Metrics Books with R application
Econometrics with R: https://www.econometrics-with-r.org/ (free, pdf and follow-along)
Applied Econometrics with R: https://www.amazon.de/Applied-Econometrics-R-Use/dp/0387773169 (up for free here)
General Grad School Metrics
Bruce Hansen's free Econometrics book (I love this): https://www.ssc.wisc.edu/~bhansen/econometrics/Econometrics.pdf
Econometric Analysis, by W. H. Greene (good ugrad to grad text)
General Ugrad Metrics
Other resources I highly recommend:
Econ Replication Wiki (set to software --> R and find tons of models in R): https://replication.uni-goettingen.de/wiki/index.php/R
Macroeconomic Model Database (focuses on Matlab but still useful for replication purposes): https://www.macromodelbase.com/
Edit: more info