philsf / philsf.workflow Goto Github PK

We could probably use sed to systematically update the version number in all relevant files

• scripts
• templates
• READMEs

• Remove signatures table
• include version in document code (v01)

• report
  • #23
  • #20
• SAP
  • philsf/philsfmisc#63
• Protocol
  • philsf/philsfmisc#64
• README

Don't auto-download the PDFs, show them in the browser instead.

We forgot to include the new scripts templates in SAR-init after creating them.

Improvements in readability, and structure of the repo README

• document
• style
• README

Include the new best practices after the good experiences tested in SAR-2021-003 and SAR-2021-004.

• figure caption with knitr and here
• source input in SAP, just as results is sourced in SAR
• include analytical_mockup structure by default in documents
• Availability secion in documents

Most links are broken.

• document
• style
• README

Now that there are more than one document type, change the header and footer to acknowledge

Header

• Document type
• document address
• consultant page

Footer

• consultant name/e-mail
• document type (report, SAP, protocol, etc)
• document version
• year
• page

obs: Consider creating first page header/footer for better reading flow

Some tasks are not being executed when there are special chars in a dir/path, including spaces.

We need to escape every variable that contains a path when passing it to a command like git.

Create a .Rbuildignore file to pass the devtools check.

Include

Options:

• Version a copy of the current template (will require updates whenever the template changes)
• Auto-generate a template calling R CMD from the shell (future-proof)

• scripts
• config files
• routine documentation

• fit summary headers in first page with 0,20 cm spacing below
• footer link to main page instead of linktree (check hyperlink)
• TableNormal left alignment

• objective
• Minimalistic list of documents
• link to portfolio

Github doesn't offer good render of pander tables in the simple format, but rather we must use rmarkdown format.

Set table.style in panderOptions in all templates.

After running basefiles, include a standard line + comment to ignore private datasets.

Don't commit this change to allow opt-out of this option in the workflow.

Use SAR (Statistical Analysis Report) instead of "data analysis" in pt)

• yyyy-SAR-NN-v01

• yyyy-SAP-NN-v01

• SAR_pt

  • template
  • style

• SAR_en

  • template
  • style

• SAP_pt

  • template
  • style

• SAP_en

  • template
  • style

• scripts

• README

• Consider batch renaming all previous report for easier identification of documents;

• Consider including semantinc information in the document code

  • pro: easier to know the contents by looking at filename
  • con: longer/clunkier codes/filenames

The SAR-sync script could accept an argument to sync one one remote, instead of all of them. Ideally filter lsit of available remotes from given arguments

It would be nice to use best practices and declare workflow versions in relevant files.

• scripts
• templates
• READMEs

We've been ignoring table sizes for far too long. It's time to pick a size.

Tables with too many columns (e.g. analytical data) can be divided into smaller tables, but we don't want too many subdibisions

Tested in SAR-2021-003:

• 120
• 160
• (go higher?)

philsf-biostat/org#35

Now that there are more than one document template, the filename styles.docx clashes when more than one template is used in the same project. Create individual filenames for each style to avoid this.

Create mockup examples for objects required for the documents templates, or disable the objects in the templates. results.R must run for it to be enabled by default.

• analytical_mockup for SAP templates
• enable results in SAR templates
• disable tab_desc?
• disable tab_inf?

install checks for !Linux to configure the environment for Windows. This is wrong.

We should check for MINGW64/MINGW32 instead to set that environment.

pander() is throwing a warning that it can't handle the output of as_kable().

Check if it has ever worked (and how). We are passing the "caption" argument to pander(), but kable() also accepts it.

Maybe it is time to configure knitr::kable() to the options we're using with pander() and switch.

SAR-sync et al issues warnings when the current branch is not available in the remote to be fetched.
We can do better, by tweaking the ignored strings

So we shall.

• Template report code
• Template report style
• scripts
• README

• change Date field
• include second [title], before doc history
• update link in Availability

• SAR template
• SAP template
• Protocol template
• scripts names
• scripts vars
• scripts messages

After #4 and #7 we will need to provide an argument to SAR-new to choose which README to use when creating a new SAR repo

Create a new Rmarkdown template to create Protocols for future studies and projects.

Use the same formatting choices as the report template.

For the templates to appear in the templates list we need an R package structure.

We might need to change the repo name

The github_document format from rmarkdown automatically creates a .md file that is compatible with GFM. This file is suitable for online visualization, complete with figures and links.

This might be a useful output format for reports, although it may disrupt current practices.

One could also replicate this behavior by setting

• using keep_md
• setting pander table.syle to rmarkdown by default

• Don't print availability URL as code
• Enable results in SAR docs
• name all code chunks

Include options for the most frequent content?

• Availability / optional SAP
• significance
• data cleaning
• analytical data
• descriptive analysis
• inferential analysis

Most scripts detect usage mistake only when user doesn't provide any arguments.

A major overhaul of all scripts arguments processing is needed.

• detect simple argument mistakes
• standardize usage instructions
• provide a simple example within help
• consider including a help argument

Create a template with a standard agreement of how I approach the consulting:

• Scope
  • All analyses will be previously agreed upon in an initial communications (meeting/e-mail)
  • All analyses will be written in the Analytical Plan (SAP)
  • Client will be asked to review and approve the SAP
• Online publishing (public) portfolio
  • The analysis will may be published in the portfolio, at the consultant's discretion.
  • The data will NOT be published online
  • Client can require an embargo date before the public publishing (no justification asked).
    In such a case, the date must be set before the start of the consulting
• Deadline
  • Define deadline for deliverable and payment
  • Client can request changes within the deadline agreed upon; after deadline expiration the report will be finalized and the consulting concluded.
  • If the consultant violates the deadline, there will be a penalty of 10% of the final price rebate, per day.
• Pricing
  • Fixed price and deadline for a simple analysis
  • Hourly rate for longer projects
• Additional requests (i.e., not included in the approved SAP)
  • Additional analyses will require a v02 of the SAR, or a new SAR (to be defined on a case basis)
  • Any of the above options will be charged separately
• Save the document in the private dir (at the moment, dataset)
  • Agreement/contract
  • Invoice

Use a similar template from the SAR/SAP documents, and send over e-mail in PDF format.

• https://github.com/philsf-biostat/org/blob/master/README_padrao.md
• update init script

Parse remote-all-set argument list to check if there is an optional list of SAR_DIRs to remote-set

• Section rename: Observations and limitations (instead of Exceptions)
• Section rename: Context (instead of Introduction)
• Use a replaceable [title] tag
• New template abbrevs
• Update template descriptive analysis
• Update template inferential analysis

• move install to bin/
• rename install and uninstall scripts to philsf.workflow-*
• don't install BM-setup anymore
• standardize script names (sync.repo -> SAR-sync, *.all)

• document
• style
• README

Include the new best practices after the good experiences tested in
SAR-2021-003 and SAR-2021-004.

• input: default dataset names
  • define data.raw from read_excel
  • define analytical and analytical_mockup
  • labels with labelling
• describe: tables setup (before inference)
  • gtsummary, gt
  • gtsummary default theme + optional pt translation
  • New packages: effectsize
• inference:
  • New packages: infer
  • template for add_p
  • template for add_difference()
• modeling:
  • New packages: broom, broom-mixed
• plots:
  • default ggplot2 theme
  • default color palette
• plots-save:
  • default fig dimensions (around 8cm)
  • output publication-ready tables
    use as_rtf() + writeLines() (commented out)
• results:
  • move modeling to before inference

Adapt the README in english from a recent analysis repo

Using here::here() produces a full path, instead of a relative path.
We need to use error = FALSE to pass a relative path that works.

Even so, we lose the ability to preview in Rstudio editor panel.
At least we can check the viz of the document in HTML.

Most consulting jobs are performed remotely, so printing and signing a document is unfeasible.