Month: December 2014

Creating new data with max values for each subject

We have a data set dat with multiple observations per subject. We want to create a subset of this data such that each subject (with ID giving the unique identifier for the subject) contributes the observation where the variable X takes it’s maximum value for that subject.

R solutions

Hadleyverse solutions

Using the excellent R package dplyr, we can do this using windowing functions included in dplyr. The following solution is available on StackOverflow, by junkka, and gets around the real possibility that multiple observations might have the same maximum value of X by choosing one of them.

library(dplyr)
dat_max <- dat %>% group_by(ID) %>% filter(row_number(X)==n())

To be a bit more explicit, row_number is a wrapper around rank, using the option ties.method=“first”. So you can use the rank function explicitly here as well.

A solution using the plyr package might be

library(plyr)
dat_max <- ddply(dat, .(ID), function(u) u[rank(u$X, ties.method='first')==nrow(u),])

A data.table solution

The data.table package also has great munging capabilities like dplyr. The same StackOverflow thread linked above also provides this solution using data.table, provided by Arun:

dt <- as.data.table(dat)
dt[dt[, .I[which.max(X)], by=ID]$V1]

Using SQL statements via sqldf

The sqldf package allows an easy implementation of using SQL statements on data frame objects. As Ryan mentions in the comments, the possibilities of solving our problem using sqldf is straightforward:

library(sqldf)
bl <- sqldf("select ID, max(X) from dat group by ID")
names(bl)[2] <- 'X'
sqldf('select * from bl LEFT JOIN dat using(ID, X)')

Python solutions

Using pandas

In Python, the excellent pandas package allows us to do similar operations. The following example is from this thread on StackOverflow.

import pandas as pd
df = DataFrame({’Sp’:[‘a’,’b‘,’c’,’d‘,’e’,’f’], ‘Mt’:[‘s1’, ‘s1’, ‘s2’,’s2‘,’s2’,’s3’], ‘Value’:[1,2,3,4,5,6], ‘count’:[3,2,5,10,10,6]})
df.iloc[df.groupby([‘Mt’]).apply(lambda x: x[‘count’].idxmax())]

You could also do (from the same thread)

df.sort(‘count’, ascending=False).groupby(‘Mt’, as_index=False).first()

but it is about 50% slower.

Using pandasql

The package pandasql is a port of sqldf to Python developed by
yhat. Using this package, we can mimic the sqldf solution given above:

from pandasql import sqldf
sqldf('select Sp, Mt, Value, max(count) from df group by Mt', globals())
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