diff --git a/docs/articles/Using-the-DRR-Template.html b/docs/articles/Using-the-DRR-Template.html index 9a3eff1..c605d0f 100644 --- a/docs/articles/Using-the-DRR-Template.html +++ b/docs/articles/Using-the-DRR-Template.html @@ -128,11 +128,15 @@

Project Set-up

Reproducible Reports

-

The following is for users who are using the DRR template file to -generate a data release report using RMarkdown.

-

Standard Code Chunks +

Code Chunks

+

The DRR Template takes advantage of rmarkdown code chunks to help +generate a reproducible report. The template includes all of the +required code chunks. Some of these code chunks need to be edited to +generate the report, others should not be edited. Below is description +of each code chunk in the DRR Template and instructions on how to (and +when not to) edit them.

In addition to the report outline and a description of content for each section, the template includes four standard code chunks.

YAML Header:

@@ -265,11 +269,80 @@

Standard Code Chunks -

Citations +

Editing the Text

+

The following text in the body of the DRR template will need to be +edited to customize it to each data package.

+
+

Data Records +

+

This is a required section and consists of two subheadings:

+
    +

  • Data inputs - an optional subsection used to +describe datasets that the data package is based on if it is a +re-analysis, reorganization, or re-integration of prevously existing +data sets.

    • +

  • Summary of datasts created - this is a required +section used to explain each data record associated with the work (for +instance, a data package), including the DOI indicating where this +information is stored. It shoudl also provide an overview of the data +files and their formats. Each external data record should be +cited.

    • +
+

Sample text is included that uses r code to incorporate previously +specified parameters such as the data package title, file names, and +DOI.

+

A code for a sample table summarizing the contents of the data +package (except the metadata) is provided.

+
+
+

Data Quality +

+

This is a required section. and the text includes multiple suggested +text elements and code for an example table defining data flagging +codes. Near future development here will incorporate additional optional +tables to summarize the data quality based on the flags in the data +sets.

+
+
+

Usage Notes +

+

This is a required section that should contain brief instructions to +assist other researchers with reuse of the data. This may include +discussion of software packages (with appropriate citations) that are +suitable for analysing the assay data files, suggested downstream +processing steps (e.g. normalization, etc.), or tips for integrating or +comparing the data records with other datasets. Authors are encouraged +to provide code, programs or data-processing workflows if they may help +others understand or use the data.

+
-

Automating Citations +

Methods

+

This is a required section that cites previous methods used but +should also be detailed enough in describing data production including +the experimental design, data acquisition assays, and any computational +processing (e.g. normalization, QA, QC) such that others can understand +the methods without referring to associated publications.

+

Optional sub-sections within the methods include:

+
    +
  • Data Collection and Sampling
    • +
  • Additional Data Sources
    • +
  • Data Processing
    • +
  • Code availability
    • +
+
+

+
+

References +

+

This required section includes full bibliographic references for each +paper, chapter, book, data package, dataset, protocol, etc cited within +the DRR. Each item in the Reference section should be specifically cited +in-text as well.

+
+
Automating Citations +

To automate citations, add the citation in bibtex format to the file “references.bib”. You can manually copy and paste the bibtex for each reference in, or you can search for it from within Rstudio. From within @@ -348,89 +421,17 @@

Automating Citations -

Manual citations -

+
+
Manual citations +

If you would like to format your citations manually, please feel free -to do so. Make sure to look at the References section for how to -properly format each citation type.

-
-

-
-
-

Editing the Text -

-

The following text in the body of the DRR template will need to be -edited to customize it to each data package.

-
-

Data Records -

-

This is a required section and consists of two subheadings:

-
    -

  • Data inputs - an optional subsection used to -describe datasets that the data package is based on if it is a -re-analysis, reorganization, or re-integration of prevously existing -data sets.

    • -

  • Summary of datasts created - this is a required -section used to explain each data record associated with the work (for -instance, a data package), including the DOI indicating where this -information is stored. It shoudl also provide an overview of the data -files and their formats. Each external data record should be -cited.

    • -
-

Sample text is included that uses r code to incorporate previously -specified parameters such as the data package title, file names, and -DOI.

-

A code for a sample table summarizing the contents of the data -package (except the metadata) is provided.

-
-
-

Data Quality -

-

This is a required section. and the text includes multiple suggested -text elements and code for an example table defining data flagging -codes. Near future development here will incorporate additional optional -tables to summarize the data quality based on the flags in the data -sets.

-
-
-

Usage Notes -

-

This is a required section that should contain brief instructions to -assist other researchers with reuse of the data. This may include -discussion of software packages (with appropriate citations) that are -suitable for analysing the assay data files, suggested downstream -processing steps (e.g. normalization, etc.), or tips for integrating or -comparing the data records with other datasets. Authors are encouraged -to provide code, programs or data-processing workflows if they may help -others understand or use the data.

-
-
-

Methods -

-

This is a required section that cites previous methods used but -should also be detailed enough in describing data production including -the experimental design, data acquisition assays, and any computational -processing (e.g. normalization, QA, QC) such that others can understand -the methods without referring to associated publications.

-

Optional sub-sections within the methods include:

-
    -
  • Data Collection and Sampling
    • -
  • Additional Data Sources
    • -
  • Data Processing
    • -
  • Code availability
    • -
-
-
-

References -

-

This required section includes full bibliographic references for each -paper, chapter, book, data package, dataset, protocol, etc cited within -the DRR.

+to do so. Make sure to look at the References section of the DRR +Template for how to properly format each citation type.

There are numerous examples of proper formatting for each of these. Future versions of the DRR will enable automatic reference formatting given a correctly formatted bibtex file with the references (.bib).

+

Figures

@@ -545,6 +546,18 @@

Tables

+

Non-reproducible Reports +

+

You can generate a .docx document manually without ussing the DRR +Template. The .docx, if properly formatted, can be ingested by the +publication software. Assuming the manually created .docx also has all +the required components and information, it can pass the review process +and be published. The final product should be indistinguishable from one +generated using the DRR Template.

+

Manually generating a .docx for DRR publication is not suggested and +not supported.

+
+

Publishing DRRs

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 23c641a..286504f 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,5 +5,5 @@ articles: DRR_Purpose_and_Scope: DRR_Purpose_and_Scope.html Starting-a-DRR: Starting-a-DRR.html Using-the-DRR-Template: Using-the-DRR-Template.html -last_built: 2024-02-09T20:36Z +last_built: 2024-02-09T20:53Z