Following is a response from DHS Research & Data Analysis Director, Tom Pullum:
I just did this with Stata, using code that I will paste below. I hope you can convert to R. The KR file includes all children born in the past five years. It includes 90 children who have died (b5=0), for whom b16 is a dot for Not Applicable. It includes 54 children who are not living with the mother, for whom b16 is 0. All the other children in the KR file merge successfully with the PR file.
use "C:\Users\26216\ICF\Analysis - Shared Resources\Data\DHSdata\TGKR71FL.DTA"
keep v001 v002 b*
tab b16,m
gen hv001=v001
gen hv002=v002
gen hvidx=b16
sort hv001 hv002 hvidx
save e:\DHS\DHS_data\scratch\temp.dta, replace
use "C:\Users\26216\ICF\Analysis - Shared Resources\Data\DHSdata\TGPR71FL.DTA"
keep hv001 hv002 hvidx hv101-hv105
sort hv001 hv002 hvidx
merge hv001 hv002 hvidx using e:\DHS\DHS_data\scratch\temp.dta
tab b16 _merge,m