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rrrlw / TDAstats

R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.
https://rrrlw.github.io/TDAstats
GNU General Public License v3.0
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Suggestion for improving the vignettes #8

Closed ShotaOchi closed 5 years ago

ShotaOchi commented 5 years ago

Hi, We can improve the vignettes. Honestly , there are several parts I don't understand in the vignettes. What is @roadmap-ph in the vignette "Introduction to persistent homology with TDAstats"? I think it's kind for newcomers like me if you explain what is @roadmap-ph. I listed the parts I don't understand below.

The parts I don't understand (click here)

The parts I don't understand in "Introduction to persistent homology with TDAstats" * @roadmap-ph * [@Rcpp-paper] * [@ggplot2-book]

The parts I don't understand in "Hypothesis testing with TDAstats" * @resampling-book * @hyptest * [@wasserstein-calc] * @resampling-book


By the way, references are missing in the vignettes, although there are sections for references in the bottoms of the vignettes.
You should list some references or remove the sections for references.
Thanks!

rrrlw commented 5 years ago

Thank you for opening this issue. The problem is that in-text and parenthetical references are not being replaced correctly (leaving behind text like @roadmap-ph, which actually refers to a cited work), and the References section is not being populated. This issue has been fixed in the development version of TDAstats, it just hasn't been uploaded to CRAN yet (will do so soon).

The following lines of code will install the development version and load the corrected vignettes with the references working as intended:

devtools::install_github("rrrlw/TDAstats", build_vignettes = TRUE)
vignette("intro", package = "TDAstats") # loads first vignette
vignette("inference", package = "TDAstats") # loads second vignette

I will leave this issue open until I upload a new version of TDAstats to CRAN. Please let me know if the code above does not work for you.

ShotaOchi commented 5 years ago

The code worked on my machine. I confirmed the problems were fixed.

rrrlw commented 5 years ago

An updated version of TDAstats has been uploaded to CRAN (v0.4.0 here). Thank you for helping improve TDAstats, please let me know if you have any further issues.