Hi Jeff, It works on well on a dataset with 100000 rows and I figure it will
work well with the “real” dataset. You’ve been of great help and I am starting
to make headway.
It creates a new dataframe (result), as shown below that doesn’t quite have the
result as I would want it.
ID admin_period start end ddays
J1/3 1 5/11/07 8/13/07 94
J1/3 2 8/13/07 11/12/07 91
J1/3 3 11/12/07 2/4/08 84
J1/3 4 2/4/08 5/5/08 91
J1/3 5 5/5/08 5/4/09 364
J1/3 6 5/4/09 5/17/10 378
J1/3 7 5/17/10 5/16/11 364
J10/1 1 5/11/07 8/13/07 94
J10/1 2 8/13/07 11/12/07 91
J10/1 3 11/12/07 2/4/08 84
J10/1 4 2/4/08 5/5/08 91
J10/1 5 5/5/08 5/8/09 368
J10/1 6 5/8/09 5/17/10 374
J10/1 7 5/17/10 5/16/11 364
J102/1 1 5/15/07 8/15/07 92
J102/1 2 8/15/07 11/13/07 90
J102/1 3 11/13/07 2/5/08 84
J102/1 4 2/5/08 5/6/08 91
J102/1 5 5/6/08 5/5/09 364
J102/1 6 5/5/09 5/19/10 379
My supervisor doesn’t want me to create a new dataset, she’s afraid I might
lose some data…I cannot fight that.
Like you mentioned earlier, I might be mixing up things which I think is what
you alluded to earlier.
After consultation with my supervisor, this is what we’ve agreed. For every
individual, given the start and end date, create a new column (say, diff_days)
and for every row that falls within the range of start and end_date, get the
difference between the date in that row and start date and add it to the
diff_days column. Below is an example of the result. As it can be seen
5/11/2007 is the start while 2/4/2008 is the end. The diff_days has been
populated excluding the end date and that is because that is the start of the
study in 2008 that will continue into 2009 and thus from 2/4/2008, I should
compute diff_days till 2009 and so no (I hope this makes sense).
ID date drug_admin year month diff_days
R1/3 5/11/2007 Y 2007 5 0
R1/3 5/16/2007 2007 5 6
R1/3 5/22/2007 2007 5 11
R1/3 5/28/2007 2007 5 17
R1/3 1/14/2008 2008 1 248
R1/3 1/21/2008 2008 1 255
R1/3 1/28/2008 2008 1 263
R1/3 2/4/2008 Y 2008 2
Regards
-------------------------------------------------------------------------------
Kevin Wame
On 7/3/16, 10:09 PM, "Jeff Newmiller" <jdnew...@dcn.davis.ca.us> wrote:
Typo on the second line
result <- ( result0
%>% select( -admin_period1 )
%>% inner_join( result0 %>% select( ID, admin_period1, end=start )
, by = c( ID="ID", admin_period ="admin_period1" )
)
%>% mutate( ddays = end - start )
)
--
Sent from my phone. Please excuse my brevity.
On July 3, 2016 11:55:14 AM PDT, Kevin Wamae <kwa...@kemri-wellcome.org> wrote:
>Hi Jeff, “likes its Excel”, I don’t follow. Pardon me for any mix up.
>
>Thanks for the code. After running it, this is the error I get.
>
>Error: cannot join on columns 'admin_period' x 'admin_period1': index
>out of bounds
>
>Regards
>-------------------------------------------------------------------------------
>Kevin Wame | Ph.D. Student (IDeAL)
>KEMRI-Wellcome Trust Collaborative Research Programme
>Centre for Geographic Medicine Research
>P.O. Box 230-80108, Kilifi, Kenya
>
>
>On 7/3/16, 9:34 PM, "Jeff Newmiller" <jdnew...@dcn.davis.ca.us> wrote:
>
>I still get the impression from your mixing of information types that
>you are thinking like this is Excel.
>
>Perhaps something like
>
>drug_study$admin_period <- ave( "Y" == drug_study$drug_admin,
>drug_study$ID, FUN=cumsum )
>library(dplyr)
>result0 <- ( drug_study
> %>% filter( 0 != admin_period )
> %>% group_by( ID, admin_period )
> %>% summarise( start = min( date ) )
> %>% mutate( admin_period1 = admin_period -1 )
> )
>result <- ( result0
> %>% select( -admin_period )
> %>% inner_join( result0 %>% select( ID, admin_period1, end=start )
> , by = c( ID="ID", admin_period ="admin_period1" )
> )
> %>% mutate( ddays = end - start )
> )
>--
>Sent from my phone. Please excuse my brevity.
>
>On July 3, 2016 10:24:51 AM PDT, Kevin Wamae
><kwa...@kemri-wellcome.org> wrote:
>>HI Jeff, it’s been an uphill task working with the dataset and I am
>not
>>the first to complain. Nonetheless, data-cleaning is ongoing and since
>>I cannot wait for that to get done, I decided to make the most of what
>>the dataset looks like at this time. It appears the process may take a
>>while.
>>
>>Thanks for the script. From the output, I noticed that “result”
>>contains the first and last date for each of the individuals and not
>>taking into account the variable “drug-admin”.
>>
>>ID start end
>>J1/3 1/5/09 12/25/10
>>R1/3 1/4/07 12/15/08
>>R10/1 1/4/07 3/5/12
>>
>>My aim is to pick the date, for example in 2007, where drug-admin ==
>>“Y” as my start and the date in the subsequent year (2008 in this
>case)
>>where drug-admin == “Y” as my end. Then, I should populate the
>variable
>>“study_id” with “start” up to the entry just above the one whose date
>>matches “end”, as the output below shows (I hope its structure is
>>maintained as I have copied it from R-Studio). The goal for now is to
>>then get difference in days between “date” and “study_id” and still
>get
>>to keep that column for “study_id” as I might use it later.
>>
>>From the output, it can be seen that for this individual, the dates
>run
>>from 2007 to 2008. However, for some individuals, the dates run from
>>2008-2009, 2009-2010 and so on. Therefore, I need to make the script
>>deal with all the years as the dates range from 2001-2016
>>
>>ID date drug_admin year month study_id
>>R1/3 5/11/07 Y 2007 5 5/11/07
>>R1/3 5/16/07 2007 5 5/11/07
>>R1/3 5/22/07 2007 5 5/11/07
>>R1/3 5/28/07 2007 5 5/11/07
>>R1/3 6/5/07 2007 6 5/11/07
>>R1/3 6/11/07 2007 6 5/11/07
>>R1/3 6/18/07 2007 6 5/11/07
>>R1/3 6/25/07 2007 6 5/11/07
>>R1/3 7/2/07 2007 7 5/11/07
>>R1/3 7/16/07 2007 7 5/11/07
>>R1/3 7/29/07 2007 7 5/11/07
>>R1/3 8/2/07 2007 8 5/11/07
>>R1/3 8/7/07 2007 8 5/11/07
>>R1/3 8/13/07 2007 8 5/11/07
>>R1/3 9/18/07 2007 9 5/11/07
>>R1/3 9/24/07 2007 9 5/11/07
>>R1/3 10/6/07 2007 10 5/11/07
>>R1/3 10/8/07 2007 10 5/11/07
>>R1/3 10/15/07 2007 10 5/11/07
>>R1/3 10/22/07 2007 10 5/11/07
>>R1/3 10/29/07 2007 10 5/11/07
>>R1/3 11/8/07 2007 11 5/11/07
>>R1/3 11/12/07 2007 11 5/11/07
>>R1/3 11/19/07 2007 11 5/11/07
>>R1/3 11/29/07 2007 11 5/11/07
>>R1/3 12/6/07 2007 12 5/11/07
>>R1/3 12/10/07 2007 12 5/11/07
>>R1/3 12/21/07 2007 12 5/11/07
>>R1/3 1/7/08 2008 1 5/11/07
>>R1/3 1/14/08 2008 1 5/11/07
>>R1/3 1/21/08 2008 1 5/11/07
>>R1/3 1/28/08 2008 1 5/11/07
>>R1/3 2/4/08 Y 2008 2
>>
>>
>>Regards
>>-------------------------------------------------------------------------------
>>Kevin Wame
>>
>>###############################################################
>>
>>###############################################################
>>
>>
>>
>>On 7/3/16, 7:05 PM, "Jeff Newmiller" <jdnew...@dcn.davis.ca.us> wrote:
>>
>>result <- setNames( data.frame( aggregate( date~ID, data=drug_study,
>>FUN=min ), aggregate( date~ID, data=drug_study, FUN=max )[2] ), c(
>>"ID", "start", "end" ) )
>>
>>
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