How to pick colums from a ragged array?

Hello,

Inline.
Em 23-10-2012 14:53, Stuart Leask escreveu:
I too had a parsimonious solution that was also fooled by IDs that had a duplicate date that wasn't the first date, but was the same as another ID's duplicate+first.

The right answer
From this data:
ID <- c(58,58,58,58,167,167,323,323,323,323,323,323,323
,547,794,814,814,814,814,814,814,841,841,841,841,841
,841,841,841,841,910,910,910,910,910,910,999,1019,1019
,1019)

DATE <-
  c(20060821,20061207,20080102,20090904,20040205,20040205,20051111
  ,20060111,20071119,20080107,20080407,20080521,20080711,20041005
  ,20070905,20020814,20021125,20040429,20040429,20071205,20080227
  ,20050421,20050421,20060428,20060602,20060816,20061025,20061129
  ,20070112,20070514, 19870508,20040205,20040205, 20091120,20091210
  ,20091224,20050503,19870508,19870508,19880330)

  id.d <- cbind (ID,DATE )

is:

167, 841  and 1019 - correct.
814 910 - incorrect. Although there are duplicate dates, they are not the first date.

-----Original Message-----
From: arun [mailto:smartpink111 at yahoo.com]
Sent: 23 October 2012 14:29
To: Stuart Leask
Cc: R help
Subject: Re: [R] [r] How to pick colums from a ragged array?

Hi,
Also one more thing:
This should get the dates which are duplicated.  In my first reply, I was looking for the duplicated rows. Sorry for that!

id.d<-data.frame(ID,DATE)

new1<-id.d[duplicated(id.d$DATE)|duplicated(id.d$DATE,fromLast=TRUE),]

new2<-new1[order(new1$ID,new1$DATE),]
  tapply(new2$ID,new2$DATE,head,1)
#19870508 20040205 20040429 20050421
   #   910      167      814      841

But, still the result is not that you wanted, because 910's date is the earliest date when compared to 1019.
new1[order(new1$ID,new1$DATE),]
#     ID     DATE
#5   167 20040205
#6   167 20040205
#18  814 20040429
#19  814 20040429
#22  841 20050421
#23  841 20050421
#31  910 19870508
#32  910 20040205
#33  910 20040205
#38 1019 19870508
#39 1019 19870508

A.K.

----- Original Message -----
From: Stuart Leask <Stuart.Leask at nottingham.ac.uk>
To: arun <smartpink111 at yahoo.com>
Cc: Petr PIKAL <petr.pikal at precheza.cz>
Sent: Tuesday, October 23, 2012 9:15 AM
Subject: RE: [R] [r] How to pick colums from a ragged array?

Sorry Arun, but when I run it I get an error:

ID <- c(58,58,58,58,167,167,323,323,323,323,323,323,323
+ ,547,794,814,814,814,814,814,814,841,841,841,841,841
+ ,841,841,841,841,910,910,910,910,910,910,999,1019,1019
+ ,1019)
DATE <-
+  c(20060821,20061207,20080102,20090904,20040205,20040205,20051111
+  ,20060111,20071119,20080107,20080407,20080521,20080711,20041005
+  ,20070905,20020814,20021125,20040429,20040429,20071205,20080227
+  ,20050421,20050421,20060428,20060602,20060816,20061025,20061129
+  ,20070112,20070514, 19870508,20040205,20040205, 20091120,20091210
+  ,20091224,20050503,19870508,19870508,19880330)
  id.d <- cbind (ID,DATE )
new1<-id.d[duplicated(id.d)|duplicated(id.d,fromLast=TRUE),]

tapply(new1$ID,new1$DATE,head,1)
Error in new1$DATE : $ operator is invalid for atomic vectors
The error comes from the fact that id.d is a matrix, Arun is using one 
of the list or data.frame ways of accessing the elements. Try new1[, 
"ID"] and new1[, "DATE"].
Anyway I believe the solution will give all duplicates' first rows, not 
the first rows of the duplicates in first row of each ID.

Rui Barradas

-----Original Message-----
From: arun [mailto:smartpink111 at yahoo.com]
Sent: 23 October 2012 14:05
To: Stuart Leask
Cc: R help; Petr PIKAL
Subject: Re: [R] [r] How to pick colums from a ragged array?

HI,
I was not following the thread.
May be this is what you are looking for:
new1<-id.d[duplicated(id.d)|duplicated(id.d,fromLast=TRUE),]

tapply(new1$ID,new1$DATE,head,1)
#19870508 20040205 20040429 20050421
   #  1019      167      814      841
A.K.

----- Original Message -----
From: Stuart Leask <Stuart.Leask at nottingham.ac.uk>
To: PIKAL Petr <petr.pikal at precheza.cz>; "r-help at r-project.org" <r-help at r-project.org>
Cc:
Sent: Tuesday, October 23, 2012 8:28 AM
Subject: Re: [R] [r] How to pick colums from a ragged array?

Hi there.

Not sure I follow what you are doing.

I want a list of all the IDs that have duplicate DATE entries, only when the DATE is the earliest (or last) date for that ID.

I have refined my test dataset, to include some tests (e.g. 910 has the same dup as 1019, but for 910 it's not the earliest date):

ID <- c(58,58,58,58,167,167,323,323,323,323,323,323,323
,547,794,814,814,814,814,814,814,841,841,841,841,841
,841,841,841,841,910,910,910,910,910,910,999,1019,1019
,1019)

DATE <-
c(20060821,20061207,20080102,20090904,20040205,20040205,20051111
,20060111,20071119,20080107,20080407,20080521,20080711,20041005
,20070905,20020814,20021125,20040429,20040429,20071205,20080227
,20050421,20050421,20060428,20060602,20060816,20061025,20061129
,20070112,20070514, 19870508,20040205,20040205, 20091120,20091210
,20091224,20050503,19870508,19870508,19880330)

Correct output:
"167"  "841"  "1019"

Stuart

-----Original Message-----
From: PIKAL Petr [mailto:petr.pikal at precheza.cz]
Sent: 23 October 2012 13:15
To: Stuart Leask; r-help at r-project.org
Subject: RE: [r] How to pick colums from a ragged array?

Hi

Rui's answer brought me to more elaborated solution which still needs data frame to be ordered by date

fff<-function(data, first=TRUE, remove=FALSE) {

testfirst <- function(x) x[1,2]==x[2,2]
testlast <- function(x) x[length(x),2]==x[length(x)-1,2]

if(first) sel <- as.numeric(names(which(sapply(split(data, data[,1]), testfirst)))) else sel <- as.numeric(names(which(sapply(split(data, data[,1]), testlast))))

if (remove) data[data[,1]!=sel,] else data[data[,1]==sel,] }

fff(id.d)
     ID     DATE
31 910 20091105
32 910 20091105
33 910 20091117
34 910 20091119
35 910 20091120
36 910 20091210
37 910 20091224
38 910 20091224

fff(id.d, remove=T)
      ID     DATE
1    58 20060821
2    58 20061207
3    58 20080102
4    58 20090904
5   167 20040205
6   167 20040323
7   323 20051111
8   323 20060111
9   323 20071119
10  323 20080107
11  323 20080407
12  323 20080521
13  323 20080711
14  547 20041005
15  794 20070905
16  814 20020814
17  814 20021125
18  814 20040429
19  814 20040429
20  814 20071205
21  814 20080227
22  841 20050421
23  841 20060130
24  841 20060428
25  841 20060602
26  841 20060816
27  841 20061025
28  841 20061129
29  841 20070112
30  841 20070514
39  999 20050503
40 1019 19870508
41 1019 19880223
42 1019 19880330
43 1019 19880330
Regards
Petr

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
project.org] On Behalf Of PIKAL Petr
Sent: Tuesday, October 23, 2012 1:49 PM
To: Stuart Leask; r-help at r-project.org
Subject: Re: [R] [r] How to pick colums from a ragged array?

Hi

I did not check your code and rather followed your explanation. BTW,
thanks for test data.

small change in data frame to make DATE as Date class

datum<-as.Date(as.character(DATE), format="%Y%m%d") id.d <-
data.frame(ID,datum )

ordering by date

id.d<-id.d[order(id.d$datum),]

two functions to test if first two dates are the same or last two
dates are the same

testfirst <- function(x) x[1,2]==x[2,2] testlast <- function(x)
x[length(x),2]==x[length(x)-1,2]

change one last date in the data frame to be the same as previous

id.d[35,2]<-id.d[36,2]

and here are results

sapply(split(id.d, id.d$ID), testlast)
    58   167   323   547   794   814   841   910   999  1019  FALSE
FALSE FALSE    NA    NA FALSE FALSE  TRUE    NA FALSE

sapply(split(id.d, id.d$ID), testfirst)
    58   167   323   547   794   814   841   910   999  1019  FALSE
FALSE FALSE    NA    NA FALSE FALSE FALSE    NA FALSE

Now you can select ID which is true and remove it from your data
which(sapply(split(id.d, id.d$ID), testlast))

and use it for your data frame to subset/remove id.d$ID ==
as.numeric(names(which(sapply(split(id.d, id.d$ID), testlast))))  [1]
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
FALSE [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
FALSE FALSE [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
FALSE TRUE  TRUE [37]  TRUE  TRUE  TRUE  TRUE

However I am not sure if this is exactly what you want.

Regards
Petr

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
project.org] On Behalf Of Stuart Leask
Sent: Tuesday, October 23, 2012 11:38 AM
To: r-help at r-project.org
Subject: [R] [r] How to pick colums from a ragged array?

I have a large dataset (~1 million rows) of three variables: ID
(patient's name), DATE (of appointment) and DIAGNOSIS (given on that
date).
Patients may have been assigned more than one diagnosis at any one
appointment - leading to two rows, same ID and DATE but different
DIAGNOSIS.
The diagnoses may change between appointments.

I want to subset the data in two ways:

-          define groups of patients by the first diagnosis given

-          define groups of patients by the last diagnosis given.

The problem:
Unfortunately, a small number of patients have been given more than
one diagnosis at their first (or last) appointment. These
individuals I need to identify and remove, as it's not possible to
say uniquely what their first (or last) diagnosis was. So I need to
identify and remove these individuals which have pairs of rows with
the same ID
and
(lowest or highest) DATE. The size of the dataset precludes the
option
of doing this by eye.

I suspect there is a very elegant way of doing this in R.

This is what I've come up with:

-          Sort by DATE then ID

-          Make a ragged array of DATE by ID

-          Remove IDs that only occur once.

-          Subtract the first and second DATEs. Remove IDs for which
this = zero, as this will only be true for IDs for which the
appointment is recorded twice (because there were two diagnoses
recorded on this date).

-          (Then do the same to get the 'last appointment'
duplicates,
by reversing the initial sort by DATE.)

I am stuck at the 'Subtract dates' step: I would like to get the
data out of the ragged array by columns (so e.g. I end up with a
matrix of ID, 1st DATE, 2nd DATE). But I can't get the dates out by
column from the ragged array.

I hope someone can help. My ugly code is below, with some data for
testing.

Stuart

Dr Stuart John Leask DM FRCPsych MB BChir MA Clinical Senior
Lecturer and Honorary Consultant Pychiatrist Institute of Mental
Health, Innovation Park Triumph Road, Nottingham, Notts. NG7 2TU. UK
Tel. +44
115 82 30419
stuart.leask at nottingham.ac.uk<mailto:stuart.leask at nottingham.ac.uk>
Google 'Dr Stuart Leask'

ID <- c(58,58,58,58,167,167,323,323,323,323,323,323,323
,547,794,814,814,814,814,814,814,841,841,841,841,841
,841,841,841,841,910,910,910,910,910,910,999,1019,1019
,1019)

DATE <-
c(20060821,20061207,20080102,20090904,20040205,20040323,20051111
,20060111,20071119,20080107,20080407,20080521,20080711,20041005
,20070905,20020814,20021125,20040429,20040429,20071205,20080227
,20050421,20060130,20060428,20060602,20060816,20061025,20061129
,20070112,20070514,20091105,20091117,20091119,20091120,20091210
,20091224,20050503,19870508,19880223,19880330)

id.d <- cbind (ID,DATE )
rag.a  <-  split ( id.d [ ,2 ], id.d [ ,1])               # create
ragged array, 1-n DATES for every NAME

# Inelegant attempt to remove IDs that only have one entry:

rag.s <-tapply  (id.d [ ,2], id.d [ ,1], sum)             #add up
the dates per row # Since DATE is in 'year mo da', if there's only
one date, sum will
be
less than 2100000:
rag.t <- rag.s [ rag.s > 21000000 ]
multi.dates <- rownames ( rag.t )                         # all the
IDs
with >1 date
rag.am <- rag.a [ multi.dates ]                           # rag.am
only
has IDs with > 1 Date

# But now I'm stuck.
# Each row of the array is rag.am$ID.
# So I can't pick columns of DATEs from the ragged array.

This message and any attachment are intended solely for the
addressee and may contain confidential information. If you have
received this message in error, please send it back to me, and
immediately delete
it.
Please do not use, copy or disclose the information contained in
this message or in any attachment.  Any views or opinions expressed
by the author of this email do not necessarily reflect the views of
the University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage
your computer system:
you are advised to perform your own checks. Email communications
with the University of Nottingham may be monitored as permitted by
UK legislation.
     [[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.
______________________________________________
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.
______________________________________________
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.

This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it.   Please do not use, copy or disclose the information contained in this message or in any attachment.  Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.

This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system:
you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

______________________________________________
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.

How to pick colums from a ragged array?

Thread (3 messages)