite uses the testthat package to write and run tests. (Please ensure you have the latest version of testthat (or at least v0.11.0), as older versions stored the tests in a different directory, and may not test properly.) See the tests/testthat directory for examples. You can run the test suite via Build -> Test Package.

New features should include inline Roxygen documentation. You can generate all .Rd documents from the Roxygen code using Build -> Document, or using Make as describe below.

Finally, you can use Build -> Build and Reload or Build -> Clean and Rebuild to load an updated version of propertee in your current RStudio session. Alternatively, to install the developed version permanently, use Build -> Build Binary Version, followed by

install.packages("../propertee_VERSION.tgz", repo=NULL)

You can revert back to the current CRAN version by

remove.packages("propertee")
install.packages("propertee")

If you prefer not to use RStudio, you can develop using Make.

  • make test: Run the full test suite.
  • make document: Update all documentation from Roxygen inline comments.
  • make interactive: Start up an interactive session with propertee loaded. (make interactive-emacs starts the session inside emacs.)
  • make check: Run R CMD check on the package
  • make build: Build a binary package.
  • make vignette: Builds any vignettes in vignettes/ directory
  • make clean: Removes files built by make vignette, make document or make check. Should not be generally necessary, but can be useful for debugging.

When your change is ready, make a pull request on github.

White space changes

To ease searches of the commit history:

  • Commit white space changes only when they occur on lines with substantive changes.
  • Avoid committing trailing white spaces.

In RStudio, there are options to enable automatically removing white space as the end of lines and trailing whitespaces in the Settings, Code -> Saving.

In emacs, you can remove white spaces at ends of lines with M-x delete-trailing-whitespace. To do this automatically whenever you save, add the following to your init file:

(add-hook 'before-save-hook (lambda ()
                             (delete-trailing-whitespace)))

To remove trailing lines when saving, you can also add this:

(setq delete-trailing-lines t)

Referring to functions

When documentation refers to another function (internal to the package or otherwise), please include the trailing (), as that will help pkgdown provide an appropriate link (see https://pkgdown.r-lib.org/articles/linking.html).

E.g. \code{lm()} or \code{cov_adj()} or \code{lme4::lmer()}.

Vignettes or simulations

Vignettes and simulations should go in the /vignettes/ folder. Anything that should not be built by R check (especially anything that builds very slowly, or introduces dependencies not specified in DESCRIPTION) should go in the /vignettes/not-for-cran. (The not-for-cran folder is in the .Rbuildignore file.)

Note that ALL .Rmd files in /vignettes/ get built during building of the reference site. To exclude a .Rmd file, it needs to start with “_“. E.g. myslowvignette.Rmd -> _myslowvignette.Rmd.