Improve documentation - required time windows

[gowthamrao]

Many users have expressed surprise when they discover that CohortDiagnostics computes characterization for time windows that were not explicitly specified. This issue arises because certain time windows are required, as indicated in the code section: RunDiagnostics.R#L409-L419.

CohortDiagnostics/R/RunDiagnostics.R

Lines 409 to 419 in 03c40ab

	# Adding required temporal windows required in results viewer
	requiredTemporalPairs <-
	list(
	c(-365, 0),
	c(-30, 0),
	c(-365, -31),
	c(-30, -1),
	c(0, 0),
	c(1, 30),
	c(31, 365),
	c(-9999, 9999)

For example, even when the default covariate settings are modified, these required time windows are still computed:

customCovariateSettings <- CohortDiagnostics::getDefaultCovariateSettings()
customCovariateSettings$temporalStartDays <- c(-1095, -30)
customCovariateSettings$temporalEndDays <- c(0, 0)

Originally (and continues to be), CohortDiagnostics was intended for phenotype development and evaluation, and the FeatureExtraction covariate settings were not exposed. Over time, likely due to demand for using CohortDiagnostics as a characterization tool, these settings were made public. However, a design decision to enforce certain time windows was implemented. As a result, users are often surprised by seeing outputs for time windows they did not specify.

It would be beneficial to either improve the documentation to clearly state this behavior or reconsider the design to allow more flexibility in specifying time windows.