I have problems with the output after I bin the a numerical vector.
I am trying to bin the length of stay, which was calculated beforehand with difftime function. It does not make sense to provide the whole code since this is only the background. Yet, when I bin, I do not get the right answer. Here is the length of stay assigned it with los.
dput(los)
c(61.0416666666667, 61.0416666666667, 61.0416666666667, 2, 2, 3, 3)
Here are my breaks. I used na.rm inside as tried several methods. I passed na.rm with TRUE, FALSE and took it out of my breaks.
breaks <- c(0, 0.8, 0.16,
1.0, 1.8, 1.16,
2.0, 2.8, 2.16,
3.0, 3.8, 3.16,
4.0, 4.8, 4.16,
5.0, 5.8, 5.16,
6.0, 6.8, 6.16,
7.0, 14.0, 21.0, 28.0, max(los)) #, , na.rm = FALSE
Nevertheless, the next code tried
dt_los$losbinned <- cut(dt_los$LOS,
breaks = breaks,
labels = c("0hrs", "8hrs", "16hrs", "1 d",
"1 d 8hrs", "1 d 16hrs", "2 d",
"2 d 8hrs", "2 d 16hrs", "3 d",
"3 d 8hrs", "3 d 16hrs", "4 d",
"4 d 8hrs", "4 d 16hrs", "5 d",
"5 d 8hrs", "5 d 16hrs", "6 d",
"6 d 8hrs","6 d 16hrs", "7 - 14 d",
"14 - 21 d", "21 - 28 d", "> 28 d"),
right = FALSE)#
with different parameters passed for the 'right' gives me this:
when right = FALSE I do not get LOS for 61.04 binned for the category ">28 d". BBut do get the right bins for the other ones 2.00 and 3.00.
structure(list(IDcol = 101:107, Admissions = structure(c(1539160200,
1539160200, 1539160200, 1539154800, 1539154800, 1539154800, 1539154800
), class = c("POSIXct", "POSIXt"), tzone = "Europe/London"),
Discharges = structure(c(1544434200, 1544434200, 1544434200,
1539327600, 1539327600, 1539414000, 1539414000), class = c("POSIXct",
"POSIXt"), tzone = "Europe/London"), Admission_type = c("Elective",
"Emergency", "Emergency", "Elective", "Emergency", "Elective",
"Emergency"), LOS = c(61.0416666666667, 61.0416666666667,
61.0416666666667, 2, 2, 3, 3), Ward_code = c("DSN", "DSN",
"DNA", "NAS", "BAS", "BAS", "BAS"), Same_day_discharge = c(FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE), Spell_type = c("Elective",
"Emergency", "Emergency", "Elective", "Emergency", "Elective",
"Emergency"), Adm_period = c(TRUE, TRUE, TRUE, TRUE, TRUE,
TRUE, TRUE), losbinned = structure(c(NA, NA, NA, 7L, 7L,
10L, 10L), .Label = c("0hrs", "8hrs", "16hrs", "1 d", "1 d 8hrs",
"1 d 16hrs", "2 d", "2 d 8hrs", "2 d 16hrs", "3 d", "3 d 8hrs",
"3 d 16hrs", "4 d", "4 d 8hrs", "4 d 16hrs", "5 d", "5 d 8hrs",
"5 d 16hrs", "6 d", "6 d 8hrs", "6 d 16hrs", "7 - 14 d",
"14 - 21 d", "21 - 28 d", "> 28 d"), class = "factor")), row.names = c(NA,
-7L), class = c("tbl_df", "tbl", "data.frame"))
when I pass right = TRUE, the output for 61.04 is binning into ">28 d" which is the desired answer, yet, I do not get the right bins for 2.0 and 3.0, which are bbinned in 1 d 16hrs for 2.0 and 2 d 16 hrs for 3. And again, these shall be binned in 2, respectively 3.
structure(list(IDcol = 101:107, Admissions = structure(c(1539160200,
1539160200, 1539160200, 1539154800, 1539154800, 1539154800, 1539154800
), class = c("POSIXct", "POSIXt"), tzone = "Europe/London"),
Discharges = structure(c(1544434200, 1544434200, 1544434200,
1539327600, 1539327600, 1539414000, 1539414000), class = c("POSIXct",
"POSIXt"), tzone = "Europe/London"), Admission_type = c("Elective",
"Emergency", "Emergency", "Elective", "Emergency", "Elective",
"Emergency"), LOS = c(61.0416666666667, 61.0416666666667,
61.0416666666667, 2, 2, 3, 3), Ward_code = c("DSN", "DSN",
"DNA", "NAS", "BAS", "BAS", "BAS"), Same_day_discharge = c(FALSE,
FALSE, FALSE, FALSE, FALSE, FALSE, FALSE), Spell_type = c("Elective",
"Emergency", "Emergency", "Elective", "Emergency", "Elective",
"Emergency"), Adm_period = c(TRUE, TRUE, TRUE, TRUE, TRUE,
TRUE, TRUE), losbinned = structure(c(25L, 25L, 25L, 6L, 6L,
9L, 9L), .Label = c("0hrs", "8hrs", "16hrs", "1 d", "1 d 8hrs",
"1 d 16hrs", "2 d", "2 d 8hrs", "2 d 16hrs", "3 d", "3 d 8hrs",
"3 d 16hrs", "4 d", "4 d 8hrs", "4 d 16hrs", "5 d", "5 d 8hrs",
"5 d 16hrs", "6 d", "6 d 8hrs", "6 d 16hrs", "7 - 14 d",
"14 - 21 d", "21 - 28 d", "> 28 d"), class = "factor")), row.names = c(NA,
-7L), class = c("tbl_df", "tbl", "data.frame"))
The actual and expected results should the the right bins assigned for my length of stay. For 61.04 -> ">28d", for 2 -> "2 d", for 3 -> "3 d".
If this can be done with tidyverse that would be amazing. But respecting the bins I have assigned. However, I am aware this isn't done yet. Therefore, okay with the corrected code I have came up with, but corrected.
The cut function's bins are exclusive to inclusive.
From the cut function's help: The factor level labels are constructed as "(b1, b2]", "(b2, b3]" etc. for right = TRUE and as "[b1, b2)"
In order to include the lowest value (or highest value in this case), the include.lowest=TRUE option in required. This will make the first bin exclusive to exclusive, "[b1, b2]".
Try:
labels<-c("0hrs", "8hrs", "16hrs", "1 d",
"1 d 8hrs", "1 d 16hrs", "2 d",
"2 d 8hrs", "2 d 16hrs", "3 d",
"3 d 8hrs", "3 d 16hrs", "4 d",
"4 d 8hrs", "4 d 16hrs", "5 d",
"5 d 8hrs", "5 d 16hrs", "6 d",
"6 d 8hrs","6 d 16hrs", "7 - 14 d",
"14 - 21 d", "21 - 28 d", "> 28 d")
dt_los$losbinned <- cut(los, breaks=breaks, labels=labels, right=FALSE, include.lowest = TRUE)