diff --git a/README.md b/README.md index 892900a..dbf8d51 100644 --- a/README.md +++ b/README.md @@ -27,32 +27,6 @@ If step 1 above fails, try the following instead: `conda env create -f environme └── utils.py - various utility functions ``` -## Testing -This project uses [pytest](https://docs.pytest.org/en/latest/). Before you push code, it is generally a good idea to run `pytest` to make sure it hasn't broken anything that is covered by the existing tests, especially if you are pushing a big commit. You can run `pytest -v` for a bit more verbose output. This will just run fast tests that only take a few seconds. You can run the slow tests that involve fully training models by including the `--runslow` flag. You can run the plotting tests by including the `--runplot` flag. - -## Installing whynot_estimators -The regular `whynot` package comes with [3 simple estimators](https://github.com/zykls/whynot/blob/master/whynot/algorithms/causal_suite.py#L47): OLS, propensity score matching, and propensity score weighted OLS. These may be sufficient for your purposes. If not, read further. - -To use more, you must install them in the `whynot_estimators` package. The `whynot_estimators` package should already have been pip installed from environment.yml. To use the additional 4 estimators [here](https://github.com/zykls/whynot/blob/master/whynot/algorithms/causal_suite.py#L53), you must install them as follows: -``` -python -m whynot_estimators install ip_weighting -python -m whynot_estimators install matching -python -m whynot_estimators install causal_forest -python -m whynot_estimators install tmle -``` - -Depending on your operating system, you may have issues with these installs because conda doesn't always play well with r. - -For example, on MacOS, I had trouble installing the `Matching` R package and the `dbarts` R package that is used in the `tmle` R package. I just followed [this answer StackOverflow answer](https://stackoverflow.com/a/55875539) and ran the following r code inside the `gen` conda env to fix the issue: - -```r -(gen) $ r -> Sys.setenv(CONDA_BUILD_SYSROOT="/") -> install.packages("Matching") -> install.packages("tmle") -> install.packages("dbarts") -``` - ## Loading RealCause pre-computed datasets