-
Notifications
You must be signed in to change notification settings - Fork 0
/
panel.gaps.R
135 lines (82 loc) · 6.41 KB
/
panel.gaps.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
## Internal function, do not export
## Assumes that the data are all for a single patient (same id) and sorted in increasing order of t1.name
identify.panel.gaps.one.patient <- function(patient.dat, t1.name, t2.name, first.value = 0, expected.gap.between = 0){
require(data.table)
setDT(patient.dat)
gap.first.row <- (patient.dat[1, get(t1.name) > first.value])
n <- patient.dat[, .N]
if(n == 1){
res <- gap.first.row
}
if(n > 1){
t2.values <- patient.dat[1:(n-1), get(t2.name)]
gaps.other.rows <- patient.dat[2:n, get(t1.name) > t2.values + expected.gap.between]
res <- c(gap.first.row, gaps.other.rows)
}
return(res)
}
# Exportable function: panel.gaps
# Determines whether each record was preceded by a gap (missing period) of observation.
# dat: a data.frame structured as a panel data set.
# id.name: The (character) name of an identifying variable within the data.frame dat. Values from this variable are used to track subjects across multiple rows of data.
# t1.name: The (character) name of a time-tracking variable within the data.frame dat. Since panel data sets include intervals of time [t1, t2), the selected variable for t1.name should represent the left endpoints t1.
# t2.name: The (character) name of a time-tracking variable within the data.frame dat. Since panel data sets include intervals of time [t1, t2), the selected variable for t2.name should represent the right endpoints t2.
# gap.name: a (character) value for the name of the variable specifying whether a gap is observed before this record.
# first.value: The (numeric) expected beginning time of the observation period.
# expected.gap.between: The (numeric) amount of time expected between the end of one record and the next; zero by default.
panel.gaps <- function(dat, id.name = "id", t1.name = "t1", t2.name = "t2", gap.name = "gap_before", first.value = 0, expected.gap.between = 0){
if(is.data.frame(x = dat) == FALSE){
stop("Error: dat must be a data.frame object.")
}
all.variable.names <- unique(names(dat))
if((id.name %in% all.variable.names) == FALSE){
stop("Error: id.name must be a variable name from names(dat).")
}
if((t1.name %in% all.variable.names) == FALSE){
stop("Error: t1.name must be a variable name from names(dat).")
}
if((t2.name %in% all.variable.names) == FALSE){
stop("Error: t2.name must be a variable name from names(dat).")
}
require(data.table)
format.dt <- is.data.table(x = dat)
if(format.dt == FALSE){
setDT(x = dat)
}
setorderv(x = dat, cols = c(id.name, t1.name), order = 1)
dat[, eval(gap.name) := identify.panel.gaps.one.patient(patient.dat = .SD, t1.name = t1.name, t2.name = t2.name, first.value = first.value, expected.gap.between = expected.gap.between), by = id.name]
if(format.dt == FALSE){
setDF(x = dat)
}
return(dat[])
}
# Exportable function: first.panel.gap
# Determines the time point of the first gap (missing period) of observation for each unique subject.
# dat: a data.frame structured as a panel data set.
# id.name: The (character) name of an identifying variable within the data.frame dat. Values from this variable are used to track subjects across multiple rows of data.
# t1.name: The (character) name of a time-tracking variable within the data.frame dat. Since panel data sets include intervals of time [t1, t2), the selected variable for t1.name should represent the left endpoints t1.
# t2.name: The (character) name of a time-tracking variable within the data.frame dat. Since panel data sets include intervals of time [t1, t2), the selected variable for t2.name should represent the right endpoints t2.
# gap.name: a (character) value for the name of the variable specifying whether a gap is observed before this record.
# first.value: The (numeric) expected beginning time of the observation period.
# expected.gap.between: The (numeric) amount of time expected between the end of one record and the next; zero by default.
# append.to.table: The (logical) value specifying whether the calculated quantities should be appended (TRUE) as a new variable to the existing data or not (FALSE, default).
first.panel.gap <- function(dat, id.name = "id", t1.name = "t1", t2.name = "t2", gap.name = "gap_before", first.value = 0, expected.gap.between = 0, append.to.table = F){
the.gaps <- panel.gaps(dat = dat, id.name = id.name, t1.name = t1.name, t2.name = t2.name, gap.name = gap.name, first.value = first.value, expected.gap.between = expected.gap.between)
res <- first.event(dat = the.gaps, id.name = id.name, t1.name = t1.name, outcome.names = gap.name, append.to.table = append.to.table)
return(res)
}
# Exportable function: last.panel.gap
# Determines the time point of the last gap (missing period) of observation for each unique subject.
# dat: a data.frame structured as a panel data set.
# id.name: The (character) name of an identifying variable within the data.frame dat. Values from this variable are used to track subjects across multiple rows of data.
# t1.name: The (character) name of a time-tracking variable within the data.frame dat. Since panel data sets include intervals of time [t1, t2), the selected variable for t1.name should represent the left endpoints t1.
# t2.name: The (character) name of a time-tracking variable within the data.frame dat. Since panel data sets include intervals of time [t1, t2), the selected variable for t2.name should represent the right endpoints t2.
# gap.name: a (character) value for the name of the variable specifying whether a gap is observed before this record.
# first.value: The (numeric) expected beginning time of the observation period.
# expected.gap.between: The (numeric) amount of time expected between the end of one record and the next; zero by default.
# append.to.table: The (logical) value specifying whether the calculated quantities should be appended (TRUE) as a new variable to the existing data or not (FALSE, default).
last.panel.gap <- function(dat, id.name, t1.name, t2.name, gap.name = "gap_before", first.value = 0, expected.gap.between = 0, append.to.table = F){
the.gaps <- panel.gaps(dat = dat, id.name = id.name, t1.name = t1.name, t2.name = t2.name, gap.name = gap.name, first.value = first.value, expected.gap.between = expected.gap.between)
res <- last.event(dat = the.gaps, id.name = id.name, t1.name = t1.name, outcome.names = gap.name, append.to.table = append.to.table)
return(res)
}