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El-Tahtawy, Ahmed

2013-Sep-09 15:46 UTC

[R] replacing Na's with values on different records

I'm sure I'm missing something really obvious in the "for
loop"...

Here is simplified data for 3 patients, we need filling in Na's with same WT
for each patient, AUC halved for visit 3, doubled for visit 5 for the same
patient, based on visit 4


for(i in unique(u3s$ID)){                             #fill in same Wt for each
patient
  u3s$WT <- ifelse(is.na(u3s$WT),u3s$WT[u3s$visit == "4"],u3s$WT)

  for(j in length(u3s$ID1)){                        #fill in .5 AUC for visit 3,
2*AUC for visit 5

    u3s$AUC24 <- ifelse(is.na(u3s$AUC24),u3s$AUC24[u3s$visit ==
"4"]*0.5,u3s$AUC24)
    u3s$AUC24 <- ifelse(!is.na(u3s$AUC24),u3s$AUC24[u3s$visit ==
"4"]*1.0,u3s$AUC24)
    u3s$AUC24 <- ifelse(is.na(u3s$AUC24),u3s$AUC24[u3s$visit ==
"4"]*2.0,u3s$AUC24)
  }
}

Current-
ID

visit

AUC

Wight

ID1

101

3





1

101

4

10

13

2

101

5





3

102

3





4

102

4

4

10

5

102

5





6

103

3





7

103

4

6

9

8

103

5





9


Desired-

ID

visit

AUC

Wight

ID1

101

3

5

13

1

101

4

10

13

2

101

5

20

13

3

102

3

2

10

4

102

4

4

10

5

102

5

8

10

6

103

3

3

9

7

103

4

6

9

8

103

5

12

9

9



Your help is greatly appreciated...


Best Regards

	[[alternative HTML version deleted]]

arun

2013-Sep-09 16:49 UTC

head link

[R] replacing Na's with values on different records

Hi,
Please ?dput() your example dataset.? Not sure this helps or not.
u3s<- read.table(text="Current-ID visit AUC Wight ID1
101 3 . . 1
101 4 10 13 2
101 5? . . 3
102 3 .? . 4
102 4 4 10 5
102 5 . . 6
103 3 . . 7
103 4 6 9 8
103 5 . .
9",sep="",header=TRUE,na.strings=".",check.names=FALSE)

u3d<- read.table(text="Desired-ID visit AUC Wight ID1
101 3 5 13 1
101 4 10 13 2
101 5 20 13 3
102 3 2 10 4
102 4 4 10 5
102 5 8 10 6
103 3 3 9 7
103 4 6 9 8
103 5 12 9 9",sep="",header=TRUE,check.names=FALSE)

?u3s1<-unsplit(lapply(split(u3s,u3s$`Current-ID`),function(x)
{(x$AUC<-as.integer(x$AUC[!is.na(x$AUC)]/2)* (2^(0:floor(log(4,2)))));
x$Wight<- x$Wight[!is.na(x$Wight)];x }),u3s$`Current-ID`)

attr(u3s1,"row.names")<- attr(u3d,"row.names")
colnames(u3s1)<- colnames(u3d)
all.equal(u3s1,u3d)
#[1] TRUE

A.K.


I'm sure I'm missing something really obvious in the "for
loop"...

Here is simplified data for 3 patients, we need filling in Na's 
with same WT for each patient, AUC halved for visit 3, doubled for visit
 5 for the same patient, based on visit 4 


for(i in unique(u3s$ID)){ ? ? ? ? ? ? ? ? ? ? ? ? ? ? #fill in same Wt for each
patient
? u3s$WT <- ifelse(is.na(u3s$WT),u3s$WT[u3s$visit == "4"],u3s$WT) 

? for(j in length(u3s$ID1)){ ? ? ? ? ? ? ? ? ? ? ? ?#fill in .5 AUC for visit 3,
2*AUC for visit 5

? ? u3s$AUC24 <- ifelse(is.na(u3s$AUC24),u3s$AUC24[u3s$visit ==
"4"]*0.5,u3s$AUC24)
? ? u3s$AUC24 <- ifelse(!is.na(u3s$AUC24),u3s$AUC24[u3s$visit ==
"4"]*1.0,u3s$AUC24)
? ? u3s$AUC24 <- ifelse(is.na(u3s$AUC24),u3s$AUC24[u3s$visit ==
"4"]*2.0,u3s$AUC24)
? } 
} 

Current- 
ID 

visit 

AUC 

Wight 

ID1 

101 

3 





1 

101 

4 

10 

13 

2 

101 

5 





3 

102 

3 





4 

102 

4 

4 

10 

5 

102 

5 





6 

103 

3 





7 

103 

4 

6 

9 

8 

103 

5 





9 


Desired- 

ID 

visit 

AUC 

Wight 

ID1 

101 

3 

5 

13 

1 

101 

4 

10 

13 

2 

101 

5 

20 

13 

3 

102 

3 

2 

10 

4 

102 

4 

4 

10 

5 

102 

5 

8 

10 

6 

103 

3 

3 

9 

7 

103 

4 

6 

9 

8 

103 

5 

12 

9 

9 



Your help is greatly appreciated... 


Best Regards

arun

2013-Sep-09 22:23 UTC

head link

[R] replacing Na's with values on different records

HI Ahmed,

No problem.

You got the error because one of the IDs had all NAs for AUC24.



Also, In your dataset, there are NAs in BLADDERWALL, BLADDERWALLC, AUC12d, 
Cmaxd,? in addition to WT, and AUC24.?? Do you want to follow any particular 
methodology for filling the NAs in these columns? or the filling of NAs 
are only applicable to AUC24.? 


res<-unsplit(lapply(split(u3s,u3s$ID),function(x) { x$AUC24<-
if(all(is.na(x$AUC24))) NA else as.integer(x$AUC24[!is.na(x$AUC24)]/2)*
(2^(0:floor(log(4,2))));x$WT<- if(all(is.na(x$WT))) NA else
x$WT[!is.na(x$WT)];x}),u3s$ID)
res
#?? ID PERIOD DOSE VOL1stD MCC BLADDERWALL visit VOL1stDC MCCC BLADDERWALLC
#1 101???? p1 0.03????? 22? 72???????? 2.9???? 3?????? -8? -21????????? 1.2
#2 101???? p2 0.06????? 24? 80???????? 1.0???? 4?????? -6? -13???????? -0.7
#3 101???? p3 0.12????? 17? 59???????? 4.6???? 5????? -13? -34????????? 2.9
#4 102???? p1 0.03?????? 5? 25???????? 0.3???? 3????? -10? -20???????? -1.3
#5 102???? p2 0.06????? 67 125????????? NA???? 4?????? 52?? 80?????????? NA
#6 102???? p3 0.12????? 10? 24???????? 0.2???? 5?????? -5? -21???????? -1.4
#7 103???? p1 0.03?????? 6? 15???????? 0.0???? 3????? -23? -20???????? -0.1
#8 103???? p2 0.06????? 58? 72???????? 0.8???? 4?????? 29?? 37????????? 0.7
#9 103???? p3 0.12????? 15? 35???????? 0.5???? 5????? -14??? 0????????? 0.4
?#? AUC12d Cmaxd Cmind?? WT???????????????? PHENO RACE SEX???? AGE_y AUC24
#1????? NA??? NA??? NA 12.7????????????????????????? 1?? 2 1.8152448??? NA
#2????? NA??? NA??? NA 12.7????????????????????????? 1?? 2 1.8152448??? NA
#3????? NA??? NA??? NA 12.7????????????????????????? 1?? 2 1.8152448??? NA
#4????? NA??? NA??? NA 13.4 Extensive Metabolizer??? 1?? 1 2.1465338??? 10
#5 10.1150? 2.98???? 0 13.4 Extensive Metabolizer??? 1?? 1 2.1465338??? 20
#6????? NA??? NA??? NA 13.4 Extensive Metabolizer??? 1?? 1 2.1465338??? 40
#7????? NA??? NA??? NA 10.0????????????????????????? 1?? 1 0.5010404???? 4
#8? 4.5817? 1.41???? 0 10.0????????????????????????? 1?? 1 0.5010404???? 8
#9????? NA??? NA??? NA 10.0????????????????????????? 1?? 1 0.5010404??? 16




A.K.


----- Original Message -----
From: "El-Tahtawy, Ahmed" <Ahmed.El-Tahtawy at pfizer.com>
To: arun <smartpink111 at yahoo.com>
Cc: 
Sent: Monday, September 9, 2013 6:06 PM
Subject: RE: replacing Na's with values on different records

Dear Arun,

Thanks a million for the sophisticated code- it is little above my skill level.
I never saw brilliant use of function x like this before!!( I am a clinical
Pharmacologist who loves to explore patient data!!). it seems impossible to use
for loop or a simpler function I guess?

The code worked with the simple data, tried to use it with actual data and got
an error!!

################################################################################
dput(head(u3s,9))? ?  # only 3 patients

structure(list(ID = c(101L, 101L, 101L, 102L, 102L, 102L, 103L, 
103L, 103L), PERIOD = c("p1", "p2", "p3",
"p1", "p2", "p3", "p1",
"p2", "p3"), DOSE = c("0.03", "0.06",
"0.12", "0.03", "0.06",
"0.12", "0.03", "0.06", "0.12"), VOL1stD
= c(22L, 24L, 17L, 5L,
67L, 10L, 6L, 58L, 15L), MCC = c(72L, 80L, 59L, 25L, 125L, 24L, 
15L, 72L, 35L), BLADDERWALL = c(2.9, 1, 4.6, 0.3, NA, 0.2, 0, 
0.8, 0.5), visit = c(3L, 4L, 5L, 3L, 4L, 5L, 3L, 4L, 5L), VOL1stDC = c(-8L, 
-6L, -13L, -10L, 52L, -5L, -23L, 29L, -14L), MCCC = c(-21L, -13L, 
-34L, -20L, 80L, -21L, -20L, 37L, 0L), BLADDERWALLC = c(1.2, 
-0.7, 2.9, -1.3, NA, -1.4, -0.1, 0.7, 0.4), AUC12d = c(NA, NA, 
NA, NA, 10.115, NA, NA, 4.5817, NA), Cmaxd = c(NA, NA, NA, NA, 
2.98, NA, NA, 1.41, NA), Cmind = c(NA, NA, NA, NA, 0, NA, NA, 
0, NA), WT = c(NA, 12.7, NA, NA, 13.4, NA, NA, 10, NA), PHENO = c("", 
"", "", "Extensive Metabolizer", "Extensive
Metabolizer", "Extensive Metabolizer",
"", "", ""), RACE = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L), SEX = c(2L,
2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L), AGE_y = c(1.815244771, 1.815244771, 
1.815244771, 2.146533786, 2.146533786, 2.146533786, 0.501040412, 
0.501040412, 0.501040412), AUC24 = c(NA, NA, NA, NA, 20.23, NA, 
NA, 9.1634, NA)), .Names = c("ID", "PERIOD",
"DOSE", "VOL1stD",
"MCC", "BLADDERWALL", "visit",
"VOL1stDC", "MCCC", "BLADDERWALLC",
"AUC12d", "Cmaxd", "Cmind", "WT",
"PHENO", "RACE", "SEX", "AGE_y",
"AUC24"), row.names = c(NA, 9L), class = "data.frame")
######################################################################
Here is your code- changed current ID to ID & AUC to AUC24 to match actual
data

u3s1<-unsplit(lapply(split(u3s,u3s$"ID"),function(x) {
? (x$AUC24<-as.integer(x$AUC24[!is.na(x$AUC24)]/2)* (2^(0:floor(log(4,2)))));
? x$WT<- x$WT[!is.na(x$WT)];
? x }),u3s$"ID")

################################################################################
Error in `$<-.data.frame`(`*tmp*`, "AUC24", value = numeric(0)) : 
? replacement has 0 rows, data has 3




Thank you again for your time and help..
Ahmed 
.


-----Original Message-----
Fr
3 5:00 PM
To: El-Tahtawy, Ahmed
Subject: Re: replacing Na's with values on different records

HI Ahmed,
No problem.? Don't know if you didn't get the reply or not.? This is
what I sent..
u3s<- read.table(text="Current-ID visit AUC Wight ID1
101 3 . . 1
101 4 10 13 2
101 5? . . 3
102 3 .? . 4
102 4 4 10 5
102 5 . . 6
103 3 . . 7
103 4 6 9 8
103 5 . .
9",sep="",header=TRUE,na.strings=".",check.names=FALSE)

u3d<- read.table(text="Desired-ID visit AUC Wight ID1
101 3 5 13 1
101 4 10 13 2
101 5 20 13 3
102 3 2 10 4
102 4 4 10 5
102 5 8 10 6
103 3 3 9 7
103 4 6 9 8
103 5 12 9 9",sep="",header=TRUE,check.names=FALSE)

?u3s1<-unsplit(lapply(split(u3s,u3s$`Current-ID`),function(x)
{(x$AUC<-as.integer(x$AUC[!is.na(x$AUC)]/2)* (2^(0:floor(log(4,2)))));
x$Wight<- x$Wight[!is.na(x$Wight)];x }),u3s$`Current-ID`)

attr(u3s1,"row.names")<- attr(u3d,"row.names")
colnames(u3s1)<- colnames(u3d)
all.equal(u3s1,u3d)






----- Original Message -----
From: "El-Tahtawy, Ahmed" <Ahmed.El-Tahtawy at pfizer.com>
To: arun <s
ubject: RE: replacing Na's with values on different records

Hi Arun,

Thanks a million...
I am looking forward to seeing your replay tomorrow.

Best Regards
Ahmed 
.


-----Original Message-----
F
13 4:17 PM
To: El-Tahtawy, Ahmed
Subject: Re: replacing Na's with values on different records

HI Ahmed,

I already sent the reply.? Let me know if that works.
A.K.




----- Original Message -----
From: "El-Tahtawy, Ahmed" <Ahmed.El-Tahtawy at pfizer.com>
To: "smartpink
 2013 2:50 PM
Subject: RE: replacing Na's with values on different records

Greeting,

Thank you for your quick response.

There are 5 columns and only 3 patients. the actual data has 50 variables and so
many patients; but a simplified version is made to help focus on the main
problem. I used dput as suggested and there an "L" added to all
numbers!!

Please let me know if you have any more questions...

head(u3s,10)
?? ID visit AUC Wight ID1
1 101? ?? 3? NA? ? NA?? 1
2 101? ?? 4? 10? ? 13?? 2
3 101? ?? 5? NA? ? NA?? 3
4 102? ?? 3? NA? ? NA?? 4
5 102? ?? 4?? 4? ? 10?? 5
6 102? ?? 5? NA? ? NA?? 6
7 103? ?? 3? NA? ? NA?? 7
8 103? ?? 4?? 6? ?? 9?? 8
9 103? ?? 5? NA? ? NA?? 9
> dput(u3s)structure(list(ID = c(101L, 101L, 101L, 102L, 102L, 102L, 103L, 103L, 103L),
visit = c(3L, 4L, 5L, 3L, 4L, 5L, 3L, 4L, 5L), AUC = c(NA, 10L, NA, NA, 4L, NA,
NA, 6L, NA), Wight = c(NA, 13L, NA, NA, 10L, NA, NA, 9L, NA), ID1 = 1:9), .Names
= c("ID", "visit", "AUC", "Wight",
"ID1"), class = "data.frame", row.names = c(NA, -9L))

Best Regards
Ahmed
.



, Ahmed
Subject: replacing Na's with values on different records

HI,

The example dataset "Current" and "Desired" are mangled by
HTML.? It is not clear how many columns you have.? I tried it like this, but
still it is still not clear..

ID visit AUC Wight ID1
101 3 1 101 4
10 13 2 101 5
3 102 3 4 102
4 4 10 5 102
5 6 103 3 7
103 4 6 9 8
103 5 9?? ####two elements are missing.

Please use ?dput()
For e.g.
dput(head(dataset,20))

<quote author='El-Tahtawy, Ahmed'>
I'm sure I'm missing something really obvious in the "for
loop"...

Here is simplified data for 3 patients, we need filling in Na's with same WT
for each patient, AUC halved for visit 3, doubled for visit 5 for the same
patient, based on visit 4


for(i in unique(u3s$ID)){? ? ? ? ? ? ? ? ? ? ? ? ? ?? #fill in same Wt for each
patient
? u3s$WT <- ifelse(is.na(u3s$WT),u3s$WT[u3s$visit == "4"],u3s$WT)

? for(j in length(u3s$ID1)){? ? ? ? ? ? ? ? ? ? ? ? #fill in .5 AUC for visit 3,
2*AUC for visit 5

? ? u3s$AUC24 <- ifelse(is.na(u3s$AUC24),u3s$AUC24[u3s$visit
="4"]*0.5,u3s$AUC24)
? ? u3s$AUC24 <- ifelse(!is.na(u3s$AUC24),u3s$AUC24[u3s$visit
="4"]*1.0,u3s$AUC24)
? ? u3s$AUC24 <- ifelse(is.na(u3s$AUC24),u3s$AUC24[u3s$visit
="4"]*2.0,u3s$AUC24)
? }
}

Current-
ID

visit

AUC

Wight

ID1

101

3





1

101

4

10

13

2

101

5





3

102

3





4

102

4

4

10

5

102

5





6

103

3





7

103

4

6

9

8

103

5





9


Desired-

ID

visit

AUC

Wight

ID1

101

3

5

13

1

101

4

10

13

2

101

5

20

13

3

102

3

2

10

4

102

4

4

10

5

102

5

8

10

6

103

3

3

9

7

103

4

6

9

8

103

5

12

9

9



Your help is greatly appreciated...


Best Regards

??? [[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

</quote>
Quoted from: 
http://r.789695.n4.nabble.com/replacing-Na-s-with-values-on-different-records-tp4675696.html


_____________________________________
Sent from http://r.789695.n4.nabble.com

arun

2013-Sep-10 14:53 UTC

head link

[R] replacing Na's with values on different records

HI,

You should take out the as.integer()
res<- unsplit(lapply(split(u3s,u3s$ID),function(x) { x$AUC24<-
if(all(is.na(x$AUC24))) NA else round(x$AUC24[!is.na(x$AUC24)]/2*
(2^(0:floor(log(4,2)))),3);x$WT<- if(all(is.na(x$WT))) NA else
x$WT[!is.na(x$WT)];x}),u3s$ID)
?res$AUC24
#[1]???? NA???? NA???? NA 10.115 20.230 40.460? 4.582? 9.163 18.327

Regarding the other question about AUC24 with NA in the first entry, you should
try this:
u3s1<- u3s
?u3s1$AUC24[1]<- 2
u3sNew<- rbind(u3s1,u3s,u3s,u3s)
u3sNew$ID[10:36]<- rep(104:112,each=3)
u3sNew$AUC24[c(12,19:22,27,28,30)]<- c(20,2,4,8,10.115,18.3268,2,8)

#Modified added ?round()

res<- unsplit(lapply(split(u3sNew,u3sNew$ID),function(x) {
??? ??? ??? ??? indx<-!is.na(x$AUC24)
??? ??? ??? ??? x1<- x$AUC24[indx]
??? ??? ??? ??? x2<- 2^(0:floor(log(4,2)))
??? ??? ??? ??? ?x$AUC24<-round(if(sum(indx)==3) {
??? ??? ??? ??? ??? x$AUC24
??? ??? ??? ??? ??? }
??? ??? ??? ??? ?else if( sum(indx)==2)??? {
??? ??? ??? ??? ???? ?if(which(!indx)==2|which(!indx)==3) {
??? ??? ??? ??? ? ??? ?x1[1]* x2
??? ??? ??? ??? ??? ?? }??? 
??? ??? ??? ??? ???? ? else (x1[1]/2)*x2
??? ??? ??? ??? ??? ??? ??? ??? ???? 
??? ??? ??? ??? ??? } 
??? ??? ??? ??? else if( sum(indx)==1) {
??? ??? ??? ??? ?? if(which(indx)==1) {
??? ??? ??? ??? ??? x1*x2
??? ??? ??? ??? ??? } 
??? ??? ??? ??? ???? else if(which(indx)==2){
??? ??? ??? ??? ???? (x1/2)*x2
??? ??? ??? ??? ??? }??? ??? ??? ??? 
??? ??? ??? ??? ???? else (x1/4)*x2
??? ??? ??? ??? ? }
??? ??? ??? ??? ?else NA,3)
??? ??? ??? ??? x$WT<- if(all(is.na(x$WT))){
??? ??? ??? ??? ??? ??? ??? ?NA
??? ??? ??? ??? ??? }
??? ??? ??? ??? ?else x$WT[!is.na(x$WT)]
??? ??? ??? ??? ?? x}),u3sNew$ID)

?res$AUC24
# [1]? 2.000? 4.000? 8.000 10.115 20.230 40.460? 4.582? 9.163 18.327? 5.000
#[11] 10.000 20.000 10.115 20.230 40.460? 4.582? 9.163 18.327? 2.000? 4.000
#[21]? 8.000 10.115 20.230 40.460? 4.582? 9.163 18.327? 2.000? 4.000? 8.000
#[31] 10.115 20.230 40.460? 4.582? 9.163 18.327

?u3sNew$AUC24
?#[1]? 2.0000????? NA????? NA????? NA 20.2300????? NA????? NA? 9.1634????? NA
#[10]????? NA????? NA 20.0000????? NA 20.2300????? NA????? NA? 9.1634????? NA
#[19]? 2.0000? 4.0000? 8.0000 10.1150 20.2300????? NA????? NA? 9.1634 18.3268
#[28]? 2.0000????? NA? 8.0000????? NA 20.2300????? NA????? NA? 9.1634????? NA
A.K.




----- Original Message -----
From: "El-Tahtawy, Ahmed" <Ahmed.El-Tahtawy at pfizer.com>
To: arun <smartpink111 at yahoo.com>
Cc: 
Sent: Tuesday, September 10, 2013 10:39 AM
Subject: RE: replacing Na's with values on different records

Hi Arun,

Thanks for the code. I just applied it and it ran like a charm!!
I ran the code with the first child (AUC24=NA) before seeking your help, but
gave me the same error!!

One last question- I tried to use round(3), but AUC24 didn't change.

res<-unsplit(lapply(split(u3s,u3s$ID),function(x) { 
? x$AUC24<- if(all(is.na(x$AUC24))) NA else
round(as.integer(x$AUC24[!is.na(x$AUC24)]/2)* (2^(0:floor(log(4,2)))),3);
x$WT<- if(all(is.na(x$WT))) NA else x$WT[!is.na(x$WT)];x}),u3s$ID)


Thanks again...
Ahmed 
.


-----Original Message-----
From: arun [mailto:smartpink111 at yahoo.com] 
Sent: Monday, September 09, 2013 6:24 PM
To: R help
Cc: El-Tahtawy, Ahmed
Subject: Re: replacing Na's with values on different records

HI Ahmed,

No problem.

You got the error because one of the IDs had all NAs for AUC24.



Also, In your dataset, there are NAs in BLADDERWALL, BLADDERWALLC, AUC12d,
Cmaxd,? in addition to WT, and AUC24.?? Do you want to follow any particular
methodology for filling the NAs in these columns? or the filling of NAs are only
applicable to AUC24.?


res<-unsplit(lapply(split(u3s,u3s$ID),function(x) { x$AUC24<-
if(all(is.na(x$AUC24))) NA else as.integer(x$AUC24[!is.na(x$AUC24)]/2)*
(2^(0:floor(log(4,2))));x$WT<- if(all(is.na(x$WT))) NA else
x$WT[!is.na(x$WT)];x}),u3s$ID) res #?? ID PERIOD DOSE VOL1stD MCC BLADDERWALL
visit VOL1stDC MCCC BLADDERWALLC
#1 101???? p1 0.03????? 22? 72???????? 2.9???? 3?????? -8? -21????????? 1.2
#2 101???? p2 0.06????? 24? 80???????? 1.0???? 4?????? -6? -13???????? -0.7
#3 101???? p3 0.12????? 17? 59???????? 4.6???? 5????? -13? -34????????? 2.9
#4 102???? p1 0.03?????? 5? 25???????? 0.3???? 3????? -10? -20???????? -1.3
#5 102???? p2 0.06????? 67 125????????? NA???? 4?????? 52?? 80?????????? NA
#6 102???? p3 0.12????? 10? 24???????? 0.2???? 5?????? -5? -21???????? -1.4
#7 103???? p1 0.03?????? 6? 15???????? 0.0???? 3????? -23? -20???????? -0.1
#8 103???? p2 0.06????? 58? 72???????? 0.8???? 4?????? 29?? 37????????? 0.7
#9 103???? p3 0.12????? 15? 35???????? 0.5???? 5????? -14??? 0????????? 0.4
?#? AUC12d Cmaxd Cmind?? WT???????????????? PHENO RACE SEX???? AGE_y AUC24
#1????? NA??? NA??? NA 12.7????????????????????????? 1?? 2 1.8152448??? NA
#2????? NA??? NA??? NA 12.7????????????????????????? 1?? 2 1.8152448??? NA
#3????? NA??? NA??? NA 12.7????????????????????????? 1?? 2 1.8152448??? NA
#4????? NA??? NA??? NA 13.4 Extensive Metabolizer??? 1?? 1 2.1465338??? 10
#5 10.1150? 2.98???? 0 13.4 Extensive Metabolizer??? 1?? 1 2.1465338??? 20
#6????? NA??? NA??? NA 13.4 Extensive Metabolizer??? 1?? 1 2.1465338??? 40
#7????? NA??? NA??? NA 10.0????????????????????????? 1?? 1 0.5010404???? 4
#8? 4.5817? 1.41???? 0 10.0????????????????????????? 1?? 1 0.5010404???? 8
#9????? NA??? NA??? NA 10.0????????????????????????? 1?? 1 0.5010404??? 16




A.K.


----- Original Message -----
From: "El-Tahtawy, Ahmed" <Ahmed.El-Tahtawy at pfizer.com>
To: arun <smartpink111 at yahoo.com>
Cc: 
Sent: Monday, September 9, 2013 6:06 PM
Subject: RE: replacing Na's with values on different records

Dear Arun,

Thanks a million for the sophisticated code- it is little above my skill level.
I never saw brilliant use of function x like this before!!( I am a clinical
Pharmacologist who loves to explore patient data!!). it seems impossible to use
for loop or a simpler function I guess?

The code worked with the simple data, tried to use it with actual data and got
an error!!

################################################################################
dput(head(u3s,9))? ?? # only 3 patients

structure(list(ID = c(101L, 101L, 101L, 102L, 102L, 102L, 103L, 103L, 103L),
PERIOD = c("p1", "p2", "p3", "p1",
"p2", "p3", "p1", "p2", "p3"),
DOSE = c("0.03", "0.06", "0.12", "0.03",
"0.06", "0.12", "0.03", "0.06",
"0.12"), VOL1stD = c(22L, 24L, 17L, 5L, 67L, 10L, 6L, 58L, 15L), MCC =
c(72L, 80L, 59L, 25L, 125L, 24L, 15L, 72L, 35L), BLADDERWALL = c(2.9, 1, 4.6,
0.3, NA, 0.2, 0, 0.8, 0.5), visit = c(3L, 4L, 5L, 3L, 4L, 5L, 3L, 4L, 5L),
VOL1stDC = c(-8L, -6L, -13L, -10L, 52L, -5L, -23L, 29L, -14L), MCCC = c(-21L,
-13L, -34L, -20L, 80L, -21L, -20L, 37L, 0L), BLADDERWALLC = c(1.2, -0.7, 2.9,
-1.3, NA, -1.4, -0.1, 0.7, 0.4), AUC12d = c(NA, NA, NA, NA, 10.115, NA, NA,
4.5817, NA), Cmaxd = c(NA, NA, NA, NA, 2.98, NA, NA, 1.41, NA), Cmind = c(NA,
NA, NA, NA, 0, NA, NA, 0, NA), WT = c(NA, 12.7, NA, NA, 13.4, NA, NA, 10, NA),
PHENO = c("", "", "", "Extensive
Metabolizer", "Extensive Metabolizer", "Extensive
Metabolizer", "", "", ""), RACE = c(1L, 1L,
1L, 1L, 1L,
 1L, 1L, 1L, 1L), SEX = c(2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L), AGE_y =
c(1.815244771, 1.815244771, 1.815244771, 2.146533786, 2.146533786, 2.146533786,
0.501040412, 0.501040412, 0.501040412), AUC24 = c(NA, NA, NA, NA, 20.23, NA, NA,
9.1634, NA)), .Names = c("ID", "PERIOD", "DOSE",
"VOL1stD", "MCC", "BLADDERWALL",
"visit", "VOL1stDC", "MCCC",
"BLADDERWALLC", "AUC12d", "Cmaxd",
"Cmind", "WT", "PHENO", "RACE",
"SEX", "AGE_y", "AUC24"), row.names = c(NA, 9L),
class = "data.frame")
######################################################################
Here is your code- changed current ID to ID & AUC to AUC24 to match actual
data

u3s1<-unsplit(lapply(split(u3s,u3s$"ID"),function(x) {
? (x$AUC24<-as.integer(x$AUC24[!is.na(x$AUC24)]/2)* (2^(0:floor(log(4,2)))));
? x$WT<- x$WT[!is.na(x$WT)];
? x }),u3s$"ID")

################################################################################
Error in `$<-.data.frame`(`*tmp*`, "AUC24", value = numeric(0)) : 
? replacement has 0 rows, data has 3




Thank you again for your time and help..
Ahmed
.


-----Original Message-----
From: arun [mailto:smartpink111 at yahoo.com] 
Sent: Monday, September 09, 2013 5:00 PM
To: El-Tahtawy, Ahmed
Subject: Re: replacing Na's with values on different records

HI Ahmed,
No problem.? Don't know if you didn't get the reply or not.? This is
what I sent..
u3s<- read.table(text="Current-ID visit AUC Wight ID1
101 3 . . 1
101 4 10 13 2
101 5? . . 3
102 3 .? . 4
102 4 4 10 5
102 5 . . 6
103 3 . . 7
103 4 6 9 8
103 5 . .
9",sep="",header=TRUE,na.strings=".",check.names=FALSE)

u3d<- read.table(text="Desired-ID visit AUC Wight ID1
101 3 5 13 1
101 4 10 13 2
101 5 20 13 3
102 3 2 10 4
102 4 4 10 5
102 5 8 10 6
103 3 3 9 7
103 4 6 9 8
103 5 12 9 9",sep="",header=TRUE,check.names=FALSE)

?u3s1<-unsplit(lapply(split(u3s,u3s$`Current-ID`),function(x)
{(x$AUC<-as.integer(x$AUC[!is.na(x$AUC)]/2)* (2^(0:floor(log(4,2)))));
x$Wight<- x$Wight[!is.na(x$Wight)];x }),u3s$`Current-ID`)

attr(u3s1,"row.names")<- attr(u3d,"row.names")
colnames(u3s1)<- colnames(u3d)
all.equal(u3s1,u3d)






----- Original Message -----
From: "El-Tahtawy, Ahmed" <Ahmed.El-Tahtawy at pfizer.com>
To: arun <smartpink111 at yahoo.com>
Cc: 
Sent: Monday, September 9, 2013 4:48 PM
Subject: RE: replacing Na's with values on different records

Hi Arun,

Thanks a million...
I am looking forward to seeing your replay tomorrow.

Best Regards
Ahmed 
.


-----Original Message-----
From: arun [mailto:smartpink111 at yahoo.com] 
Sent: Monday, September 09, 2013 4:17 PM
To: El-Tahtawy, Ahmed
Subject: Re: replacing Na's with values on different records

HI Ahmed,

I already sent the reply.? Let me know if that works.
A.K.




----- Original Message -----
From: "El-Tahtawy, Ahmed" <Ahmed.El-Tahtawy at pfizer.com>
To: "smartpink111 at yahoo.com" <smartpink111 at yahoo.com>
Cc: 
Sent: Monday, September 9, 2013 2:50 PM
Subject: RE: replacing Na's with values on different records

Greeting,

Thank you for your quick response.

There are 5 columns and only 3 patients. the actual data has 50 variables and so
many patients; but a simplified version is made to help focus on the main
problem. I used dput as suggested and there an "L" added to all
numbers!!

Please let me know if you have any more questions...

head(u3s,10)
?? ID visit AUC Wight ID1
1 101? ?? 3? NA? ? NA?? 1
2 101? ?? 4? 10? ? 13?? 2
3 101? ?? 5? NA? ? NA?? 3
4 102? ?? 3? NA? ? NA?? 4
5 102? ?? 4?? 4? ? 10?? 5
6 102? ?? 5? NA? ? NA?? 6
7 103? ?? 3? NA? ? NA?? 7
8 103? ?? 4?? 6? ?? 9?? 8
9 103? ?? 5? NA? ? NA?? 9
> dput(u3s)structure(list(ID = c(101L, 101L, 101L, 102L, 102L, 102L, 103L, 103L, 103L),
visit = c(3L, 4L, 5L, 3L, 4L, 5L, 3L, 4L, 5L), AUC = c(NA, 10L, NA, NA, 4L, NA,
NA, 6L, NA), Wight = c(NA, 13L, NA, NA, 10L, NA, NA, 9L, NA), ID1 = 1:9), .Names
= c("ID", "visit", "AUC", "Wight",
"ID1"), class = "data.frame", row.names = c(NA, -9L))

Best Regards
Ahmed
.

-----Original Message-----
From: smartpink111 at yahoo.com [mailto:smartpink111 at yahoo.com]
Sent: Monday, September 09, 2013 12:15 PM
To: El-Tahtawy, Ahmed
Subject: replacing Na's with values on different records

HI,

The example dataset "Current" and "Desired" are mangled by
HTML.? It is not clear how many columns you have.? I tried it like this, but
still it is still not clear..

ID visit AUC Wight ID1
101 3 1 101 4
10 13 2 101 5
3 102 3 4 102
4 4 10 5 102
5 6 103 3 7
103 4 6 9 8
103 5 9?? ####two elements are missing.

Please use ?dput()
For e.g.
dput(head(dataset,20))

<quote author='El-Tahtawy, Ahmed'>
I'm sure I'm missing something really obvious in the "for
loop"...

Here is simplified data for 3 patients, we need filling in Na's with same WT
for each patient, AUC halved for visit 3, doubled for visit 5 for the same
patient, based on visit 4


for(i in unique(u3s$ID)){? ? ? ? ? ? ? ? ? ? ? ? ? ?? #fill in same Wt for each
patient
? u3s$WT <- ifelse(is.na(u3s$WT),u3s$WT[u3s$visit == "4"],u3s$WT)

? for(j in length(u3s$ID1)){? ? ? ? ? ? ? ? ? ? ? ? #fill in .5 AUC for visit 3,
2*AUC for visit 5

? ? u3s$AUC24 <- ifelse(is.na(u3s$AUC24),u3s$AUC24[u3s$visit
="4"]*0.5,u3s$AUC24)
? ? u3s$AUC24 <- ifelse(!is.na(u3s$AUC24),u3s$AUC24[u3s$visit
="4"]*1.0,u3s$AUC24)
? ? u3s$AUC24 <- ifelse(is.na(u3s$AUC24),u3s$AUC24[u3s$visit
="4"]*2.0,u3s$AUC24)
? }
}

Current-
ID

visit

AUC

Wight

ID1

101

3





1

101

4

10

13

2

101

5





3

102

3





4

102

4

4

10

5

102

5





6

103

3





7

103

4

6

9

8

103

5





9


Desired-

ID

visit

AUC

Wight

ID1

101

3

5

13

1

101

4

10

13

2

101

5

20

13

3

102

3

2

10

4

102

4

4

10

5

102

5

8

10

6

103

3

3

9

7

103

4

6

9

8

103

5

12

9

9



Your help is greatly appreciated...


Best Regards

??? [[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

</quote>
Quoted from: 
http://r.789695.n4.nabble.com/replacing-Na-s-with-values-on-different-records-tp4675696.html


_____________________________________
Sent from http://r.789695.n4.nabble.com

R help - Sep 2013 - replacing Na's with values on different records

[R] replacing Na's with values on different records

[R] replacing Na's with values on different records

[R] replacing Na's with values on different records

[R] replacing Na's with values on different records