[R] how to calculate the mean in a period of time?
arun
smartpink111 at yahoo.com
Thu May 16 20:38:32 CEST 2013
Hi,
The output you showed is not clear especially the for the scores3,
2 2 2011-09-22 3 65 2.6 0.8 0.8
2 3 2011-10-26 4 34 2.7 0.8 0.8
3 1 2011-07-17 0 NA 2.8 0.5 0.6
In the input data, the scores3 column didn't had 0.8.
This is what I got:
dat1<- read.table(text="
patient_id number responsed_at delais scores1 scores2 scores3
1 1 2010-05-26 NA 2.6 0.5 0.7
1 2 2010-07-07 42 2.5 NA NA
1 3 2010-08-14 38 2.3 NA NA
1 4 2010-10-01 48 2.5 0.7 0.6
1 5 2010-12-01 61 2.5 NA NA
2 1 2011-07-19 NA 2.5 0.8 0.5
2 2 2011-09-22 65 2.6 NA NA
2 3 2011-10-26 34 2.7 NA NA
3 1 2011-07-17 NA 2.8 0.5 0.6
3 2 2011-10-30 103 2.6 NA NA
3 3 2011-12-23 54 2.5 NA NA
",sep="",header=TRUE,stringsAsFactors=FALSE)
dat1$idx<-with(dat1,ifelse(is.na(delais)|delais<45 & delais>20, 1,ifelse(delais<60 & delais>=45,2,ifelse(delais<=90 & delais>=60,3,NA))))
library(zoo)
res<-do.call(rbind,lapply(split(dat1,dat1$patient_id),function(x) {x$idx[as.logical(cumsum(is.na(x$idx)))]<-NA; x1<-x[!is.na(x$idx),]; x1[,6:8]<-na.locf(x1[,6:8]);x2<-x1[rep(seq_len(nrow(x1)),x1$idx),]; x2$delais[duplicated(x2$delais,fromLast=TRUE)]<-0; x2$t<-seq(0,nrow(x2)-1,1);x2}))
row.names(res)<- 1:nrow(res)
res1<- res[,c(1:3,9,4:7)]
res1
# patient_id number responsed_at t delais scores1 scores2 scores3
#1 1 1 2010-05-26 0 NA 2.6 0.5 0.7
#2 1 2 2010-07-07 1 42 2.5 0.5 0.7
#3 1 3 2010-08-14 2 38 2.3 0.5 0.7
#4 1 4 2010-10-01 3 0 2.5 0.7 0.6
#5 1 4 2010-10-01 4 48 2.5 0.7 0.6
#6 1 5 2010-12-01 5 0 2.5 0.7 0.6
#7 1 5 2010-12-01 6 0 2.5 0.7 0.6
#8 1 5 2010-12-01 7 61 2.5 0.7 0.6
#9 2 1 2011-07-19 0 NA 2.5 0.8 0.5
#10 2 2 2011-09-22 1 0 2.6 0.8 0.5
#11 2 2 2011-09-22 2 0 2.6 0.8 0.5
#12 2 2 2011-09-22 3 65 2.6 0.8 0.5
#13 2 3 2011-10-26 4 34 2.7 0.8 0.5
#14 3 1 2011-07-17 0 NA 2.8 0.5 0.6
A.K.
________________________________
From: GUANGUAN LUO <guanguanluo at gmail.com>
To: arun <smartpink111 at yahoo.com>
Sent: Thursday, May 16, 2013 12:05 PM
Subject: Re: how to calculate the mean in a period of time?
Hello, AK,
now i have a problem really complicated for me,
Now my table is like this:
patient_id number responsed_at delais scores1 scores2 scores3
1 1 2010-05-26 NA 2.6 0.5 0.7
1 2 2010-07-07 42 2.5 NA NA
1 3 2010-08-14 38 2.3 NA NA
1 4 2010-10-01 48 2.5 0.7 0.6
1 5 2010-12-01 61 2.5 NA NA
2 1 2011-07-19 NA 2.5 0.8 0.5
2 2 2011-09-22 65 2.6 NA NA
2 3 2011-10-26 34 2.7 NA NA
3 1 2011-07-17 NA 2.8 0.5 0.6
3 2 2011-10-30 103 2.6 NA NA
3 3 2011-12-23 54 2.5 NA NA
explications: delais = the date of "responsed_at" - the date of precedent "responsed_at"
scores1 is measured every month
scores2 and 3 are measured every three months
first thing is : if the 20<delais <45, this count one month of delais
if the 45<=delais <60, this count two month of delais,so add one line with the copy of the precedent line,and change the delais to 0
if the 60 <= delais <=90, this count three month of delais, so add two lines with the copy of the precedent line,and change these two delais to 0
if the delais >90, delete all the following lines
and add a column "t", "t" means the month, "t" is in order
second thing is :
I want to replace NA of scores2 and scores3 with the precedent scores
and finally get a table like this:
patient_id number responsed_at t delais scores1 scores2 scores3
1 1 2010-05-26 0 NA 2.6 0.5 0.7 # scores2 and 3 are mesured every 3
1 2 2010-07-07 1 42 2.5 0.5 0.7 ## months,replace the following with precedent numbers
1 3 2010-08-14 2 38 2.3 0.5 0.7 # copy this line
1 3 2010-08-14 3 0 2.3 0.5 0.7 # add one line here and change delais to 0
1 4 2010-10-01 4 48 2.5 0.7 0.6
1 4 2010-10-01 5 0 2.5 0.7 0.6
1 4 2010-10-01 6 0 2.5 0.7 0.6
1 5 2010-12-01 7 61 2.5 0.7 0.6
2 1 2011-07-19 0 NA 2.5 0.8 0.5
2 1 2011-07-19 1 0 2.5 0.8 0.5
2 1 2011-07-19 2 0 2.5 0.8 0.5
2 2 2011-09-22 3 65 2.6 0.8 0.8
2 3 2011-10-26 4 34 2.7 0.8 0.8
3 1 2011-07-17 0 NA 2.8 0.5 0.6
(3 2 2011-10-30 103 2.6 0.5 0.6)# delete these 2 line
(3 3 2011-12-23 54 2.5 0.5 0.6) ## and delete the following lines of this patient because the delais is 103 which superior to 90
Do you know how can i get this?
Thank you so much
GG
2013/5/9 GUANGUAN LUO <guanguanluo at gmail.com>
Hello,
>Because according to the database, the first time of collecting the data is just for an entry, an inclusion of the patients. What i should focus on is the difference between two month. If i don't include the t0, i think i will lose the information. I don't know if this is pertinent.
>Thank you very much for your help, AK
>
>GG
>
>
>
>2013/5/9 arun <smartpink111 at yahoo.com>
>
>HI GG,
>>I did the code according the calculation shown by you. For example, in the first case, you had scores of (0+1+2+3)/4, which is not 3 months. It is 3+ initial month. After that it is only 3 months that is repeating. So, my code is doing this:
>> 1st group (the scores)
>>(0+1+2+3)/4
>>2nd group( scores)
>>(5+6+7)/3
>>3rd group
>>(8+9+10)/3
>>
>>Here, the months are used only for illustration. I am taking the mean of the scores.
>>
>>So, if you are only doing every 3 months, why do you need to combine the initial scores with the first 3 months? Anyway, I did what you asked for.
>>
>>
>>Regards,
>>Arun
>>
>>
>>________________________________
>>From: GUANGUAN LUO <guanguanluo at gmail.com>
>>To: arun <smartpink111 at yahoo.com>
>>Sent: Thursday, May 9, 2013 4:19 AM
>>
>>Subject: Re: how to calculate the mean in a period of time?
>>
>>
>>
>>Hi,Thank you so much for your help. I have seen your code. It's very complicated. The time 0 is the beginning of collecting all the information.
>>
>>The time 1 is the first month when follow the patients, time 2 is the second month ect. If i want to calculate the means of every 3 month do you think i should do like this?
>>
>>GG
>>
>>2013/5/7 arun <smartpink111 at yahoo.com>
>>
>>Hi,
>>>Your question is still not clear.
>>>May be this helps:
>>>
>>>dat2<- read.table(text="
>>>
>>>patient_id t scores
>>>1 0 1.6
>>>1 1 2.6
>>>1 2 2.2
>>>1 3 1.8
>>>2 0 2.3
>>>2 2 2.5
>>>2 4 2.6
>>>2 5 1.5
>>>",sep="",header=TRUE)
>>>
>>>library(plyr)
>>> dat2New<-ddply(dat2,.(patient_id),summarize,t=seq(min(t),max(t)))
>>> res<-join(dat2New,dat2,type="full")
>>>res1<-do.call(rbind,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$patient_id),scores=mean(y1$scores,na.rm=TRUE))}) ) }))
>>> row.names(res1)<-1:nrow(res1)
>>>res1$period<-with(res1,ave(patient_id,patient_id,FUN=seq))
>>> res1
>>># patient_id scores period
>>>#1 1 2.05 1
>>>#2 2 2.40 1
>>>#3 2 2.05 2
>>>
>>>
>>>A.K.
>>>
>>>
>>>
>>>
>>>________________________________
>>>From: GUANGUAN LUO <guanguanluo at gmail.com>
>>>To: arun <smartpink111 at yahoo.com>
>>>Sent: Tuesday, May 7, 2013 11:29 AM
>>>Subject: Re: how to calculate the mean in a period of time?
>>>
>>>
>>>
>>>
>>>Yes ， as you have said, probably , it's not continuous.
>>>
>>>
>>>2013/5/7 arun <smartpink111 at yahoo.com>
>>>
>>>Hi,
>>>>Your question is not clear. You mentioned to calculate the mean of 3 months, but infact you added the scores for t=0,1,2,3 as first 3 months, then possibly 4,5,6 as the next. So, it is not exactly three months. Isn't it?
>>>>
>>>>
>>>>Dear R experts,
>>>>sorry to trouble you again.
>>>>My data is like this now :
>>>>patient_id t scores
>>>>1 0 1.6
>>>>1 1 2.6
>>>>1 2 2.2
>>>>1 3 1.8
>>>>2 0 2.3
>>>>2 2 2.5
>>>>2 4 2.6
>>>>2 5 1.5
>>>>
>>>>I want to calculate the mean of period of 3 months, just get a table like this
>>>>
>>>>patient_id period scores
>>>>1 1 2.05 (1.6+2.6+2.2+1.8)/4
>>>>2 1 2.4 (2.3+2.5)/2
>>>>2 2 2.05 (2.6+1.5)/2
>>>>
>>>>thank you in avance
>>>>
>>>
>>
>
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