subtotal, submean, aggregate

Dear All,

I would like to make partial sums (or means or any other function) of
the values in intervals along a sequence (spatial transect) where groups
are defined.

For instance:

habitats<-rep(c("meadow","forest","meadow","pasture"),c(10,5,12,6))
observations<-rpois(length(habitats),2)
transect<-data.frame(observations=observations,habitats=habitats)

aggregate() is not suitable for my purpose because I want a result
respecting the order of the habitats encountered although they may have
the same name (and not pooling each group on each level of the factor
created). For instance, the output of the ideal function
mynicefunction() would be something as:

mynicefunction(transect$observations, by=list(transect$habitats),sum)
meadow     16
forest      9
meadow     21
pasture    17

and not

aggregate(transect$observations,by=list(transect$habitats),sum)
 Group.1  x
1  forest  9
2  meadow 37
3 pasture 17

Did anybody hear about such a function already written in R? If no, any
idea to make it simple and elegant to write?

Cheers,

Patrick Giraudoux

Dear All,

I would like to make partial sums (or means or any other function) of 
the values in intervals along a sequence (spatial transect) where groups 
are defined.

For instance:

habitats<-rep(c("meadow","forest","meadow","pasture"),c(10,5,12,6))
observations<-rpois(length(habitats),2)
transect<-data.frame(observations=observations,habitats=habitats)

aggregate() is not suitable for my purpose because I want a result 
respecting the order of the habitats encountered although they may have 
the same name (and not pooling each group on each level of the factor 
created). For instance, the output of the ideal function 
mynicefunction() would be something as:

mynicefunction(transect$observations, by=list(transect$habitats),sum)
meadow     16
forest      9
meadow     21
pasture    17

and not

aggregate(transect$observations,by=list(transect$habitats),sum)
  Group.1  x
1  forest  9
2  meadow 37
3 pasture 17

Did anybody hear about such a function already written in R? If no, any 
idea to make it simple and elegant to write?

Cheers,

Patrick Giraudoux

Excellent! I was messing with this problem since the early afternoon.
Actually the discrepancy you noticed remaining comes from negative
difference in
diff(as.numeric(transect[,2]))
One can work it around using  abs(diff(as.numeric(transect[,2]))). This
makes:

runno <- cumsum(c(TRUE, abs(diff(as.numeric(transect[,2])))!=0))
aggregate(transect[,1], list(obs = transect[,2], runno = runno), sum)

I did not know about this use of diff, which was the key point... and then
cumsum for polishing. Really great and also elegant (concise). I like it!

Thanks a lot!!!

Cheers,

Patrick


Gabor Grothendieck a ??crit :
Create another variable that gives the run number and aggregate on

habitat and run number removing the run number after

cumsum(c(TRUE, diff(as.numeric(transect[,2])) !=0))

list(obs = transect[,2], runno = runno), sum)[,-2]

same as your example but I think there are some

output.

<patrick.giraudoux at univ-fcomte.fr> wrote:

Dear All,

function) of

where groups

instance:

is not suitable for my purpose because I want a result

of the habitats encountered although they may have

pooling each group on each level of the factor

output of the ideal function

as:

by=list(transect$habitats),sum)

not

Group.1 x

function already written in R? If no, any

to write?

Giraudoux

mailing
list

read the posting guide!

Yes right. Checking some examples, all come out OK.


same as your example but I think there are some errors in your example
output.
Simply the 'errors' observed come simply from the seed in
rpois(length(habitats),2)
It is unlikely it is the same on your and my computer...

Cheers,

Patrick


Gabor Grothendieck a ??crit :
We are just comparing the difference to 0 so it does not matter if its
positive

the runno you calculate with the abs is identical to the one

without the abs:

abs(diff(as.numeric(transect[,2])))!=0))

diff(as.numeric(transect[,2])))!=0)

2/26/06, Patrick Giraudoux
<patrick.giraudoux at univ-fcomte.fr> wrote:

Excellent! I was messing with this problem since the early
afternoon.

negative

using abs(diff(as.numeric(transect[,2]))). This

cumsum(c(TRUE,
abs(diff(as.numeric(transect[,2])))!=0))

transect[,2], runno = runno), sum)

which was the key point... and then

also elegant (concise). I like it!

lot!!!

variable that gives the run number and aggregate on

both the

habitat and run number removing the run number after

aggregating:

cumsum(c(TRUE, diff(as.numeric(transect[,2])) !=0))

aggregate(transect[,1],

list(obs = transect[,2], runno = runno), sum)[,-2]

This does not give the

same as your example but I think there are some

errors in your example

output.

On 2/26/06, Patrick Giraudoux

<patrick.giraudoux at univ-fcomte.fr> wrote:

Dear All,

I would like to make partial sums (or means or any other

function) of

the values in intervals along a sequence (spatial transect)

where groups

are defined.

instance:

habitats<-rep(c("meadow","forest","meadow","pasture"),c(10,5,12,6))

is not suitable for my purpose because I want a result

respecting the order

of the habitats encountered although they may have

the same name (and not

pooling each group on each level of the factor

created). For instance, the

output of the ideal function

mynicefunction() would be something

as:

mynicefunction(transect$observations,

by=list(transect$habitats),sum)

meadow 16

not

aggregate(transect$observations,by=list(transect$habitats),sum)
Group.1 x

1 forest 9

function already written in R? If no, any

idea to make it simple and elegant

to write?

Cheers,

Giraudoux

mailing

read the posting
guide!