[R] alternative for multiple if_else statements
Kevin Wamae
KWamae at kemri-wellcome.org
Fri Feb 23 06:13:13 CET 2018
Dear Eric, thank you for that observation.
I realised that some of the participants have duplicated “survey_start” dates and when I corrected this, the code works.
Regards
------------------
Kevin Wamae
From: Eric Berger <ericjberger at gmail.com>
Date: Thursday, 22 February 2018 at 15:16
To: Kevin Wamae <KWamae at kemri-wellcome.org>
Cc: "R-help at r-project.org" <R-help at r-project.org>
Subject: Re: [R] alternative for multiple if_else statements
Hi Kevin,
I ran the code on the full data set and was able to reproduce the problem that you are facing.
My guess is that you have an error in your intuition and/or logic, and that this relates to the use of the subscript [1].
Specifically, on the full dataset, the condition
trialData$date[trialData$survey_start == "Y" & trialData$year == 2013 & trialData$site == "site_1"]
yields 412 matches, of which there are 9 unique ones, specifically
April 2,3,4,5,8,10,11,16,17
In the full data set the first element that appears, i.e. subscript[1], is "2013-04-04".
In the filtered data set the first element that appears is "2013-04-05".
I hope that is enough information for you to make further progress from here.
Best,
Eric
On Thu, Feb 22, 2018 at 1:28 PM, Kevin Wamae <KWamae at kemri-wellcome.org<mailto:KWamae at kemri-wellcome.org>> wrote:
Dear Eric, wow, this seems to do the trick. But I have encountered a problem.
I have tested it on the larger dataset and it seems to work on a filtered dataset but not on the whole dataset (attached). See below script..
#load packages
Library(dplyr)
#load data
trialData <- fread("trialData.txt") %>% mutate(date = as.Date(date,"%d/%m/%Y"))
#create blank variable
trialData$survey_year <- rep(NA_character_, nrow(trialData))
#attempt 1 fails: code for survey
trialData$survey_year[trialData$date >= trialData$date[trialData$survey_start == "Y" & trialData$year == 2013 & trialData$site == "site_1"][1] & trialData$date < trialData$date[trialData$month == 4 & trialData$year == 2014 & trialData$site == "site_1"][1]] <- "survey_2013"
#filter trialData
trialData <- trialData %>% filter(id == "id_786/3")
#attempt 2 works: code for survey
trialData$survey_year[trialData$date >= trialData$date[trialData$survey_start == "Y" & trialData$year == 2013 & trialData$site == "site_1"][1] & trialData$date < trialData$date[trialData$month == 4 & trialData$year == 2014 & trialData$site == "site_1"][1]] <- "survey_2013"
From: Eric Berger <ericjberger at gmail.com<mailto:ericjberger at gmail.com>>
Date: Thursday, 22 February 2018 at 13:05
To: Kevin Wamae <KWamae at kemri-wellcome.org<mailto:KWamae at kemri-wellcome.org>>
Cc: "R-help at r-project.org<mailto:R-help at r-project.org>" <R-help at r-project.org<mailto:R-help at r-project.org>>
Subject: Re: [R] alternative for multiple if_else statements
Hi,
1. I think the reason that the different ordering leads to different results is because of the following:
date[ some condition is true ][1]
will give you an NA if there are no rows where 'some condition holds'.
In the code that 'works' you don't have such a situation, but in the code that 'does not work' you presumably hit an NA before you get to the result that you really want.
2. I am not a big fan of your "nested if" layout. I think you could rewrite it more clearly - and without nesting - with something like
> trialData$survey_year <- rep(NA_character_, nrow(trialData))
> trialData$survey_year[ condition for survey_2007 ] <- "survey_2007"
> trialData$survey_year[ condition for survey_2008 ] <- "survey_2008"
> etc
HTH,
Eric
On Wed, Feb 21, 2018 at 10:33 PM, Kevin Wamae <KWamae at kemri-wellcome.org<mailto:KWamae at kemri-wellcome.org>> wrote:
Hi, I am having trouble trying to figure out why if_else is behaving the way it is, it may be my code or the way the data is structured.
Below is a snapshot of a database am working on and it represents a longitudinal survey of study participants in a trial with weekly follow up.
The variable "survey_start" represents the start of the study-defined one year follow up (which we called "survey_year").
I am trying to populate all subsequent entries for each participant, per survey year, with the entry "survey" followed by an underscore and the respective year, eg. survey_2014.
There are missing entries such as the participant represented here, wasn't available at the start of the 2015 survey. Also, some participants don’t have complete one-year follow ups but I still need to include them.
I have written two codes, first one fails while the second works, the only difference being I have reversed the order in which the entries are populated in the second code (from 2007-2016 to 2016-2007) and removed the if_else statement for 2015. Also noticed, that for the second code, which spans the years 2007-2016 (less 2015), if a participants entries start from 2010-2016, the code fails.
Kindly assist in figuring this out...or better yet, an alternative.
trialData <- structure(list(study = c("site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1", "site_1", "site_1", "site_1", "site_1", "site_1",
"site_1", "site_1"), studyno = c("child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1", "child_1", "child_1", "child_1", "child_1",
"child_1", "child_1"), date = structure(c(16078, 16085, 16092,
16098, 16104, 16115, 16121, 16129, 16135, 16140, 16146, 16156,
16162, 16168, 16177, 16185, 16191, 16195, 16203, 16210, 16217,
16225, 16234, 16237, 16246, 16253, 16262, 16269, 16278, 16283,
16288, 16297, 16304, 16311, 16319, 16326, 16332, 16337, 16346,
16353, 16360, 16366, 16370, 16381, 16384, 16395, 16399, 16407,
16415, 16422, 16444, 16452, 16454, 16467, 16474, 16477, 16484,
16490, 16501, 16508, 16514, 16520, 16529, 16533, 16539, 16550,
16556, 16564, 16566, 16578, 16582, 16593, 16599, 16604, 16613,
16620, 16623, 16635, 16636, 16654, 16660, 16666, 16673, 16681,
16688, 16693, 16702, 16706, 16714, 16721, 16728, 16734, 16745,
16749, 16757, 16764, 16769, 16778, 16785, 16792, 16805, 16812,
16819, 16830, 16832, 16839, 16846, 16856, 16862, 16867, 16877,
16884, 16890, 16898, 16904, 16912, 16917, 16923, 16936, 16938,
16953, 16960, 16966, 16973, 16980), class = "Date"), year = c(2014L,
2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L,
2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L,
2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L,
2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L,
2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L, 2014L,
2014L, 2014L, 2014L, 2014L, 2015L, 2015L, 2015L, 2015L, 2015L,
2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L,
2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L,
2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L,
2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L,
2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L,
2016L, 2016L, 2016L, 2016L, 2016L, 2016L, 2016L, 2016L, 2016L,
2016L, 2016L, 2016L, 2016L, 2016L, 2016L, 2016L, 2016L, 2016L,
2016L, 2016L, 2016L, 2016L, 2016L, 2016L, 2016L), month = c(1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L,
5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L,
8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L,
12L, 12L, 12L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L,
4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 7L, 7L, 7L,
7L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L,
11L, 11L, 11L, 11L, 12L, 12L, 12L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L,
6L, 6L), survey_start = c("", "", "", "", "", "", "", "", "",
"", "", "", "", "", "", "", "", "Y", "", "", "", "", "", "",
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "",
"", "", "", "", "", "", "Y", "", "", "", "", "", "", "", "",
"", "", "", "", "", "")), class = "data.frame", row.names = c(NA,
-125L), .Names = c("study", "studyno", "date", "year", "month",
"survey_start"))
code 1 fails:
trialData <- trialData %>% arrange(studyno, date) %>% group_by(studyno) %>%
mutate(survey_year = if_else(date >= date[survey_start == "Y" & year == 2007 & study == "site_1"][1] & date < date[month == 5 & year == 2008 & study == "site_1"][1], "survey_2007",
if_else(date >= date[survey_start == "Y" & year == 2008 & study == "site_1"][1] & date < date[month == 4 & year == 2009 & study == "site_1"][1], "survey_2008",
if_else(date >= date[survey_start == "Y" & year == 2009 & study == "site_1"][1] & date < date[month == 5 & year == 2010 & study == "site_1"][1], "survey_2009",
if_else(date >= date[survey_start == "Y" & year == 2010 & study == "site_1"][1] & date < date[month == 5 & year == 2011 & study == "site_1"][1], "survey_2010",
if_else(date >= date[survey_start == "Y" & year == 2011 & study == "site_1"][1] & date < date[month == 4 & year == 2012 & study == "site_1"][1], "survey_2011",
if_else(date >= date[survey_start == "Y" & year == 2012 & study == "site_1"][1] & date < date[month == 4 & year == 2013 & study == "site_1"][1], "survey_2012",
if_else(date >= date[survey_start == "Y" & year == 2013 & study == "site_1"][1] & date < date[month == 4 & year == 2014 & study == "site_1"][1], "survey_2013",
if_else(date >= date[survey_start == "Y" & year == 2014 & study == "site_1"][1] & date < date[month == 4 & year == 2015 & study == "site_1"][1], "survey_2014",
if_else(date >= date[survey_start == "Y" & year == 2015 & study == "site_1"][1] & date < date[month == 3 & year == 2016 & study == "site_1"][1], "survey_2015",
if_else(date >= date[survey_start == "Y" & year == 2016 & study == "site_1"][1], "survey_2016","")))))))))))
code 2 works:
trialData <- trialData %>% arrange(studyno, date) %>% group_by(studyno) %>%
mutate(survey_year = if_else(date >= date[survey_start == "Y" & year == 2016 & study == "site_1"][1] , "survey_2016",
if_else(date >= date[survey_start == "Y" & year == 2014 & study == "site_1"][1] & date < date[month == 4 & year == 2015 & study == "site_1"][1], "survey_2014",
if_else(date >= date[survey_start == "Y" & year == 2013 & study == "site_1"][1] & date < date[month == 4 & year == 2014 & study == "site_1"][1], "survey_2013",
if_else(date >= date[survey_start == "Y" & year == 2012 & study == "site_1"][1] & date < date[month == 4 & year == 2013 & study == "site_1"][1], "survey_2012",
if_else(date >= date[survey_start == "Y" & year == 2011 & study == "site_1"][1] & date < date[month == 4 & year == 2012 & study == "site_1"][1], "survey_2011",
if_else(date >= date[survey_start == "Y" & year == 2010 & study == "site_1"][1] & date < date[month == 5 & year == 2011 & study == "site_1"][1], "survey_2010",
if_else(date >= date[survey_start == "Y" & year == 2009 & study == "site_1"][1] & date < date[month == 5 & year == 2010 & study == "site_1"][1], "survey_2009",
if_else(date >= date[survey_start == "Y" & year == 2008 & study == "site_1"][1] & date < date[month == 4 & year == 2009 & study == "site_1"][1], "survey_2008",
if_else(date >= date[survey_start == "Y" & year == 2007 & study == "site_1"][1] & date < date[month == 5 & year == 2008 & study == "site_1"][1], "survey_2007",""))))))))))
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