Why are my dplyr group_by & summarize not working properly? (name-collision with plyr)

I believe you've loaded plyr after dplyr, which is why you are getting an overall summary instead of a grouped summary.

This is what happens with plyr loaded last.

library(dplyr)
library(plyr)
df %>%
      group_by(DRUG,FED) %>%
      summarize(mean=mean(AUC0t, na.rm=TRUE), 
                low = CI90lo(AUC0t), 
                 high= CI90hi(AUC0t),
                 min=min(AUC0t, na.rm=TRUE),
                 max=max(AUC0t,na.rm=TRUE), 
                 sd= sd(AUC0t, na.rm=TRUE))

  mean low high min max sd
1  150 105  195 100 200 50

Now remove plyr and try again and you get the grouped summary.

detach(package:plyr)
df %>%
      group_by(DRUG,FED) %>%
      summarize(mean=mean(AUC0t, na.rm=TRUE), 
                low = CI90lo(AUC0t), 
                 high= CI90hi(AUC0t),
                 min=min(AUC0t, na.rm=TRUE),
                 max=max(AUC0t,na.rm=TRUE), 
                 sd= sd(AUC0t, na.rm=TRUE))

Source: local data frame [4 x 8]
Groups: DRUG

  DRUG FED mean low high min max  sd
1    0   0  150 150  150 150 150 NaN
2    0   1  NaN  NA   NA  NA  NA NaN
3    1   0  100 100  100 100 100 NaN
4    1   1  200 200  200 200 200 NaN

A variant of aosmith's answer that might help some folks out. Direct R to call dplyr's functions directly. Good trick when one package interferes with another.

df %>%
      dplyr::group_by(DRUG,FED) %>%
      dplyr::summarize(mean=mean(AUC0t, na.rm=TRUE), 
                low = CI90lo(AUC0t), 
                 high= CI90hi(AUC0t),
                 min=min(AUC0t, na.rm=TRUE),
                 max=max(AUC0t,na.rm=TRUE), 
                 sd= sd(AUC0t, na.rm=TRUE))

Or you could consider using data.table

library(data.table)
setDT(df)  # set the data frame as data table
df[, list(mean = mean(AUC0t, na.rm=TRUE),
          low = CI90lo(AUC0t), 
          high = CI90hi(AUC0t), 
          min = as.double(min(AUC0t, na.rm=TRUE)),
          max = as.double(max(AUC0t, na.rm=TRUE)), 
          sd = sd(AUC0t, na.rm=TRUE)),
   by=list(DRUG, FED)]

#    DRUG FED mean low high min  max sd
# 1:    1   0  100 100  100 100  100 NA
# 2:    1   1  200 200  200 200  200 NA
# 3:    0   1  NaN  NA   NA Inf -Inf NA
# 4:    0   0  150 150  150 150  150 NA
# Warning messages:
#   1: In min(AUC0t, na.rm = TRUE) :
#   no non-missing arguments to min; returning Inf
# 2: In max(AUC0t, na.rm = TRUE) :
#   no non-missing arguments to max; returning -Inf