When you have a constrained set of character string values that are allowed for a function argument, like in method here (https://github.com/shuowencs/SortedEffects/blob/master/R/u.Subpop.R#L44), you can specify them in the function signature as a vector c("ols", "logit", ...) and then use match.arg() to retrieve the default and validate a user-supplied value against that list of allowed values.

That prevents you from having to write code like: https://github.com/shuowencs/SortedEffects/blob/master/R/PEestimate.R#L19

Rather than giving errors that ask for a correct argument value, the errors might be improved by saying what values are allowed (e.g., https://github.com/shuowencs/SortedEffects/blob/master/R/u.Subpop.R#L48 and subsequent lines).

For bootstrap draws, why set a default value that you don't personally recommend? https://github.com/shuowencs/SortedEffects/blob/master/R/u.Subpop.R#L26

Explicitly return the output object: https://github.com/shuowencs/SortedEffects/blob/master/R/u.Subpop.R#L130

And the out object:
https://github.com/shuowencs/SortedEffects/blob/master/R/PEestimate.R#L99

Missing variable definitions for wage2015 data: https://github.com/shuowencs/SortedEffects/blob/master/R/data.R#L33

If plotting functions are meant to be convenient quick-use tools for the interactive user, I would be inclined to set default values to arguments like xlab and ylab so it's clear what is being presented: https://github.com/shuowencs/SortedEffects/blob/master/R/u.Subpop.R#L190

That's done in some places (e.g., https://github.com/shuowencs/SortedEffects/blob/master/R/SPE.R#L223) but it would be good to be consistent across the whole package.

It's generally bad practice to set options() inside functions (https://github.com/shuowencs/SortedEffects/blob/master/R/PEestimate.R#L17). If you do it, you should reset to the previous value.