-
Notifications
You must be signed in to change notification settings - Fork 4
/
prisma.R
101 lines (87 loc) · 3.51 KB
/
prisma.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
#' generate PRISMA statement flow chart
#'
#' generate PRISMA statement flow chart for use in retrospective medical
#' research
#' @param found Records found through database searching
#' @param found_other Additional records identified through other sources
#' @param no_dupes Records after duplicates removed
#' @param screened Records screened
#' @param screen_exclusions Records excluded
#' @param full_text Full-text articles assessed for eligibility
#' @param full_text_exclusions Full-text articles excluded with reasons
#' @param qualitative Studies included in qualitative analysis
#' @param quantitative Studies included in quantitative synthesis
#' (meta-analysis)
#' @param reasons Reaons for full text exclusion (as string)
#' @param ... Further arguments are passed to \code{grViz}
#' @source
#' \url{http://www.prisma-statement.org/PRISMAStatement/FlowDiagram.aspx}
#' @examples
#' prisma(1, 2, 3, 4, 5, 6, 7, 8, 9, "Incorrect design n=10")
#' @export
prisma <- function(found, found_other,
no_dupes,
screened, screen_exclusions,
full_text, full_text_exclusions,
qualitative,
quantitative, reasons,...) {
stopifnot(length(found) == 1)
stopifnot(length(found_other) == 1)
stopifnot(length(no_dupes) == 1)
stopifnot(length(screened) == 1)
stopifnot(length(screen_exclusions) == 1)
stopifnot(length(full_text) == 1)
stopifnot(length(full_text_exclusions) == 1)
stopifnot(length(qualitative) == 1)
stopifnot(length(quantitative) == 1)
stopifnot(found == floor(found))
stopifnot(found_other == floor(found_other))
stopifnot(no_dupes == floor(no_dupes))
stopifnot(screened == floor(screened))
stopifnot(screen_exclusions == floor(screen_exclusions))
stopifnot(full_text == floor(full_text))
stopifnot(full_text_exclusions == floor(full_text_exclusions))
stopifnot(qualitative == floor(qualitative))
stopifnot(quantitative == floor(quantitative))
stopifnot(found >= 0)
stopifnot(found_other >= 0)
stopifnot(no_dupes >= 0)
stopifnot(screened >= 0)
stopifnot(screen_exclusions >= 0)
stopifnot(full_text >= 0)
stopifnot(full_text_exclusions >= 0)
stopifnot(qualitative >= 0)
stopifnot(quantitative >= 0)
requireNamespace("DiagrammeR")
dot_template <- 'digraph prisma {
node [shape="box", width=3.5, style=filled, tooltip="PRISMA Flowchart", fillcolor=white];
graph [splines=ortho, nodesep=1, tooltip="PRISMA Flowchart"]
a -> nodups;
b -> nodups;
a [label="Records identified through\ndatabase searching\n(n = %d)"];
b [label="Additional records identified\nthrough other sources\n(n = %d)"]
nodups -> incex;
nodups [label="Records after duplicates removed\n(n = %d)"];
incex -> {ex; ft}
incex [label="Records screened\n(n = %d)"];
ex [label="Records excluded\n(n = %d)"];
{rank=same; incex ex}
ft -> {qual; ftex};
ft [label="Full-text articles assessed\nfor eligibility\n(n = %d)"];
{rank=same; ft ftex}
ftex [label="Full-text articles excluded,\n(n = %d)"];
qual -> quant
qual [label="Studies included in qualitative synthesis\n(n = %d)"];
quant [label="Studies included in\nquantitative synthesis\n(meta-analysis)\n(n = %d)"];
reasons [label="Reasons for full-text exclusion\n%s"]
ftex -> reasons
}'
DiagrammeR::grViz(
sprintf(dot_template,
found, found_other,
no_dupes,
screened, screen_exclusions,
full_text, full_text_exclusions,
qualitative, quantitative, reasons),
...)
}