Kevin Wamae
2016-Jul-02 09:57 UTC
[R] R - Populate Another Variable Based on Multiple Conditions | For a Large Dataset
I have a drug-trial study dataset (attached image).
Since its a large and complex dataset (at least to me) and I hope to be as clear
as possible with my question.
The dataset is from a study where individuals are given drugs and followed up
over a period spanning two consecutive years. Individuals do not start treatment
on the same day and once they start, the variable "drug-admin" is
marked "x" as well as the time they stop treatment in the following
year.
There exists another variable, "study_id", that I hope to populate as
can be seen in the dataset, with the following conditions:
For every individual
? if the individual has entries that show they received drugs both on the
start and end date (marked with the "x")
? if the start of drug administration falls in month == 2 | 3 and end of
administration falls in month == 2 | 4
? then, using the date that marks the start of drug administration, populate
the variable _"study_id"_ in all the rows that fall within the
timeframe that the individual was given drugs but excluding the end of drug
administration.
I have tried my level best and while I have explored several examples online, I
haven't managed to solve this. The dataset contains close to 6000
individuals spanning 10 years and my best bet was to use a loop which keeps
crushing R after running for close to 30min. I have also read that dplyr may do
the job but my attempts have been in vain.
sample code
-------------------------------------------------------------------------------------------------------------------------------------------------------------------
individual <- unique (df$ID) #vector of individuals
datalength <- dim(df)[1] #number of rows in dataframe
for (i in 1:length(individual)) {
for (j in 1:datalength) {
start_admin <- df[(df$year == 2007] & df$drug_admin == "x"
& c(df$month == 2 | df$month == 3),1] #capture date of start
end_admin <- df[(df$year == 2008] & df$drug_admin == "x"
& c(df$month == 2 | df$month == 4),1] #capture date of end
if(df[datalength,1] == individual(i) & df[datalength,2] >=
start_admin & df[datalength,2] < end_admin) {
df[datalength,6] <- start_admin #populate respective row if condition
is met
}
}
}
-------------------------------------------------------------------------------------------------------------------------------------------------------------------
Above is the code that keeps failing..
Any help is highly appreciated....
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Jeff Newmiller
2016-Jul-02 16:37 UTC
[R] R - Populate Another Variable Based on Multiple Conditions | For a Large Dataset
I can understand you not wanting to supply your actual data online, but only you know what your data looks like so only you can create a simulated data set that we could show you how to work with. -- Sent from my phone. Please excuse my brevity. On July 2, 2016 2:57:39 AM PDT, Kevin Wamae <KWamae at kemri-wellcome.org> wrote:>I have a drug-trial study dataset (attached image). > >Since its a large and complex dataset (at least to me) and I hope to be >as clear as possible with my question. >The dataset is from a study where individuals are given drugs and >followed up over a period spanning two consecutive years. Individuals >do not start treatment on the same day and once they start, the >variable "drug-admin" is marked "x" as well as the time they stop >treatment in the following year. >There exists another variable, "study_id", that I hope to populate as >can be seen in the dataset, with the following conditions: > >For every individual >? if the individual has entries that show they received drugs both >on the start and end date (marked with the "x") >? if the start of drug administration falls in month == 2 | 3 and >end of administration falls in month == 2 | 4 >? then, using the date that marks the start of drug administration, >populate the variable _"study_id"_ in all the rows that fall within the >timeframe that the individual was given drugs but excluding the end of >drug administration. >I have tried my level best and while I have explored several examples >online, I haven't managed to solve this. The dataset contains close to >6000 individuals spanning 10 years and my best bet was to use a loop >which keeps crushing R after running for close to 30min. I have also >read that dplyr may do the job but my attempts have been in vain. > >sample code >------------------------------------------------------------------------------------------------------------------------------------------------------------------- >individual <- unique (df$ID) #vector of individuals >datalength <- dim(df)[1] #number of rows in dataframe > >for (i in 1:length(individual)) { > for (j in 1:datalength) { >start_admin <- df[(df$year == 2007] & df$drug_admin == "x" & c(df$month >== 2 | df$month == 3),1] #capture date of start >end_admin <- df[(df$year == 2008] & df$drug_admin == "x" & c(df$month >== 2 | df$month == 4),1] #capture date of end > >if(df[datalength,1] == individual(i) & df[datalength,2] >= start_admin >& df[datalength,2] < end_admin) { >df[datalength,6] <- start_admin #populate respective row if condition >is met > } > } > } > >------------------------------------------------------------------------------------------------------------------------------------------------------------------- > >Above is the code that keeps failing.. > >Any help is highly appreciated.... > > >______________________________________________________________________ > >This e-mail contains information which is confidential. It is intended >only for the use of the named recipient. If you have received this >e-mail in error, please let us know by replying to the sender, and >immediately delete it from your system. Please note, that in these >circumstances, the use, disclosure, distribution or copying of this >information is strictly prohibited. KEMRI-Wellcome Trust Programme >cannot accept any responsibility for the accuracy or completeness of >this message as it has been transmitted over a public network. Although >the Programme has taken reasonable precautions to ensure no viruses are >present in emails, it cannot accept responsibility for any loss or >damage arising from the use of the email or attachments. Any views >expressed in this message are those of the individual sender, except >where the sender specifically states them to be the views of >KEMRI-Wellcome Trust Programme. >______________________________________________________________________ > > >------------------------------------------------------------------------ > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >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.
Kevin Wamae
2016-Jul-02 22:41 UTC
[R] R - Populate Another Variable Based on Multiple Conditions | For a Large Dataset
Hi Jeff, sorry for referring to you as Jennifer earlier, accept my apologies. I attached a sample dataset in the question, am afraid it must have failed to attach. I have attached it again.. Regards ------------------------------------------------------------------------------- Kevin Kariuki On 7/2/16, 7:37 PM, "Jeff Newmiller" <jdnewmil at dcn.davis.ca.us> wrote: I can understand you not wanting to supply your actual data online, but only you know what your data looks like so only you can create a simulated data set that we could show you how to work with. -- Sent from my phone. Please excuse my brevity. On July 2, 2016 2:57:39 AM PDT, Kevin Wamae <KWamae at kemri-wellcome.org> wrote:>I have a drug-trial study dataset (attached image). > >Since its a large and complex dataset (at least to me) and I hope to be >as clear as possible with my question. >The dataset is from a study where individuals are given drugs and >followed up over a period spanning two consecutive years. Individuals >do not start treatment on the same day and once they start, the >variable "drug-admin" is marked "x" as well as the time they stop >treatment in the following year. >There exists another variable, "study_id", that I hope to populate as >can be seen in the dataset, with the following conditions: > >For every individual >? if the individual has entries that show they received drugs both >on the start and end date (marked with the "x") >? if the start of drug administration falls in month == 2 | 3 and >end of administration falls in month == 2 | 4 >? then, using the date that marks the start of drug administration, >populate the variable _"study_id"_ in all the rows that fall within the >timeframe that the individual was given drugs but excluding the end of >drug administration. >I have tried my level best and while I have explored several examples >online, I haven't managed to solve this. The dataset contains close to >6000 individuals spanning 10 years and my best bet was to use a loop >which keeps crushing R after running for close to 30min. I have also >read that dplyr may do the job but my attempts have been in vain. > >sample code >------------------------------------------------------------------------------------------------------------------------------------------------------------------- >individual <- unique (df$ID) #vector of individuals >datalength <- dim(df)[1] #number of rows in dataframe > >for (i in 1:length(individual)) { > for (j in 1:datalength) { >start_admin <- df[(df$year == 2007] & df$drug_admin == "x" & c(df$month >== 2 | df$month == 3),1] #capture date of start >end_admin <- df[(df$year == 2008] & df$drug_admin == "x" & c(df$month >== 2 | df$month == 4),1] #capture date of end > >if(df[datalength,1] == individual(i) & df[datalength,2] >= start_admin >& df[datalength,2] < end_admin) { >df[datalength,6] <- start_admin #populate respective row if condition >is met > } > } > } > >------------------------------------------------------------------------------------------------------------------------------------------------------------------- > >Above is the code that keeps failing.. > >Any help is highly appreciated.... > > >______________________________________________________________________ > >This e-mail contains information which is confidential. It is intended >only for the use of the named recipient. If you have received this >e-mail in error, please let us know by replying to the sender, and >immediately delete it from your system. Please note, that in these >circumstances, the use, disclosure, distribution or copying of this >information is strictly prohibited. KEMRI-Wellcome Trust Programme >cannot accept any responsibility for the accuracy or completeness of >this message as it has been transmitted over a public network. Although >the Programme has taken reasonable precautions to ensure no viruses are >present in emails, it cannot accept responsibility for any loss or >damage arising from the use of the email or attachments. Any views >expressed in this message are those of the individual sender, except >where the sender specifically states them to be the views of >KEMRI-Wellcome Trust Programme. >______________________________________________________________________ > > >------------------------------------------------------------------------ > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >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 e-mail contains information which is confidential. It is intended only for the use of the named recipient. If you have received this e-mail in error, please let us know by replying to the sender, and immediately delete it from your system. Please note, that in these circumstances, the use, disclosure, distribution or copying of this information is strictly prohibited. KEMRI-Wellcome Trust Programme cannot accept any responsibility for the accuracy or completeness of this message as it has been transmitted over a public network. Although the Programme has taken reasonable precautions to ensure no viruses are present in emails, it cannot accept responsibility for any loss or damage arising from the use of the email or attachments. Any views expressed in this message are those of the individual sender, except where the sender specifically states them to be the views of KEMRI-Wellcome Trust Programme. ______________________________________________________________________ -------------- next part -------------- A non-text attachment was scrubbed... Name: XsOgd.png Type: image/png Size: 100935 bytes Desc: XsOgd.png URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20160702/c493765e/attachment.png>