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Merge pull request #12 from chriscpritchard/shiny-update
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Fixed blank line regression
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@nealhaddaway
nealhaddaway authored Jul 7, 2021
2 parents 2b105e9 + 1eb00d8 commit 8299e6c
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Showing 6 changed files with 168 additions and 83 deletions.
235 changes: 160 additions & 75 deletions R/PRISMA_flowdiagram.R
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,11 @@ PRISMA_flowdiagram <- function (data,
} else {
other_excludedh <- 3.5
}

#remove previous box if both values are zero
if (is.na(previous_studies) == TRUE && is.na(previous_reports) == TRUE) {
previous <- FALSE
}

if(previous == TRUE){
xstart <- 0
ystart <- 0
Expand All @@ -104,26 +108,43 @@ PRISMA_flowdiagram <- function (data,
12->19;\n")
h_adj1 <- 0
h_adj2 <- 0
previous_nodes <- paste0("node [shape = box,

#conditional studies and reports - empty text if blank
if(is.na(previous_studies) == TRUE) {
cond_prevstud <- ''
} else {
cond_prevstud <- stringr::str_wrap(paste0(previous_studies_text,
" (n = ",
previous_studies,
")"),
width = 40)
}
if(is.na(previous_reports) == TRUE) {
cond_prevrep <- ''
} else {
cond_prevrep <- paste0(stringr::str_wrap(previous_reports_text,
width = 40),
"\n(n = ",
previous_reports,
')')
}
if (is.na(previous_studies) == TRUE || is.na(previous_reports) == TRUE) {
dbl_br <- ''
} else {
dbl_br <- "\n\n"
}
previous_nodes <- paste0("node [shape = box,
fontsize = ", fontsize,",
fontname = ", font,",
fontname = ", font, ",
color = ", greybox_colour, "]
1 [label = '", previous_text, "', style = 'rounded,filled', width = 3.5, height = 0.5, pos='",xstart+1,",",ystart+8.25,"!', tooltip = '", tooltips[1], "']
node [shape = box,
fontname = ", font, ",
color = ", greybox_colour, "]
2 [label = '",paste0(stringr::str_wrap(paste0(previous_studies_text,
" (n = ",
previous_studies,
")"),
width = 40),
"\n\n",
paste0(stringr::str_wrap(previous_reports_text,
width = 40),
"\n(n = ",
previous_reports,
')')),
2 [label = '",paste0(cond_prevstud,
dbl_br,
cond_prevrep),
"', style = 'filled', width = 3.5, height = 0.5, pos='",xstart+1,",",ystart+7,"!', tooltip = '", tooltips[2], "']")
finalnode <- paste0("
node [shape = box,
Expand Down Expand Up @@ -157,8 +178,7 @@ PRISMA_flowdiagram <- function (data,
h_adj2 <- 1.4
prev_rank1 <- ""
prevnode1 <- ""
prevnode2 <- ""

prevnode2 <- ""
}
if(side_boxes == TRUE){
sidebox <- paste0("node [shape = box,
Expand All @@ -173,6 +193,9 @@ PRISMA_flowdiagram <- function (data,
} else {
sidebox <- ""
}
if (is.na(website_results) == TRUE && is.na(organisation_results) == TRUE && is.na(citations_results) == TRUE) {
other <- FALSE
}
if(other == TRUE){
if (is.data.frame(other_excluded) == TRUE){
other_excluded_data <- paste0(':',
Expand All @@ -187,6 +210,31 @@ PRISMA_flowdiagram <- function (data,
other_excluded_data <- paste0('\n', '(n = ', other_excluded, ')')
}
B <- paste0("B [label = '', pos='",xstart+13,",",ystart+1.5,"!', tooltip = '']")

if (is.na(website_results) == FALSE) {
cond_websites <- paste0(website_results_text,
" (n = ",
website_results,
')\n')
} else {
cond_websites <- ''
}
if (is.na(organisation_results) == FALSE) {
cond_organisation <- paste0(organisation_results_text,
" (n = ",
organisation_results,
')\n')
} else {
cond_organisation <- ''
}
if (is.na(citations_results) == FALSE) {
cond_citation <- paste0(citations_results_text,
" (n = ",
citations_results,
')')
} else {
cond_citation <- ''
}
cluster2 <- paste0("subgraph cluster2 {
edge [color = White,
arrowhead = none,
Expand Down Expand Up @@ -216,18 +264,9 @@ PRISMA_flowdiagram <- function (data,
fontname = ", font, ",
color = ", greybox_colour, "]
14 [label = '", paste0('Records identified from:\n',
website_results_text,
" (n = ",
website_results,
')\n',
organisation_results_text,
" (n = ",
organisation_results,
')\n',
citations_results_text,
" (n = ",
citations_results,
')'),
cond_websites,
cond_organisation,
cond_citation),
"', style = 'filled', width = 3.5, height = 0.5, pos='",xstart+13,",",ystart+7,"!', tooltip = '", tooltips[6], "']
node [shape = box,
Expand Down Expand Up @@ -279,7 +318,85 @@ PRISMA_flowdiagram <- function (data,
othernodeB <- ""

}
if (any(!grepl("\\D", dbr_excluded)) == FALSE){
dbr_excluded_data <- paste0(':',
paste(paste('\n',
dbr_excluded[,1],
' (n = ',
dbr_excluded[,2],
')',
sep = ''),
collapse = ''))
} else {
dbr_excluded_data <- paste0('\n', '(n = ', dbr_excluded, ')')
}

if (is.na(database_results) == FALSE) {
cond_database <- paste0(database_results_text,
' (n = ',
database_results,
')\n')
} else {
cond_database <- ''
}
if (is.na(register_results) == FALSE) {
cond_register <- paste0(register_results_text,
' (n = ',
register_results,
')')
} else {
cond_register <- ''
}

if (is.na(duplicates) == FALSE) {
cond_duplicates <- paste0(stringr::str_wrap(paste0(duplicates_text,
' (n = ',
duplicates,
')'),
width = 42),
'\n')
} else {
cond_duplicates <- ''
}
if (is.na(excluded_automatic) == FALSE) {
cond_automatic <- paste0(stringr::str_wrap(paste0(excluded_automatic_text,
' (n = ',
excluded_automatic,
')'),
width = 42),
'\n')
} else {
cond_automatic <- ''
}
if (is.na(excluded_other) == FALSE) {
cond_exclother <- paste0(stringr::str_wrap(paste0(excluded_other_text,
' (n = ',
excluded_other,
')'),
width = 42))
} else {
cond_exclother <- ''
}
if (is.na(duplicates) == TRUE && is.na(excluded_automatic) == TRUE && is.na(excluded_other) == TRUE) {
cond_duplicates <- paste0('(n = 0)')
}

if(is.na(new_studies) == FALSE) {
cond_newstud <- paste0(stringr::str_wrap(new_studies_text, width = 40),
'\n(n = ',
new_studies,
')\n')
} else {
cond_newstud <- ''
}
if(is.na(new_reports) == FALSE) {
cond_newreports <- paste0(stringr::str_wrap(new_reports_text, width = 40),
'\n(n = ',
new_reports,
')')
} else {
cond_newreports <- ''
}
x <- DiagrammeR::grViz(
paste0("digraph TD {
Expand All @@ -295,51 +412,31 @@ PRISMA_flowdiagram <- function (data,
node [shape = box,
fontname = ", font, ",
color = ", main_colour, "]
4 [label = '", paste0('Records identified from:\n',
database_results_text,
' (n = ',
database_results,
')\n',
register_results_text,
' (n = ',
register_results,
')'), "', width = 3.5, height = 0.5, height = 0.5, pos='",xstart+5,",",ystart+7,"!', tooltip = '", tooltips[4], "']
4 [label = '", paste0('Records identified from:\n',
cond_database,
cond_register), "', width = 3.5, height = 0.5, height = 0.5, pos='",xstart+5,",",ystart+7,"!', tooltip = '", tooltips[4], "']
node [shape = box,
fontname = ", font, ",
color = ", main_colour, "]
5 [label = '", paste0('Records removed before screening:\n',
stringr::str_wrap(paste0(duplicates_text,
' (n = ',
duplicates,
')'),
width = 42),
'\n',
stringr::str_wrap(paste0(excluded_automatic_text,
' (n = ',
excluded_automatic,
')'),
width = 42)
,'\n',
stringr::str_wrap(paste0(excluded_other_text,
' (n = ',
excluded_other,
')'),
width = 42)),
"', width = 3.5, height = 0.5, pos='",xstart+9,",",ystart+7,"!', tooltip = '", tooltips[7], "']
cond_duplicates,
cond_automatic,
cond_exclother),
"', width = 3.5, height = 0.5, pos='",xstart+9,",",ystart+7,"!', tooltip = '", tooltips[7], "']
node [shape = box,
fontname = ", font, ",
color = ", main_colour, "]
6 [label = '", paste0(records_screened_text,
6 [label = '", paste0(records_screened_text,
'\n(n = ',
records_screened,
')'), "', width = 3.5, height = 0.5, height = 0.5, pos='",xstart+5,",",ystart+5.5,"!', tooltip = '", tooltips[8], "']
node [shape = box,
fontname = ", font, ",
color = ", main_colour, "]
7 [label = '", paste0(records_excluded_text,
7 [label = '", paste0(records_excluded_text,
'\n(n = ',
records_excluded,
')'), "', width = 3.5, height = 0.5, pos='",xstart+9,",",ystart+5.5,"!', tooltip = '", tooltips[9], "']
Expand All @@ -355,15 +452,15 @@ PRISMA_flowdiagram <- function (data,
node [shape = box,
fontname = ", font, ",
color = ", main_colour, "]
9 [label = '", paste0(dbr_notretrieved_reports_text,
9 [label = '", paste0(dbr_notretrieved_reports_text,
'\n(n = ',
dbr_notretrieved_reports,
')'), "', width = 3.5, height = 0.5, pos='",xstart+9,",",ystart+4.5,"!', tooltip = '", tooltips[11], "']
node [shape = box,
fontname = ", font, ",
color = ", main_colour, "]
10 [label = '", paste0(dbr_assessed_text,
10 [label = '", paste0(dbr_assessed_text,
'\n(n = ',
dbr_assessed,
')'), "', width = 3.5, height = 0.5, pos='",xstart+5,",",ystart+3.5,"!', tooltip = '", tooltips[14], "']
Expand All @@ -374,25 +471,13 @@ PRISMA_flowdiagram <- function (data,
fillcolor = White,
style = filled]
11 [label = '", paste0(dbr_excluded_text,
paste(paste('\n',
dbr_excluded[,1],
' (n = ',
dbr_excluded[,2],
')',
sep = ''),
collapse = '')), "', width = 3.5, height = 0.5, pos='",xstart+9,",",ystart+dbr_excludedh,"!', tooltip = '", tooltips[15], "']
dbr_excluded_data), "', width = 3.5, height = 0.5, pos='",xstart+9,",",ystart+dbr_excludedh,"!', tooltip = '", tooltips[15], "']
node [shape = box,
fontname = ", font, ",
color = ", main_colour, ", fillcolor = '', style = solid]
12 [label = '", paste0(stringr::str_wrap(new_studies_text, width = 40),
'\n(n = ',
new_studies,
')\n',
stringr::str_wrap(new_reports_text, width = 40),
'\n(n = ',
new_reports,
')'), "', width = 3.5, height = 0.5, pos='",xstart+5,",",ystart+1.5,"!', tooltip = '", tooltips[18], "']
12 [label = '", paste0(cond_newstud,
cond_newreports), "', width = 3.5, height = 0.5, pos='",xstart+5,",",ystart+1.5,"!', tooltip = '", tooltips[18], "']
",othernodes,

Expand Down
2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ A static version is produced otherwise. <a href="https://srflowdiagram.github.io
See the interactive template here.</a><br>

Please cite as:<br>
Neal R Haddaway, Chris C Pritchard and Luke A McGuinness (2020). PRISMA2020: R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams (Version 0.0.2). doi: <a href="https://doi.org/10.5281/zenodo.4287835" target="_blank">10.5281/zenodo.4287835</a><br>
Neal R Haddaway, Chris C Pritchard and Luke A McGuinness (2021). PRISMA2020: R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams (Version 0.0.2). doi: <a href="https://doi.org/10.5281/zenodo.4287835" target="_blank">10.5281/zenodo.4287835</a><br>
<a id="raw-url" href="https://raw.githubusercontent.com/nealhaddaway/PRISMA2020/master/inst/extdata/citation.ris">Citation in .ris format (right click 'Save Link As')</a>

<!-- badges: start -->
Expand Down
4 changes: 2 additions & 2 deletions inst/CITATION
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,10 @@ citEntry(
entry = "Manual",
title = "PRISMA2020: R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams (Version 0.0.2)",
author = "Neal R Haddaway, Chris C Pritchard and Luke A McGuinness",
year = "2020",
year = "2021",
doi = "10.5281/zenodo.4287835",
textVersion = paste(
"Neal R Haddaway, Chris C Pritchard and Luke A McGuinness (2020).",
"Neal R Haddaway, Chris C Pritchard and Luke A McGuinness (2021).",
"PRISMA2020: R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams (Version 0.0.2)",
"zenodo. https://doi.org/10.5281/zenodo.4287835"
)
Expand Down
2 changes: 1 addition & 1 deletion inst/extdata/citation.ris
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ AU - Pritchard, C. C.
AU - McGuinness, L. A.
DO - 10.5281/zenodo.4287835
PB - Zenodo
PY - 2020
PY - 2021
ST - PRISMA2020: R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams (Version 0.0.2)
TI - PRISMA2020: R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams (Version 0.0.2)
UR - http://doi.org/10.5281/zenodo.4287835
Expand Down
6 changes: 3 additions & 3 deletions inst/shiny-examples/PRISMA_flowdiagram/app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -56,10 +56,10 @@ ui <- tagList(
hr(),
'Please cite as:',
br(),
'Neal R Haddaway, Chris C Pritchard, Luke A McGuinness. (2020). PRISMA2020: R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams (Version 0.0.2). Zenodo.',
'Neal R Haddaway, Chris C Pritchard, Luke A McGuinness. (2021). PRISMA2020: R package and ShinyApp for producing PRISMA 2020 compliant flow diagrams (Version 0.0.2). Zenodo.',
tags$a(href="http://doi.org/10.5281/zenodo.4287835", "http://doi.org/10.5281/zenodo.4287835"),
br(),
tags$a(href="Haddaway_Pritchard_and_McGuinness2020.ris", "Download citation (.ris)", download=NA, target="_blank")
tags$a(href="Haddaway_Pritchard_and_McGuinness2021.ris", "Download citation (.ris)", download=NA, target="_blank")
)
),

Expand All @@ -76,7 +76,7 @@ ui <- tagList(
'Jack Wasey (advisor)', br(),
br(),
tags$a(href="https://github.com/nealhaddaway/PRISMA2020", tags$img(height = 40, width = 40, src = "https://pngimg.com/uploads/github/github_PNG40.png")),
'Created November 2020, Updated June 2021'
'Created November 2020, Updated July 2021'
)
)
),
Expand Down
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