R/screen_abstracts.R
In mjwestgate/bibviewr: Tools to Support Evidence Synthesis
Defines functions
screen_abstracts
Documented in
screen_abstracts
screen_abstracts <- function(
x = NULL,
max_file_size
){
# set file size if requested, ensuring to reset on exit
if(!missing(max_file_size)){
initial_file_size <- options("shiny.maxRequestSize")
options(shiny.maxRequestSize = max_file_size * 1024^2)
on.exit(options(initial_file_size))
}
# load data
data_in <- load_abstract_data(
data = x
)
# create ui
ui_data <- screen_abstracts_ui()
ui <- shinydashboard::dashboardPage(
title = "revtools | screen_abstracts",
ui_data$header,
ui_data$sidebar,
ui_data$body,
skin = "black"
)
# start server
server <- function(input, output, session){
# build reactive values
data <- reactiveValues(
raw = data_in$data$raw
)
progress <- reactiveValues(
order = data_in$progress$order,
available = data_in$progress$available,
current = data_in$progress$current,
row = data_in$progress$row,
max_n = data_in$progress$max_n
)
display <- reactiveValues(
notes = FALSE,
column = "label"
)
# create header image
output$header <- renderPlot({
revtools_logo(text = "screen_abstracts")
})
# DATA INPUT
## when specified, ensure input data is processed correctly
observeEvent(input$data_in, {
if(is.null(data$raw)){
data_previous <- data_in$raw
}else{
data_previous <- data$raw
}
import_result <- import_shiny(
source = input$data_in,
current_data = data_previous
)
import_result <- add_abstract_columns(import_result)
# export to reactiveValues
data$raw <- import_result
# set progress values
progress$order <- set_row_order(
data$raw,
input$order,
input$order_result
)
if(is.null(progress$current) | progress$current < 1){
progress$current <- 1
}
if(input$hide_screened){
# if(length(progress$screen_cols) > 1){
# progress$available <- which(
# apply(data$raw[, progress$screen_cols], 1, function(a){all(is.na(a))})
# )
# }else{
# progress$available <- which(is.na(data$raw[, progress$screen_cols]))
# }
progress$available <- which(is.na(data$raw$screened_abstracts))
progress$max_n <- length(progress$available)
}else{
progress$max_n <- nrow(data$raw)
progress$available <- seq_len(progress$max_n)
}
progress$row <- choose_abstract_row(
progress$order, progress$available, progress$current
)
})
# allow user to select order
output$column_selector <- renderUI({
if(input$order == "user_defined"){
available_colnames <- colnames(data$raw)
selectInput(
inputId = "order_result",
label = "Select variable to order by:",
choices = available_colnames,
selected = display$column
)
}
})
# ensure decisions about selected columns are retained
observeEvent(input$order_result, {
display$column <- input$order_result
})
# ABSTRACT SCREENING
# change order of articles as necessary
observeEvent(input$order_result_go, {
progress$order <- set_row_order(
data$raw,
input$order,
input$order_result
)
progress$current <- 1
progress$row <- choose_abstract_row(
progress$order, progress$available, progress$current
)
})
# display text for the current entry
# note that observe is necessary to force changes when input$order changes
observe({
output$citation <- renderPrint({
validate(
need(data$raw, "Import data to begin")
)
validate(
need(progress$max_n > 0,
"No unscreened data remaining\nAdd more data, or save and exit to continue")
)
if(any(colnames(data$raw) == "abstract")){
abstract_text <- data$raw$abstract[progress$row]
}else{
abstract_text <- "<em>No abstract available</em>"
}
current_status <- data$raw$screened_abstracts[progress$row]
if(is.na(current_status)){
text_color <- "black"
text_label <- ""
}else{
if(current_status == "excluded"){
text_color <- "'#993f3f'"
text_label <- "Status: Excluded"
}else{
text_color <- "'#405d99'"
text_label <- "Status: Selected"
}
}
cat(
paste0(
"<font color =", text_color, ">",
format_citation(
data$raw[progress$row, ],
abstract = FALSE,
details = (input$hide_names == FALSE),
add_html = TRUE
),
"<br>",
text_label,
"<br><br>",
abstract_text,
"</font>"
)
)
})
})
# RENDER SELECTION BUTTONS
output$selector_bar <- renderUI({
if(!is.null(data$raw)){
text_out <- HTML(
paste0(
nrow(data$raw) - length(which(is.na(data$raw$screened_abstracts))),
" entries screened | Showing entry ",
progress$current,
" of ",
progress$max_n
)
)
div(
list(
div(
style = "
display: inline-block;
vertical-align: top;
text-align: right;
width: 350px",
renderText({text_out})
),
div(
style = "
display: inline-block;
vertical-align: top;
text-align: right;
width: 20px",
renderText(" ")
),
div(
style = "
display: inline-block;
vertical-align: top;
width: 40px",
actionButton(
inputId = "abstract_10previous",
label = "<<",
width = "40px",
style = "background-color: #6b6b6b;"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
width: 40px",
actionButton(
inputId = "abstract_previous",
label = "<",
width = "40px",
style = "background-color: #6b6b6b;"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
text-align: right;
width: 100px",
actionButton(
inputId = "select_yes",
label = "Select",
style = "
background-color: #7c93c1;
color: #fff;
width: 100px"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
text-align: right;
width: 100px",
actionButton(
inputId = "select_no",
label = "Exclude",
style = "
background-color: #c17c7c;
color: #fff;
width: 100px"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
width: 40px",
actionButton(
inputId = "abstract_next",
label = ">",
width = "40px",
style = "background-color: #6b6b6b;"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
width: 40px",
actionButton(
inputId = "abstract_10next",
label = ">>",
width = "40px",
style = "background-color: #6b6b6b;"
)
)
)
)
}
})
output$render_notes_toggle <- renderUI({
if(!is.null(data$raw)){
if(progress$max_n > 0){
actionButton(
inputId = "notes_toggle",
label = "Show notes window",
style = "
background-color: #adadad;
color: #fff;
width: 200px"
)
}
}
})
# NOTES
# when toggle is triggered, invert display status of notes
observeEvent(input$notes_toggle, {
display$notes <- !display$notes
})
# render notes
output$render_notes <- renderUI({
if(display$notes){
div(
list(
br(),
textAreaInput(
inputId = "abstract_notes",
label = NULL,
value = data$raw$notes[progress$row],
resize = "both",
width = "400px",
height = "150px"
),
actionButton(
inputId = "notes_save",
label = "Save Notes",
width = "100px"
),
br()
)
)
}
})
# save notes
observeEvent(input$notes_save, {
data$raw$notes[progress$row] <- input$abstract_notes
})
# SELECTION & NAVIGATION
observeEvent(input$select_yes, {
data$raw$screened_abstracts[progress$row] <- "selected"
if(input$hide_screened){ # progress$current remains the same and progress$available changes
progress$available <- which(is.na(data$raw$screened_abstracts))
progress$max_n <- length(progress$available)
if(progress$current > progress$max_n){
progress$current <- progress$max_n
}
}else{ # i.e. if screened elements are visible, then current is used for navigation
if(progress$current < progress$max_n){
progress$current <- progress$current + 1
}
}
})
observeEvent(input$select_no, {
data$raw$screened_abstracts[progress$row] <- "excluded"
if(input$hide_screened){
progress$available <- which(is.na(data$raw$screened_abstracts))
progress$max_n <- length(progress$available)
if(progress$current > progress$max_n){
progress$current <- progress$max_n
}
}else{
if(progress$current < progress$max_n){
progress$current <- progress$current + 1
}
}
})
observeEvent(input$abstract_next, {
if((progress$current + 1) > progress$max_n){
progress$current <- progress$max_n
}else{
progress$current <- progress$current + 1
}
})
observeEvent(input$abstract_previous, {
if((progress$current - 1) > 0){
progress$current <- progress$current - 1
}
})
observeEvent(input$abstract_10previous, {
if((progress$current - 10) > 0){
progress$current <- progress$current - 10
}else{
progress$current <- 1
}
})
observeEvent(input$abstract_10next, {
if((progress$current + 10) > progress$max_n){
progress$current <- progress$max_n
}else{
progress$current <- progress$current + 10
}
})
# choose then row of the next entry when progress$current is updated
observeEvent(progress$current, {
if(!is.null(data$raw)){
progress$row <- choose_abstract_row(
progress$order, progress$available, progress$current
)
}
})
# ditto if progress$available is pinged
observeEvent(progress$available, {
if(!is.null(data$raw)){
progress$row <- choose_abstract_row(
progress$order, progress$available, progress$current
)
progress$max_n <- length(progress$available)
}
})
observeEvent(input$hide_screened, {
if(!is.null(data$raw)){
if(input$hide_screened){ # i.e. text were shown but are now hidden
# ensure that - if the currently viewed row is not selected - then it stays displayed
# if(is.na(data$raw$screened_abstracts[progress$row])){
if(progress$row %in% progress$available){
progress$current <- choose_abstract_current(
progress$order,
which(is.na(data$raw$screened_abstracts)),
progress$row
)
# this doesn't work at present
}
progress$available <- which(is.na(data$raw$screened_abstracts))
}else{
if(progress$current < 1){
progress$current <- 1
}
progress$available <- seq_len(nrow(data$raw))
}
}
})
observeEvent(progress$max_n, {
if(!is.null(data$raw) & progress$max_n < 1){
showModal(
modalDialog(
HTML(
"All articles have been screened. Would you like to save your progess?<br><br>
<i>If you have specified an object in your workspace and click 'Exit App',
your progress will be invisibly saved to that object.</i><br><br>"
),
textInput("save_filename",
label = "File Name"
),
selectInput("save_data_filetype",
label = "File Type",
choices = c("csv", "rds")
),
actionButton(
inputId = "save_data_execute",
label = "Save to File"
),
actionButton(
inputId = "exit_app_confirmed",
label = "Exit App"
),
modalButton("Cancel"),
title = "Save As",
footer = NULL,
easyClose = FALSE
)
)
}
})
# SAVE OPTIONS
observeEvent(input$save_data, {
if(is.null(data$raw)){
showModal(
modalDialog(
HTML(
"Import some data to begin<br><br>
<em>Click anywhere to exit</em>"
),
title = "Error: no data to save",
footer = NULL,
easyClose = TRUE
)
)
}else{
showModal(
modalDialog(
textInput("save_filename",
label = "File Name"
),
selectInput("save_data_filetype",
label = "File Type",
choices = c("csv", "rds")
),
actionButton("save_data_execute", "Save"),
modalButton("Cancel"),
title = "Save As",
footer = NULL,
easyClose = FALSE
)
)
}
})
observeEvent(input$save_data_execute, {
if(nchar(input$save_filename) == 0){
filename <- "revtools_abstract_screening"
}else{
if(grepl("\\.[[:lower:]]{3}$", input$save_filename)){
filename <- substr(
input$save_filename, 1,
nchar(input$save_filename) - 4
)
}else{
filename <- input$save_filename
}
}
filename <- paste(filename, input$save_data_filetype, sep = ".")
switch(input$save_data_filetype,
"csv" = {write.csv(data$raw, file = filename, row.names = FALSE)},
"rds" = {saveRDS(data$raw, file = filename)}
)
removeModal()
})
# add option to remove data
observeEvent(input$clear_data, {
shiny::showModal(
shiny::modalDialog(
HTML("If you proceed, all data will be removed from this window,
including any progress you have made screening your data.
If you have not saved your data,
you might want to consider doing that first.<br><br>
Are you sure you want to continue?<br><br>"
),
shiny::actionButton(
inputId = "clear_data_confirmed",
label = "Confirm"),
shiny::modalButton("Cancel"),
title = "Clear all data",
footer = NULL,
easyClose = FALSE
)
)
})
observeEvent(input$clear_data_confirmed, {
data$raw <- NULL
progress$current <- 1
progress$row <- NULL
display$notes <- FALSE
removeModal()
})
observeEvent(input$exit_app, {
exit_modal()
})
observeEvent(input$exit_app_confirmed, {
stopApp(returnValue = invisible(data$raw))
})
} # end server
print(shinyApp(ui, server))
}
mjwestgate/bibviewr documentation built on Jan. 11, 2020, 10:43 p.m.
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Defines functions screen_abstracts
Documented in screen_abstracts
screen_abstracts <- function(
x = NULL,
max_file_size
){
# set file size if requested, ensuring to reset on exit
if(!missing(max_file_size)){
initial_file_size <- options("shiny.maxRequestSize")
options(shiny.maxRequestSize = max_file_size * 1024^2)
on.exit(options(initial_file_size))
}
# load data
data_in <- load_abstract_data(
data = x
)
# create ui
ui_data <- screen_abstracts_ui()
ui <- shinydashboard::dashboardPage(
title = "revtools | screen_abstracts",
ui_data$header,
ui_data$sidebar,
ui_data$body,
skin = "black"
)
# start server
server <- function(input, output, session){
# build reactive values
data <- reactiveValues(
raw = data_in$data$raw
)
progress <- reactiveValues(
order = data_in$progress$order,
available = data_in$progress$available,
current = data_in$progress$current,
row = data_in$progress$row,
max_n = data_in$progress$max_n
)
display <- reactiveValues(
notes = FALSE,
column = "label"
)
# create header image
output$header <- renderPlot({
revtools_logo(text = "screen_abstracts")
})
# DATA INPUT
## when specified, ensure input data is processed correctly
observeEvent(input$data_in, {
if(is.null(data$raw)){
data_previous <- data_in$raw
}else{
data_previous <- data$raw
}
import_result <- import_shiny(
source = input$data_in,
current_data = data_previous
)
import_result <- add_abstract_columns(import_result)
# export to reactiveValues
data$raw <- import_result
# set progress values
progress$order <- set_row_order(
data$raw,
input$order,
input$order_result
)
if(is.null(progress$current) | progress$current < 1){
progress$current <- 1
}
if(input$hide_screened){
# if(length(progress$screen_cols) > 1){
# progress$available <- which(
# apply(data$raw[, progress$screen_cols], 1, function(a){all(is.na(a))})
# )
# }else{
# progress$available <- which(is.na(data$raw[, progress$screen_cols]))
# }
progress$available <- which(is.na(data$raw$screened_abstracts))
progress$max_n <- length(progress$available)
}else{
progress$max_n <- nrow(data$raw)
progress$available <- seq_len(progress$max_n)
}
progress$row <- choose_abstract_row(
progress$order, progress$available, progress$current
)
})
# allow user to select order
output$column_selector <- renderUI({
if(input$order == "user_defined"){
available_colnames <- colnames(data$raw)
selectInput(
inputId = "order_result",
label = "Select variable to order by:",
choices = available_colnames,
selected = display$column
)
}
})
# ensure decisions about selected columns are retained
observeEvent(input$order_result, {
display$column <- input$order_result
})
# ABSTRACT SCREENING
# change order of articles as necessary
observeEvent(input$order_result_go, {
progress$order <- set_row_order(
data$raw,
input$order,
input$order_result
)
progress$current <- 1
progress$row <- choose_abstract_row(
progress$order, progress$available, progress$current
)
})
# display text for the current entry
# note that observe is necessary to force changes when input$order changes
observe({
output$citation <- renderPrint({
validate(
need(data$raw, "Import data to begin")
)
validate(
need(progress$max_n > 0,
"No unscreened data remaining\nAdd more data, or save and exit to continue")
)
if(any(colnames(data$raw) == "abstract")){
abstract_text <- data$raw$abstract[progress$row]
}else{
abstract_text <- "<em>No abstract available</em>"
}
current_status <- data$raw$screened_abstracts[progress$row]
if(is.na(current_status)){
text_color <- "black"
text_label <- ""
}else{
if(current_status == "excluded"){
text_color <- "'#993f3f'"
text_label <- "Status: Excluded"
}else{
text_color <- "'#405d99'"
text_label <- "Status: Selected"
}
}
cat(
paste0(
"<font color =", text_color, ">",
format_citation(
data$raw[progress$row, ],
abstract = FALSE,
details = (input$hide_names == FALSE),
add_html = TRUE
),
"<br>",
text_label,
"<br><br>",
abstract_text,
"</font>"
)
)
})
})
# RENDER SELECTION BUTTONS
output$selector_bar <- renderUI({
if(!is.null(data$raw)){
text_out <- HTML(
paste0(
nrow(data$raw) - length(which(is.na(data$raw$screened_abstracts))),
" entries screened | Showing entry ",
progress$current,
" of ",
progress$max_n
)
)
div(
list(
div(
style = "
display: inline-block;
vertical-align: top;
text-align: right;
width: 350px",
renderText({text_out})
),
div(
style = "
display: inline-block;
vertical-align: top;
text-align: right;
width: 20px",
renderText(" ")
),
div(
style = "
display: inline-block;
vertical-align: top;
width: 40px",
actionButton(
inputId = "abstract_10previous",
label = "<<",
width = "40px",
style = "background-color: #6b6b6b;"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
width: 40px",
actionButton(
inputId = "abstract_previous",
label = "<",
width = "40px",
style = "background-color: #6b6b6b;"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
text-align: right;
width: 100px",
actionButton(
inputId = "select_yes",
label = "Select",
style = "
background-color: #7c93c1;
color: #fff;
width: 100px"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
text-align: right;
width: 100px",
actionButton(
inputId = "select_no",
label = "Exclude",
style = "
background-color: #c17c7c;
color: #fff;
width: 100px"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
width: 40px",
actionButton(
inputId = "abstract_next",
label = ">",
width = "40px",
style = "background-color: #6b6b6b;"
)
),
div(
style = "
display: inline-block;
vertical-align: top;
width: 40px",
actionButton(
inputId = "abstract_10next",
label = ">>",
width = "40px",
style = "background-color: #6b6b6b;"
)
)
)
)
}
})
output$render_notes_toggle <- renderUI({
if(!is.null(data$raw)){
if(progress$max_n > 0){
actionButton(
inputId = "notes_toggle",
label = "Show notes window",
style = "
background-color: #adadad;
color: #fff;
width: 200px"
)
}
}
})
# NOTES
# when toggle is triggered, invert display status of notes
observeEvent(input$notes_toggle, {
display$notes <- !display$notes
})
# render notes
output$render_notes <- renderUI({
if(display$notes){
div(
list(
br(),
textAreaInput(
inputId = "abstract_notes",
label = NULL,
value = data$raw$notes[progress$row],
resize = "both",
width = "400px",
height = "150px"
),
actionButton(
inputId = "notes_save",
label = "Save Notes",
width = "100px"
),
br()
)
)
}
})
# save notes
observeEvent(input$notes_save, {
data$raw$notes[progress$row] <- input$abstract_notes
})
# SELECTION & NAVIGATION
observeEvent(input$select_yes, {
data$raw$screened_abstracts[progress$row] <- "selected"
if(input$hide_screened){ # progress$current remains the same and progress$available changes
progress$available <- which(is.na(data$raw$screened_abstracts))
progress$max_n <- length(progress$available)
if(progress$current > progress$max_n){
progress$current <- progress$max_n
}
}else{ # i.e. if screened elements are visible, then current is used for navigation
if(progress$current < progress$max_n){
progress$current <- progress$current + 1
}
}
})
observeEvent(input$select_no, {
data$raw$screened_abstracts[progress$row] <- "excluded"
if(input$hide_screened){
progress$available <- which(is.na(data$raw$screened_abstracts))
progress$max_n <- length(progress$available)
if(progress$current > progress$max_n){
progress$current <- progress$max_n
}
}else{
if(progress$current < progress$max_n){
progress$current <- progress$current + 1
}
}
})
observeEvent(input$abstract_next, {
if((progress$current + 1) > progress$max_n){
progress$current <- progress$max_n
}else{
progress$current <- progress$current + 1
}
})
observeEvent(input$abstract_previous, {
if((progress$current - 1) > 0){
progress$current <- progress$current - 1
}
})
observeEvent(input$abstract_10previous, {
if((progress$current - 10) > 0){
progress$current <- progress$current - 10
}else{
progress$current <- 1
}
})
observeEvent(input$abstract_10next, {
if((progress$current + 10) > progress$max_n){
progress$current <- progress$max_n
}else{
progress$current <- progress$current + 10
}
})
# choose then row of the next entry when progress$current is updated
observeEvent(progress$current, {
if(!is.null(data$raw)){
progress$row <- choose_abstract_row(
progress$order, progress$available, progress$current
)
}
})
# ditto if progress$available is pinged
observeEvent(progress$available, {
if(!is.null(data$raw)){
progress$row <- choose_abstract_row(
progress$order, progress$available, progress$current
)
progress$max_n <- length(progress$available)
}
})
observeEvent(input$hide_screened, {
if(!is.null(data$raw)){
if(input$hide_screened){ # i.e. text were shown but are now hidden
# ensure that - if the currently viewed row is not selected - then it stays displayed
# if(is.na(data$raw$screened_abstracts[progress$row])){
if(progress$row %in% progress$available){
progress$current <- choose_abstract_current(
progress$order,
which(is.na(data$raw$screened_abstracts)),
progress$row
)
# this doesn't work at present
}
progress$available <- which(is.na(data$raw$screened_abstracts))
}else{
if(progress$current < 1){
progress$current <- 1
}
progress$available <- seq_len(nrow(data$raw))
}
}
})
observeEvent(progress$max_n, {
if(!is.null(data$raw) & progress$max_n < 1){
showModal(
modalDialog(
HTML(
"All articles have been screened. Would you like to save your progess?<br><br>
<i>If you have specified an object in your workspace and click 'Exit App',
your progress will be invisibly saved to that object.</i><br><br>"
),
textInput("save_filename",
label = "File Name"
),
selectInput("save_data_filetype",
label = "File Type",
choices = c("csv", "rds")
),
actionButton(
inputId = "save_data_execute",
label = "Save to File"
),
actionButton(
inputId = "exit_app_confirmed",
label = "Exit App"
),
modalButton("Cancel"),
title = "Save As",
footer = NULL,
easyClose = FALSE
)
)
}
})
# SAVE OPTIONS
observeEvent(input$save_data, {
if(is.null(data$raw)){
showModal(
modalDialog(
HTML(
"Import some data to begin<br><br>
<em>Click anywhere to exit</em>"
),
title = "Error: no data to save",
footer = NULL,
easyClose = TRUE
)
)
}else{
showModal(
modalDialog(
textInput("save_filename",
label = "File Name"
),
selectInput("save_data_filetype",
label = "File Type",
choices = c("csv", "rds")
),
actionButton("save_data_execute", "Save"),
modalButton("Cancel"),
title = "Save As",
footer = NULL,
easyClose = FALSE
)
)
}
})
observeEvent(input$save_data_execute, {
if(nchar(input$save_filename) == 0){
filename <- "revtools_abstract_screening"
}else{
if(grepl("\\.[[:lower:]]{3}$", input$save_filename)){
filename <- substr(
input$save_filename, 1,
nchar(input$save_filename) - 4
)
}else{
filename <- input$save_filename
}
}
filename <- paste(filename, input$save_data_filetype, sep = ".")
switch(input$save_data_filetype,
"csv" = {write.csv(data$raw, file = filename, row.names = FALSE)},
"rds" = {saveRDS(data$raw, file = filename)}
)
removeModal()
})
# add option to remove data
observeEvent(input$clear_data, {
shiny::showModal(
shiny::modalDialog(
HTML("If you proceed, all data will be removed from this window,
including any progress you have made screening your data.
If you have not saved your data,
you might want to consider doing that first.<br><br>
Are you sure you want to continue?<br><br>"
),
shiny::actionButton(
inputId = "clear_data_confirmed",
label = "Confirm"),
shiny::modalButton("Cancel"),
title = "Clear all data",
footer = NULL,
easyClose = FALSE
)
)
})
observeEvent(input$clear_data_confirmed, {
data$raw <- NULL
progress$current <- 1
progress$row <- NULL
display$notes <- FALSE
removeModal()
})
observeEvent(input$exit_app, {
exit_modal()
})
observeEvent(input$exit_app_confirmed, {
stopApp(returnValue = invisible(data$raw))
})
} # end server
print(shinyApp(ui, server))
}
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