[R] aggregate syntax for grouped column means

[Jeff Newmiller]

The semantics for na.rm are different for aggregate than for the other options. The former removes any rows that contain an NA prior to performing the computation, the latter methods work column-wise.  You have to decide which is correct for your purposes.
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Sent from my phone. Please excuse my brevity.

Juliet Hannah <juliet.hannah at gmail.com> wrote:

>I am calculating the mean of each column grouped by the variable 'id'.
>I do this using aggregate, data.table, and plyr. My aggregate results
>do not match the other two, and I am trying to figure out what is
>incorrect with my syntax. Any suggestions? Thanks.
>
>Here is the data.
>
>myData <- structure(list(var1 = c(31.59, 32.21, 31.78, 31.34, 31.61,
>31.61,
>30.59, 30.84, 30.98, 30.79, 30.79, 30.94, 31.08, 31.27, 31.11,
>30.42, 30.37, 30.29, 30.06, 30.3, 30.43, 30.61, 30.64, 30.75,
>30.39, 30.1, 30.25, 31.55, 31.96, 31.87, 30.29, 30.15, 30.37,
>29.59, 29.52, 28.96, 29.69, 29.58, 29.52, 30.21, 30.3, 30.25,
>30.23, 30.29, 30.39), var2 = c(33.78, 33.25, NA, 32.05, 32.59,
>NA, 32.24, NA, NA, 32.15, 32.39, NA, 32.4, 31.6, NA, 30.5, 30.66,
>NA, 30.6, 29.95, NA, 31.24, 30.73, NA, 30.51, 30.43, 31.17, 31.44,
>31.17, 31.18, 31.01, 30.98, 31.25, 30.44, 30.47, NA, 30.47, 30.56,
>NA, 30.6, 30.57, NA, 31, 30.8, NA), id = c("0m4", "0m4", "0m4",
>"0m5", "0m5", "0m5", "0m6", "0m6", "0m6", "0m11", "0m11", "0m11",
>"0m12", "0m12", "0m12", "205m1", "205m1", "205m1", "205m4", "205m4",
>"205m4", "205m5", "205m5", "205m5", "205m6", "205m6", "205m6",
>"205m7", "205m7", "205m7", "600m1", "600m1", "600m1", "600m3",
>"600m3", "600m3", "600m4", "600m4", "600m4", "600m5", "600m5",
>"600m5", "600m7", "600m7", "600m7")), .Names = c("var1", "var2",
>"id"), row.names = c(NA, -45L), class = "data.frame")
>
>> head(myData)
>   var1  var2  id
>1 31.59 33.78 0m4
>2 32.21 33.25 0m4
>3 31.78    NA 0m4
>4 31.34 32.05 0m5
>5 31.61 32.59 0m5
>6 31.61    NA 0m5
>
>
>
>results1 <- aggregate(. ~  id ,data=myData,FUN=mean,na.rm=T)
> head(results1,1)
>#    id  var1  var2
># 1 0m11 30.79 32.27
>
>library(data.table)
>mydt <- data.table(myData)
>setkey(mydt,id)
>results2 <- mydt[,lapply(.SD,mean,na.rm=TRUE),by=id]
> head(results2,1)
>#       id  var1  var2
># [1,] 0m11 30.84 32.27
>
>library(plyr)
>results3 <- ddply(myData,.(id),colwise(mean),na.rm=TRUE)
> head(results3,1)
>#    id  var1  var2
># 1 0m11 30.84 32.27
>
>> sessionInfo()
>R version 2.14.0 (2011-10-31)
>Platform: i386-pc-mingw32/i386 (32-bit)
>
>locale:
>[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>[5] LC_TIME=English_United States.1252
>
>attached base packages:
>[1] stats     graphics  grDevices utils     datasets  methods   base
>
>other attached packages:
>[1] plyr_1.6         data.table_1.7.3
>
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>and provide commented, minimal, self-contained, reproducible code.