[R] calcul of the mean in a period of time

[arun]

HI GG,
I should had checked with multiple t=0 only rows.
Apologies!
Check if this work: (Changed the thread name as the solution applies to that problem)

dat2<- read.csv("dat6.csv",header=TRUE,sep="\t",row.names=1)
str(dat2)
#'data.frame':    3896 obs. of  3 variables:
# $ patient_id: int  2 2 2 2 2 2 2 2 2 2 ...
# $ t         : int  0 1 2 3 4 5 6 7 8 9 ...
# $ basdai    : num  2.83 4.05 3.12 3.12 2.42 ...
 
library(plyr)
 dat2New<-ddply(dat2,.(patient_id),summarize,t=seq(min(t),max(t)))
 res<-join(dat2New,dat2,type="full")


 lst1<-lapply(split(res,res$patient_id),function(x) {x1<-x[x$t!=0,];do.call(rbind,lapply(split(x1,((x1$t-1)%/%3)+1),function(y) {y1<-if(any(y$t==1)) rbind(x[x$t==0,],y) else y; data.frame(patient_id=unique(y1$patient_id),t=head(y1$t,1),basdai=mean(y1$basdai,na.rm=TRUE))}) ) })

dat3<-dat2[unlist(with(dat2,tapply(t,patient_id,FUN=function(x) x==0 & length(x)==1)),use.names=FALSE),]
 head(dat3,3)
#    patient_id t basdai
#143         10 0  5.225
#555         37 0  2.450
#627         42 0  6.950

 lst2<-split(dat3,seq_len(nrow(dat3)))
 lst1[lapply(lst1,length)==0]<-mapply(rbind,lst1[lapply(lst1,length)==0],lst2,SIMPLIFY=FALSE)
res1<-do.call(rbind,lst1)
 row.names(res1)<- 1:nrow(res1)
 res2<- res1[,-2]
res2$period<-with(res2,ave(patient_id,patient_id,FUN=seq_along))
 #res2
#selected rows
res2[c(48:51,189:192,210:215),]
#    patient_id   basdai period
#48           9 3.625000      8
#49          10 5.225000      1 #t=0 only row
#50          11 6.018750      1
#51          11 6.000000      2
#189         36 6.166667      1
#190         37 2.450000      1 #t=0 only row
#191         38 3.100000      1
#192         38 3.575000      2
#210         41 1.918750      1
#211         41 4.025000      2
#212         41 2.975000      3
#213         41 1.725000      4
#214         42 6.950000      1 #t=0 only row
#215         44 4.300000      1

A.K.






________________________________
From: GUANGUAN LUO <guanguanluo at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, May 23, 2013 9:50 AM
Subject: Re: how to calculate the mean in a period of time?



Hello, Arun, sorry to trouble you again,
I tried your method and i found that for patient_id==10 et patient_id==37 ect, the scores are repeated 51 times, I don't understand why this occured.

Thank you so much.

GG