Hi,
Some speed comparisons:
df <- data.frame(TreeID=rep(1:6000,each=20), Age=rep(seq(1,20,1),6000))
df$Height <- exp(-0.1 + 0.2*df$Age)
df1<- df
df3<-df
library(data.table)
dt1<- data.table(df)
df$HeightGrowth <- NA
system.time({ #Rui's 2nd function
df2 <- data.matrix(df)
for(i in seq_len(nrow(df2))[-1]){
if(df2[i, "TreeID"] == df2[i - 1, "TreeID"])
df2[i, "HeightGrowth"] <- df2[i, "Height"] - df2[i - 1, "Height"]
}
})
# user system elapsed
# 1.108 0.000 1.109
system.time({for (ir in unique(df$TreeID)) { #Don's first function
in.ir <- df$TreeID == ir
df$HeightGrowth[in.ir] <- c(NA, diff(df$Height[in.ir]))
}})
# user system elapsed
#100.004 0.704 100.903
system.time({df3$delta <- c(NA,diff(df3$Height)) ##Don's 2nd function
df3$delta[df3$delta < 0] <- NA}) #####winner
# user system elapsed
# 0.016 0.000 0.014
system.time(df1$HeightGrowth <- ave(df1$Height, df1$TreeID, FUN= function(vec)
c(NA, diff(vec)))) #David's
#user system elapsed
# 0.136 0.000 0.137
system.time(dt1[,HeightGrowth:=c(NA,diff(Height)),by=TreeID])
# user system elapsed
# 0.076 0.000 0.079
identical(df1,as.data.frame(dt1))
#[1] TRUE
identical(df1,df)
#[1] TRUE
head(df1,2)
# TreeID Age Height HeightGrowth
#1 1 1 1.105171 NA
#2 1 2 1.349859 0.2446879
head(df2,2)
# TreeID Age Height HeightGrowth
#[1,] 1 1 1.105171 NA
#[2,] 1 2 1.349859 0.2446879
A.K.
----- Original Message -----
From: Trevor Walker <trevordaviswal...@gmail.com>
To: r-help@r-project.org
Cc:
Sent: Monday, June 10, 2013 1:28 PM
Subject: [R] Speed up or alternative to 'For' loop
I have a For loop that is quite slow and am wondering if there is a faster
option:
df <- data.frame(TreeID=rep(1:500,each=20), Age=rep(seq(1,20,1),500))
df$Height <- exp(-0.1 + 0.2*df$Age)
df$HeightGrowth <- NA #intialize with NA
for (i in 2:nrow(df))
{if(df$TreeID[i]==df$TreeID[i-1])
{df$HeightGrowth[i] <- df$Height[i]-df$Height[i-1]
}
}
Trevor Walker
Email: trevordaviswal...@gmail.com
[[alternative HTML version deleted]]
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