COMETS 1.3. Minor tweaks to warning messages

[steven-moore]

For batch mode, model age.1, lets replace existing warning message with "We removed one or more dummy variables that were redundant (i.e. perfectly correlated with another variable)."

Also is it possible to specify the variable?

[steven-moore]

For age 2.2., the current message is " Warning: Model Age.2.2 BMI stratified has strata (bmi_grp=4) with less than 15 observations. Model will not be run"

The second sentence here should read instead "Model will not be run for this stratum."

[steven-moore]

Updated to include milestone label

[steven-moore]

The model below: Exposure: Age Outcome: All metabolites Adjustment: multivitamin bmi_grp smk_grp

returns an error message that is likely to be uninformative to user: " argument 'pattern' has length > 1 and only the first element will be used"

[ellatemprosa]

this is actually a bug steve, good catch! i will fix this

[ellatemprosa]

for multiple adjustment vars, it was only taking the first one, i updated the code so that all vars are matched correctly and included adjspec to output to show what adjustments were added to model

[ellatemprosa]

@kailingchen please redeploy

[ellatemprosa]

addressed with this commit https://github.com/CBIIT/R-cometsAnalytics/commit/c35674a744ef6025c5f6d6f9c01a749bbc367b37

[steven-moore]

There are some wordsmithing issues we could fix, but in general I am satisfied with COMETS 1.3 as it stands and think we should move to production.

[steven-moore]

I would like to propose that we change this to a 1.4 milestone.

[ewymathe]

Warning fixed.