The data below has columns for an individual ID (with repeat observations), Date
and Fate
.
ID Date Fate
1 BHS_1149 2017-04-11 MIA
2 BHS_1154 <NA> <NA>
3 BHS_1155 <NA> <NA>
4 BHS_1156 <NA> <NA>
5 BHS_1157 <NA> Mort
6 BHS_1159 2017-04-11 Alive
7 BHS_1169 2017-04-11 Alive
8 BHS_1259 <NA> <NA>
9 BHS_1260 <NA> <NA>
10 BHS_1262 2017-04-11 MIA
11 BHS_1262 2017-07-05 Alive
12 BHS_1262 2017-12-06 Alive
13 BHS_1262 2017-12-06 MIA
14 BHS_1262 2018-01-17 Mort
For each ID I want to make a new column that represents the min Date
or max Date
when Fate
is Alive. I have tryed different combinations if including and excluding the na.rm = T
argument in the code below but still get the following warnings.
library(tidyverse)
library(lubridate)
dat %>%
group_by(ID) %>%
mutate(
#the first or min of Date
FstSurvey = min(Date),
LstAlive = max(Date[Fate == "Alive"])) %>%
as.data.frame()
ID Date Fate FstSurvey LstAlive
1 BHS_1149 2017-04-11 MIA 2017-04-11 <NA>
2 BHS_1154 <NA> <NA> <NA> <NA>
3 BHS_1155 <NA> <NA> <NA> <NA>
4 BHS_1156 <NA> <NA> <NA> <NA>
5 BHS_1157 <NA> Mort <NA> <NA>
6 BHS_1159 2017-04-11 Alive 2017-04-11 2017-04-11
7 BHS_1169 2017-04-11 Alive 2017-04-11 2017-04-11
8 BHS_1259 <NA> <NA> <NA> <NA>
9 BHS_1260 <NA> <NA> <NA> <NA>
10 BHS_1262 2017-04-11 MIA 2017-04-11 2017-12-06
11 BHS_1262 2017-07-05 Alive 2017-04-11 2017-12-06
12 BHS_1262 2017-12-06 Alive 2017-04-11 2017-12-06
13 BHS_1262 2017-12-06 MIA 2017-04-11 2017-12-06
14 BHS_1262 2018-01-17 Mort 2017-04-11 2017-12-06
Warning messages:
1: In max.default(numeric(0), na.rm = FALSE) :
no non-missing arguments to max; returning -Inf
2: In max.default(numeric(0), na.rm = FALSE) :
no non-missing arguments to max; returning -Inf
The code seems to work as expected, but I have not been able to intrepret or avoid the errors and was not able to find a solution though the max
or min
help pages. The reproducable code is included below.
dat <- structure(list(ID = c("BHS_1149", "BHS_1154", "BHS_1155", "BHS_1156",
"BHS_1157", "BHS_1159", "BHS_1169", "BHS_1259", "BHS_1260", "BHS_1262",
"BHS_1262", "BHS_1262", "BHS_1262", "BHS_1262"), Date = structure(c(1491890400,
NA, NA, NA, NA, 1491890400, 1491890400, NA, NA, 1491890400, 1499234400,
1512543600, 1512543600, 1516172400), class = c("POSIXct", "POSIXt"
), tzone = ""), Fate = c("MIA", NA, NA, NA, "Mort", "Alive",
"Alive", NA, NA, "MIA", "Alive", "Alive", "MIA", "Mort")), row.names = c(NA,
-14L), .Names = c("ID", "Date", "Fate"), class = "data.frame")
I also like to write code that don't give me errors. Here is a suggestion on how to make the same calculations without warnings. By using ordered first and last instead of min and max you dont get the weird scenarios where r interpret max(NULL) becomes Inf.
dat %>%
group_by(ID) %>%
mutate(FstSurvey = first(Date,
order_by = Date),
LstAlive = last(Date[Fate == "Alive"],
order_by = Date[Fate == "Alive"]))
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