diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index b1a98a6..7228d8f 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-31T02:36:21","documenter_version":"1.6.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-31T05:06:02","documenter_version":"1.6.0"}} \ No newline at end of file diff --git a/dev/checklist/index.html b/dev/checklist/index.html index 3cad6b5..db84fc6 100644 --- a/dev/checklist/index.html +++ b/dev/checklist/index.html @@ -10,7 +10,7 @@ df = checklist_df() df[3, "Location where item is reported"] = "Sysemtatic review is in the title." -df[3, "Location where item is reported"] = "The completed abastract is located on page one."

Additionally, the checklist() function uses checklist_df() as a template but takes a paper in PDF format, parses it using natural language processing via Flux.jl and Transformers.jl, and returns a completed checklist along with the paper's metadata, represented by the type Checklist.

source
PRISMA.checklist — Function
PRISMA.checklist(paper::AbstractString)::Checklist
+df[3, "Location where item is reported"] = "The completed abastract is located on page one."

Additionally, the checklist() function uses checklist_df() as a template but takes a paper in PDF format, parses it using natural language processing via Flux.jl and Transformers.jl, and returns a completed checklist along with the paper's metadata, represented by the type Checklist.

source
PRISMA.checklist — Function
PRISMA.checklist(paper::AbstractString)::Checklist
 PRISMA.checklist(bytes::Vector{UInt8})::Checklist

Returns a completed PRISMA checklist as the type Checklist. The Checklist type includes a completed checklist as a DataFrame and the metadata of the paper as a LittleDict. The paper argument can be a path to a pdf file or an array of bytes. This function uses the C++ library Poppler via Poppler_jll to parse the pdf and the natural language processing functionality in Julia via Flux.jl and Transformers.jl to find items from the checklist in the paper and populate the Comments or location in manuscript and Yes/No/NA columns in the DataFrame from checklist_df().

The following metadata is parsed from the pdf file and stored in the LittleDict as:

  • "title": the title of the paper
  • "subject": the subject of the paper
  • "author": the author of the paper
  • "creator": the creator of the paper
  • "producer": the producer of the paper
  • "creation date": the date the paper was created
  • "modification date": the date the paper was last modified
  • "pages": the number of pages in the paper
  • "paper size": the size of the paper
  • "paper rotation": the rotation of the paper
  • "file size": the size of the pdf file
  • "optimized": whether the pdf was optimized
  • "pdf version": the version of the pdf

All keys and values in the dictionary ar eof type String. If the parsing fails the value will be an empty string.

Arguments

  • paper::AbstractString: a path to a pdf file as a string
  • bytes::Vector{UInt8}: the pdf data as an array of bytes

Returns

  • Checklist: a completed checklist with paper metadata

Examples

Export a completed checklist to an Microsoft® Excel spreadsheet. Just make the sure the file path end with .xlsx.

using PRISMA
 
 clist = checklist("manuscript.pdf")
@@ -24,7 +24,7 @@
 df[02, "Yes/No/NA"] = "Yes"
 df[09, "Yes/No/NA"] = "Yes"
 df[10, "Yes/No/NA"] = "Yes"
-
source
PRISMA.checklist_read — Function
checklist_read(fn::AbstractString; sheetname::AbstractString="2020 PRISMA Checklist", kwargs....)::DataFrame

reads the template data from a CSV, XLSX, HTML, or JSON

Arguments

  • fn::AbstractString: the name of the file to read
  • sheetname::AbstractString="2020 PRISMA Checklist": the name of the sheet in the spreadsheet
  • kwargs...: additional arguments to be passed to the underlying

CSV.read, XLSX.readtable, HTMLTables.read, and JSON3.read functions

Returns

  • DataFrame: the template dataframe

Examples

using PRISMA: checklist_save, checklist_df, checklist_read
+
source
PRISMA.checklist_read — Function
checklist_read(fn::AbstractString; sheetname::AbstractString="2020 PRISMA Checklist", kwargs....)::DataFrame

reads the template data from a CSV, XLSX, HTML, or JSON

Arguments

  • fn::AbstractString: the name of the file to read
  • sheetname::AbstractString="2020 PRISMA Checklist": the name of the sheet in the spreadsheet
  • kwargs...: additional arguments to be passed to the underlying

CSV.read, XLSX.readtable, HTMLTables.read, and JSON3.read functions

Returns

  • DataFrame: the template dataframe

Examples

using PRISMA: checklist_save, checklist_df, checklist_read
 
 checklist_save("checklist.csv",  checklist_df())
 checklist_save("checklist.xlsx", checklist_df())
@@ -34,7 +34,7 @@
 checklist_read("checklist.csv")
 checklist_read("checklist.xlsx")
 checklist_read("checklist.json")
-checklist_read("checklist.html")
source
PRISMA.Checklist — Type
PRISMA.Checklist

This types represents a PRISMA checklist in the form of a DataFrame and the metadata of the paper that was used to generate it as a LittleDict or an small ordered dictionary withs keys and values.

Keyword Arguments

  • df::DataFrame: the checklist as a DataFrame
  • metadata::LittleDict: the metadata of the paper

Examples

using PRISMA
+checklist_read("checklist.html")
source
PRISMA.Checklist — Type
PRISMA.Checklist

This types represents a PRISMA checklist in the form of a DataFrame and the metadata of the paper that was used to generate it as a LittleDict or an small ordered dictionary withs keys and values.

Keyword Arguments

  • df::DataFrame: the checklist as a DataFrame
  • metadata::LittleDict: the metadata of the paper

Examples

using PRISMA
 
 cl::Checklist = checklist("paper.pdf")
 
@@ -42,7 +42,7 @@
 println(title)
 
 pages = cl.metadata["pages"]
-println(pages)
source
PRISMA.checklist_save — Function
checklist_save(
+println(pages)
source
PRISMA.checklist_save — Function
checklist_save(
     fn::AbstractString, 
     cl::Checklist; 
     sheetname::AbstractString="2020 PRISMA Checklist", 
@@ -55,7 +55,7 @@
 checklist_save("checklist.csv",  clist)
 checklist_save("checklist.xlsx", clist)
 checklist_save("checklist.json", clist)
-checklist_save("checklist.html", clist)
source
checklist_save(
+checklist_save("checklist.html", clist)
source
checklist_save(
     fn::AbstractString, 
     cl::Checklist; 
     sheetname::AbstractString="2020 PRISMA Checklist", 
@@ -70,4 +70,4 @@
 checklist_save("checklist.xlsx", df)
 checklist_save("checklist.json", df)
 checklist_save("checklist.html", df)
-
source
+source diff --git a/dev/flow_diagram/index.html b/dev/flow_diagram/index.html index 95698bc..3903c86 100644 --- a/dev/flow_diagram/index.html +++ b/dev/flow_diagram/index.html @@ -23,7 +23,7 @@ df = CSV.read("flow_diagram.csv", DataFrame) -PRISMA.flow_diagram(df)source
PRISMA.flow_diagram — Function
PRISMA.flow_diagram(
+PRISMA.flow_diagram(df)
source
PRISMA.flow_diagram — Function
PRISMA.flow_diagram(
     data::DataFrame=flow_diagram_df(),
     background_color::AbstractString="white",
     grayboxes::Bool=true,
@@ -59,7 +59,7 @@
 fd::PRISMA.FlowDiagram = PRISMA.flow_diagram(df, top_boxes_color="white")
 
 # save the flow diagram
-PRISMA.flow_diagram_save("flow_diagram.svg", fd)
source
PRISMA.flow_diagram_read — Function
flow_diagram_read(fn::AbstractString; sheetname::AbstractString="2020 PRISMA Flow Diagram", kwargs....)::DataFrame

reads the template data from a CSV, XLSX, HTML, or JSON file

Arguments

  • fn::AbstractString: the name of the file to read
  • `sheetname::AbstractString="2020 PRISMA Flow Diagram": the name of the sheet in the spreadsheet
  • kwargs...: additional arguments to be passed to the underlying

CSV.read, XLSX.readtable, HTMLTables.read, and JSON3.read functions

Returns

  • DataFrame: the template dataframe

Examples

using PRISMA: flow_diagram_save, flow_diagram_df, flow_diagram_read
+PRISMA.flow_diagram_save("flow_diagram.svg", fd)
source
PRISMA.flow_diagram_read — Function
flow_diagram_read(fn::AbstractString; sheetname::AbstractString="2020 PRISMA Flow Diagram", kwargs....)::DataFrame

reads the template data from a CSV, XLSX, HTML, or JSON file

Arguments

  • fn::AbstractString: the name of the file to read
  • `sheetname::AbstractString="2020 PRISMA Flow Diagram": the name of the sheet in the spreadsheet
  • kwargs...: additional arguments to be passed to the underlying

CSV.read, XLSX.readtable, HTMLTables.read, and JSON3.read functions

Returns

  • DataFrame: the template dataframe

Examples

using PRISMA: flow_diagram_save, flow_diagram_df, flow_diagram_read
 
 flow_diagram_save("flow_diagram.csv", flow_diagram_df())
 flow_diagram_save("flow_diagram.xlsx", flow_diagram_df())
@@ -69,17 +69,17 @@
 flow_diagram_read("flow_diagram.csv")
 flow_diagram_read("flow_diagram.xlsx")
 flow_diagram_read("flow_diagram.json")
-flow_diagram_read("flow_diagram.html")
source
PRISMA.FlowDiagram — Type
PRISMA.FlowDiagram

Flow diagram type for PRISMA.jl

Argument

  • dot::AbstractString: The flow diagram written in Graphviz's DOT language
source
PRISMA.flow_diagram_save — Function
PRISMA.flow_diagram_save(fn::AbstractString, fd::FlowDiagram; overwrite::Bool=false)::String

writes a FlowDiagram as either a file (i.e., any Graphviz supported format) or stdout

Arguments

  • fn::AbstractString: The name of the file to be saved.
  • fd::FlowDiagram: The flow diagram to be saved.
  • overwrite::Bool=false: Whether to overwrite the file if it already exists.

Returns

  • String: The path to the saved file.

Examples

using PRISMA
+flow_diagram_read("flow_diagram.html")
source
PRISMA.FlowDiagram — Type
PRISMA.FlowDiagram

Flow diagram type for PRISMA.jl

Argument

  • dot::AbstractString: The flow diagram written in Graphviz's DOT language
source
PRISMA.flow_diagram_save — Function
PRISMA.flow_diagram_save(fn::AbstractString, fd::FlowDiagram; overwrite::Bool=false)::String

writes a FlowDiagram as either a file (i.e., any Graphviz supported format) or stdout

Arguments

  • fn::AbstractString: The name of the file to be saved.
  • fd::FlowDiagram: The flow diagram to be saved.
  • overwrite::Bool=false: Whether to overwrite the file if it already exists.

Returns

  • String: The path to the saved file.

Examples

using PRISMA
 
 fd = PRISMA.flow_diagram()
 
 PRISMA.flow_diagram_save("flow_diagram.pdf", fd)
 PRISMA.flow_diagram_save("flow_diagram.png", fd)
-PRISMA.flow_diagram_save("flow_diagram.svg", fd)
source
PRISMA.flow_diagram_save(fn::AbstractString, df::DataFrame; sheetname::AbstractString="2020 PRISMA Flow Diagram", overwrite::Bool=false, kwargs...)::String

saves as the template for the flow diagram as a either a CSV, XLSX, HTML, or JSON file.

Arguments

  • fn::AbstractString: the name of the file to save
  • df::DataFrame: the flow diagram to save
  • sheetname::AbstractString="2020 PRISMA Flow Diagram": the name of the sheet in the spreadsheet
  • overwrite::Bool=false: whether to overwrite the file if it already exists
  • kwargs...: additional arguments to be passed to the underlying

CSV.write, XLSX.writetable, HTMLTables.write, and JSON3.write functions

Returns

  • String: the path to the saved file

Examples

using PRISMA
+PRISMA.flow_diagram_save("flow_diagram.svg", fd)
source
PRISMA.flow_diagram_save(fn::AbstractString, df::DataFrame; sheetname::AbstractString="2020 PRISMA Flow Diagram", overwrite::Bool=false, kwargs...)::String

saves as the template for the flow diagram as a either a CSV, XLSX, HTML, or JSON file.

Arguments

  • fn::AbstractString: the name of the file to save
  • df::DataFrame: the flow diagram to save
  • sheetname::AbstractString="2020 PRISMA Flow Diagram": the name of the sheet in the spreadsheet
  • overwrite::Bool=false: whether to overwrite the file if it already exists
  • kwargs...: additional arguments to be passed to the underlying

CSV.write, XLSX.writetable, HTMLTables.write, and JSON3.write functions

Returns

  • String: the path to the saved file

Examples

using PRISMA
 
 df = PRISMA.flow_diagram_df()
 
 PRISMA.flow_diagram_save("flow_diagram.csv", df)
 PRISMA.flow_diagram_save("flow_diagram.xlsx", df)
 PRISMA.flow_diagram_save("flow_diagram.html", df)
-PRISMA.flow_diagram_save("flow_diagram.json", df)
source
+PRISMA.flow_diagram_save("flow_diagram.json", df)source diff --git a/dev/index.html b/dev/index.html index 3ec89e0..35d7ea8 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -Home · PRISMA.jl
GitHub

Home

PRISMA.PRISMA — Module

PRISMA.jl

Julia package for generating checklists and flow diagrams based on the 2020 Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement (Page et al., 2021).

Functions

  • checklist_df: returns an empty PRISMA checklist as the type DataFrame

  • checklist: returns a completed PRISMA checklist as the type Checklist

  • checklist_read: reads the checklist data as a DataFrame from a data file

  • checklist_save: saves a Checklist as either a .csv, .xlsx, .html, or .json file

  • flow_diagram_df: returns the DataFrame that is used to create the flow diagram

  • flow_diagram: returns a PRISMA flow diagram as the type FlowDiagram

  • flow_diagram_read: reads the flow diagram data as a DataFrame from a data file

  • flow_diagram_save: saves a FlowDiagram to file formats supported by Graphviz

Types

  • Checklist: includes a completed checklist and paper metadata
  • FlowDiagram: the PRISMA flow diagram represented as Graphviz's DOT language

Reexports

  • DataFrames.DataFrame: both flow_diagram_df and checklist_df return a DataFrame
  • DataStructures.LittleDict: the metadata field of the Checklist type is a small ordered dictionary
  • Base.display: PRISMA adds a method for displaying the FlowDiagram type
  • Base.show: PRISMA adds new methods for showing the Checklist and FlowDiagram types
source
+Home · PRISMA.jl
GitHub

Home

PRISMA.PRISMA — Module

PRISMA.jl

Julia package for generating checklists and flow diagrams based on the 2020 Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement (Page et al., 2021).

Functions

  • checklist_df: returns an empty PRISMA checklist as the type DataFrame

  • checklist: returns a completed PRISMA checklist as the type Checklist

  • checklist_read: reads the checklist data as a DataFrame from a data file

  • checklist_save: saves a Checklist as either a .csv, .xlsx, .html, or .json file

  • flow_diagram_df: returns the DataFrame that is used to create the flow diagram

  • flow_diagram: returns a PRISMA flow diagram as the type FlowDiagram

  • flow_diagram_read: reads the flow diagram data as a DataFrame from a data file

  • flow_diagram_save: saves a FlowDiagram to file formats supported by Graphviz

Types

  • Checklist: includes a completed checklist and paper metadata
  • FlowDiagram: the PRISMA flow diagram represented as Graphviz's DOT language

Reexports

  • DataFrames.DataFrame: both flow_diagram_df and checklist_df return a DataFrame
  • DataStructures.LittleDict: the metadata field of the Checklist type is a small ordered dictionary
  • Base.display: PRISMA adds a method for displaying the FlowDiagram type
  • Base.show: PRISMA adds new methods for showing the Checklist and FlowDiagram types
source
diff --git a/dev/references/index.html b/dev/references/index.html index 024232b..4252b50 100644 --- a/dev/references/index.html +++ b/dev/references/index.html @@ -1,2 +1,2 @@ -References · PRISMA.jl
GitHub

References

+References · PRISMA.jl
GitHub

References