diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 6ae344b..89d7fb4 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-06T23:19:44","documenter_version":"1.5.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-07T01:32:11","documenter_version":"1.5.0"}} \ No newline at end of file diff --git a/dev/checklist/index.html b/dev/checklist/index.html index 5f87860..94e4075 100644 --- a/dev/checklist/index.html +++ b/dev/checklist/index.html @@ -11,7 +11,7 @@ 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 using the XLSX package.

using PRISMA, XLSX
 
 clist = checklist("manuscript.pdf")
@@ -29,4 +29,4 @@
 clist.df[02, "Yes/No/NA"] = "Yes"
 clist.df[09, "Yes/No/NA"] = "Yes"
 clist.df[10, "Yes/No/NA"] = "Yes"
-
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
source
+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
source
diff --git a/dev/flow_diagram/index.html b/dev/flow_diagram/index.html index 4f972a6..c663867 100644 --- a/dev/flow_diagram/index.html +++ b/dev/flow_diagram/index.html @@ -28,7 +28,7 @@ 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,
@@ -64,10 +64,10 @@
 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.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
+PRISMA.flow_diagram_save("flow_diagram.svg", fd)
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("flow_diagram.svg", fd)source diff --git a/dev/index.html b/dev/index.html index 0b338bd..ae9557a 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
  • 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_save: saves a FlowDiagram to any file format supported by Graphviz_jll

Types

  • Checklist: includes a completed checklist and paper metadata
  • FlowDiagram: the PRISMA flow diagram represented as Graphviz's DOT language
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
  • 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_save: saves a FlowDiagram to any file format supported by Graphviz_jll

Types

  • Checklist: includes a completed checklist and paper metadata
  • FlowDiagram: the PRISMA flow diagram represented as Graphviz's DOT language
source
diff --git a/dev/references/index.html b/dev/references/index.html index 80c1c4b..4f21c48 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