# [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:
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

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:
>>>
>>>
>>>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
>>>
>>>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
>>>>
>>>
>>
>

```