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

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

i have info frame looks this:

#df id drug fed auc0t tmax cmax 1 1 0 100 5 20 2 1 1 200 6 25 3 0 1 na 2 30 4 0 0 150 6 65

ans on. want summarize statistics on auc, tmax , cmax drug drug , fed status fed. utilize dplyr. example: auc:

ci90lo <- function(x) quantile(x, probs=0.05, na.rm=true) ci90hi <- function(x) quantile(x, probs=0.95, na.rm=true) summary <- 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))

however, output not grouped drug , fed. gives 1 line containing statistics of not faceted on drug , fed.

any thought why? , how can create right thing?

i believe you've loaded plyr after dplyr, why getting overall summary instead of grouped summary.

this happens 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 , seek 1 time again , 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 info 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

r plyr dplyr shadowing name-collision