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@cecoeco
cecoeco committed Sep 27, 2024
1 parent 94caa31 commit 5050e78
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25 changes: 24 additions & 1 deletion src/checklist.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -309,7 +309,30 @@ function checklist_df()::DataFrame
end

"""
$docstring_Checklist
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 `OrderedDict`.
## Fields
- `dataframe::DataFrame`: the checklist as a `DataFrame`
- `metadata::OrderedDict`: the metadata of the paper
## Example
```julia
using PRISMA
cl::Checklist = checklist("paper.pdf")
title = cl.metadata["title"]
println(title)
pages = cl.metadata["pages"]
println(pages)
```
"""
@kwdef mutable struct Checklist
dataframe::DataFrame = checklist_df()
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142 changes: 4 additions & 138 deletions src/checklist_docstrings.jl
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@@ -1,31 +1,3 @@
const docstring_Checklist::String =
"""
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 `OrderedDict`.
## Fields
- `dataframe::DataFrame`: the checklist as a `DataFrame`
- `metadata::OrderedDict`: the metadata of the paper
## Example
```julia
using PRISMA
cl::Checklist = checklist("paper.pdf")
title = cl.metadata["title"]
println(title)
pages = cl.metadata["pages"]
println(pages)
```
"""

const docstring_checklist::String =
"""
PRISMA.checklist(paper::AbstractString)::Checklist
Expand Down Expand Up @@ -86,61 +58,8 @@ returns a template PRISMA checklist as a `DataFrame`
```jldoctest
julia> using PRISMA
julia> checklist_df()
49×4 DataFrame
Row │ Section and Topic Item # Checklist Item Location where item is reported
│ String String String String
─────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ TITLE
2 │ Title 1 Identify the report as a systema…
3 │ ABSTRACT
4 │ Abstract 2 See the PRISMA 2020 for Abstract…
5 │ INTRODUCTION
6 │ Rationale 3 Describe the rationale for the r…
7 │ Objectives 4 Provide an explicit statement of…
8 │ METHODS
9 │ Eligibility criteria 5 Specify the inclusion and exclus…
10 │ Information sources 6 Specify all databases, registers…
11 │ Search strategy 7 Present the full search strategi…
12 │ Selection process 8 Specify the methods used to deci…
13 │ Data collection process 9 Specify the methods used to coll…
14 │ Data items 10a List and define all outcomes for…
15 │ 10b List and define all other variab…
16 │ Study risk of bias assessment 11 Specify the methods used to asse…
17 │ Effect measures 12 Specify for each outcome the eff…
18 │ Synthesis methods 13a Describe the processes used to d…
19 │ 13b Describe any methods required to…
20 │ 13c Describe any methods used to tab…
21 │ 13d Describe any methods used to syn…
22 │ 13e Describe any methods used to exp…
23 │ 13f Describe any sensitivity analyse…
24 │ Reporting bias assessment 14 Describe any methods used to ass…
25 │ Certainty assessment 15 Describe any methods used to ass…
26 │ RESULTS
27 │ Study selection 16a Describe the results of the sear…
28 │ 16b Cite studies that might appear t…
29 │ Study characteristics 17 Cite each included study and pre…
30 │ Risk of bias in studies 18 Present assessments of risk of b…
31 │ Results of individual studies 19 For all outcomes, present, for e…
32 │ Results of syntheses 20a For each synthesis, briefly summ…
33 │ 20b Present results of all statistic…
34 │ 20c Present results of all investiga…
35 │ 20d Present results of all sensitivi…
36 │ Reporting biases 21 Present assessments of risk of b…
37 │ Certainty of evidence 22 Present assessments of certainty…
38 │ DISCUSSION
39 │ Discussion 23a Provide a general interpretation…
40 │ 23b Discuss any limitations of the e…
41 │ 23c Discuss any limitations of the r…
42 │ 23d Discuss implications of the resu…
43 │ OTHER INFORMATION
44 │ Registration and protocol 24a Provide registration information…
45 │ 24b Indicate where the review protoc…
46 │ 24c Describe and explain any amendme…
47 │ Support 25 Describe sources of financial or…
48 │ Competing interests 26 Identify the report as a systema…
49 │ Availability of data, code and o… 27 Report which of the following ar…
julia> isa(checklist_df(), DataFrame)
true
```
"""
Expand All @@ -167,61 +86,8 @@ julia> using PRISMA
julia> checklist_template()
"checklist.csv"
julia> checklist_read("checklist.csv")
49×4 DataFrame
Row │ Section and Topic Item # Checklist Item Location where item is reported
│ String String String String
─────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ TITLE
2 │ Title 1 Identify the report as a systema…
3 │ ABSTRACT
4 │ Abstract 2 See the PRISMA 2020 for Abstract…
5 │ INTRODUCTION
6 │ Rationale 3 Describe the rationale for the r…
7 │ Objectives 4 Provide an explicit statement of…
8 │ METHODS
9 │ Eligibility criteria 5 Specify the inclusion and exclus…
10 │ Information sources 6 Specify all databases, registers…
11 │ Search strategy 7 Present the full search strategi…
12 │ Selection process 8 Specify the methods used to deci…
13 │ Data collection process 9 Specify the methods used to coll…
14 │ Data items 10a List and define all outcomes for…
15 │ 10b List and define all other variab…
16 │ Study risk of bias assessment 11 Specify the methods used to asse…
17 │ Effect measures 12 Specify for each outcome the eff…
18 │ Synthesis methods 13a Describe the processes used to d…
19 │ 13b Describe any methods required to…
20 │ 13c Describe any methods used to tab…
21 │ 13d Describe any methods used to syn…
22 │ 13e Describe any methods used to exp…
23 │ 13f Describe any sensitivity analyse…
24 │ Reporting bias assessment 14 Describe any methods used to ass…
25 │ Certainty assessment 15 Describe any methods used to ass…
26 │ RESULTS
27 │ Study selection 16a Describe the results of the sear…
28 │ 16b Cite studies that might appear t…
29 │ Study characteristics 17 Cite each included study and pre…
30 │ Risk of bias in studies 18 Present assessments of risk of b…
31 │ Results of individual studies 19 For all outcomes, present, for e…
32 │ Results of syntheses 20a For each synthesis, briefly summ…
33 │ 20b Present results of all statistic…
34 │ 20c Present results of all investiga…
35 │ 20d Present results of all sensitivi…
36 │ Reporting biases 21 Present assessments of risk of b…
37 │ Certainty of evidence 22 Present assessments of certainty…
38 │ DISCUSSION
39 │ Discussion 23a Provide a general interpretation…
40 │ 23b Discuss any limitations of the e…
41 │ 23c Discuss any limitations of the r…
42 │ 23d Discuss implications of the resu…
43 │ OTHER INFORMATION
44 │ Registration and protocol 24a Provide registration information…
45 │ 24b Indicate where the review protoc…
46 │ 24c Describe and explain any amendme…
47 │ Support 25 Describe sources of financial or…
48 │ Competing interests 26 Identify the report as a systema…
49 │ Availability of data, code and o… 27 Report which of the following ar…
julia> isa(checklist_read("checklist.csv"), DataFrame)
true
```
"""
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