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The method to count the number of groups in R is to use the function nlevels(). This function returns the number of levels for a factor variable, which represents the number of unique categories or groups in the variable.

To remove groups that contain missing values, one can use the na.rm argument in various functions. For example, if you have a data frame df with a factor variable called group and you want to remove all rows with missing values within each group, you could use the following code:

library(dplyr)

df %>% 
  group_by(group) %>% 
  filter(!any(is.na(.)))

This code groups the data frame df by the group variable using group_by(), and then filters out rows with missing values within each group using filter(). The any() function returns TRUE if there are any missing values within the group, and ! negates this to keep only rows without missing values. The is.na() function checks if a value is missing. The resulting data frame will only contain groups without missing values.