I have a big data which contains 4787 Observations and almost 100 variables. Questionnaire has some nested questions like selected respondents are asked to Answer Q#2 if they have answers Q#1 as YES and Q#8 would be answered by those who answered Q#4 as YES, like that data is shrinking and missing values are increasing. So, how to handle this kind of missing data in R which are systematic missing not the user-missing data.
Firstly, if I am deleting all the observation with NA, it results in losing 75% of the data and losing good data points.
Secondly, Mice package in R is for user-missing data ( situation in which respondent failed to answer the question).
Kindly help in this regard