From c3c05be6908999f42776e484fcce2ce6e972284c Mon Sep 17 00:00:00 2001 From: Aymeric Stamm Date: Tue, 4 Jul 2023 15:30:57 +0200 Subject: [PATCH] Transformed two vignettes into articles. --- .Rbuildignore | 1 + NEWS.md | 4 +- cran-comments.md | 6 + .../hierarchial-clustering.Rmd} | 7 +- vignettes/{ => articles}/input-formats.Rmd | 5 - vignettes/articles/references.bib | 110 ++++++++++++++++++ 6 files changed, 120 insertions(+), 13 deletions(-) rename vignettes/{hclust.Rmd => articles/hierarchial-clustering.Rmd} (97%) rename vignettes/{ => articles}/input-formats.Rmd (98%) create mode 100644 vignettes/articles/references.bib diff --git a/.Rbuildignore b/.Rbuildignore index 6e6361f..a3d9411 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -10,3 +10,4 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^vignettes/articles$ diff --git a/NEWS.md b/NEWS.md index 25a6f1c..f1b41f1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,8 +4,8 @@ * Median and mean centroid types are now defined on the union of individual grids; * Simplified `caps` class to avoid storing objects multiple times under different names; * Added vignette on initialization strategies for k-means; -* Added vignette on use case about the Berkeley growth study; -* Added vignette on supported input formats. +* Added article on use case about the Berkeley growth study; +* Added article on supported input formats. # fdacluster 0.2.2 diff --git a/cran-comments.md b/cran-comments.md index 769fff0..0652507 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,9 @@ +## Resubmission + +This is a resubmission in which I: + +* Moved two vignettes in articles (only available on website) to reduce package size to meet CRAN requirements. + ## Test environments * local macOS R installation, R 4.3.1 * continuous integration via GH actions: diff --git a/vignettes/hclust.Rmd b/vignettes/articles/hierarchial-clustering.Rmd similarity index 97% rename from vignettes/hclust.Rmd rename to vignettes/articles/hierarchial-clustering.Rmd index 499b975..ca9b608 100644 --- a/vignettes/hclust.Rmd +++ b/vignettes/articles/hierarchial-clustering.Rmd @@ -1,10 +1,5 @@ --- -title: "Hierarchical agglomerative clustering" -output: rmarkdown::html_vignette -vignette: > - %\VignetteIndexEntry{Hierarchical agglomerative clustering} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} +title: "Hierarchical clustering" --- ```{r, include = FALSE} diff --git a/vignettes/input-formats.Rmd b/vignettes/articles/input-formats.Rmd similarity index 98% rename from vignettes/input-formats.Rmd rename to vignettes/articles/input-formats.Rmd index 62d5682..26e537d 100644 --- a/vignettes/input-formats.Rmd +++ b/vignettes/articles/input-formats.Rmd @@ -1,10 +1,5 @@ --- title: "Supported input formats" -output: rmarkdown::html_vignette -vignette: > - %\VignetteIndexEntry{Input formats} - %\VignetteEngine{knitr::rmarkdown} - %\VignetteEncoding{UTF-8} bibliography: references.bib --- diff --git a/vignettes/articles/references.bib b/vignettes/articles/references.bib new file mode 100644 index 0000000..b10d3c7 --- /dev/null +++ b/vignettes/articles/references.bib @@ -0,0 +1,110 @@ +@book{ramsay2005functional, + author = {Ramsay, J. and Silverman, B.W.}, + isbn = {978-0-387-40080-8}, + lccn = {2005923773}, + publisher = {Springer}, + series = {Springer {Series} in {Statistics}}, + title = {Functional {Data} {Analysis}}, + year = {2005} +} + +@article{sangalli2010k, + title={K-mean alignment for curve clustering}, + author={Sangalli, L.M. and Secchi, P. and Vantini, S. and Vitelli, V.}, + journal={Computational Statistics \& Data Analysis}, + volume={54}, + number={5}, + pages={1219--1233}, + year={2010}, + doi={10.1016/j.csda.2009.12.008} +} + +@article{vantini2012on, + author = {Vantini, S.}, + doi = {10.1007/s11749-011-0268-9}, + journal = {Test}, + number = {4}, + pages = {676--696}, + title = {On the definition of phase and amplitude variability in functional data analysis}, + volume = {21}, + year = {2012} +} + +@article{marron2015functional, + title={Functional data analysis of amplitude and phase variation}, + author={Marron, J.S. and Ramsay, J.O. and Sangalli, L.M. and Srivastava, A.}, + journal={Statistical Science}, + pages={468--484}, + year={2015}, + doi={10.1214/15-STS524} +} + +@article{marron2014statistics, + title={Statistics of time warpings and phase variations}, + author={Marron, J.S. and Ramsay, J.O. and Sangalli, L.M. and Srivastava, A.}, + year={2014} +} + +@article{tucker2013generative, + title={Generative models for functional data using phase and amplitude separation}, + author={Tucker, J.D. and Wu, W. and Srivastava, A.}, + journal={Computational Statistics \& Data Analysis}, + volume={61}, + pages={50--66}, + year={2013}, + doi={10.1016/j.csda.2012.12.001} +} + +@inproceedings{arthur2007k, + title={K-means++ the advantages of careful seeding}, + author={Arthur, D. and Vassilvitskii, S.}, + booktitle={Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms}, + pages={1027--1035}, + year={2007} +} + +@article{sola2018micro, + title={A micro Lie theory for state estimation in robotics}, + author={Sola, Joan and Deray, Jeremie and Atchuthan, Dinesh}, + journal={arXiv preprint arXiv:1812.01537}, + year={2018} +} + +@article{tuddenham1954physical, + title={Physical growth of California boys and girls from birth to age 18, Calif. Publ}, + author={Tuddenham, R and Snyder, M}, + journal={Child Deve}, + volume={1}, + pages={183364}, + year={1954} +} + +@book{ramsay2006functional, + title={Functional Data Analysis}, + author={Ramsay, J.O. and Silverman, B.W.}, + series={Springer series in statistics}, + year={2006}, + publisher={Springer Verlag} +} + +@article{happ2020object, + title={Object-Oriented Software for Functional Data}, + volume={93}, + url={https://www.jstatsoft.org/index.php/jss/article/view/v093i05}, + doi={10.18637/jss.v093.i05}, + number={5}, + journal={Journal of Statistical Software}, + author={Happ-Kurz, Clara}, + year={2020}, + pages={1–38} +} + +@book{silverman2002applied, +title = "Applied Functional Data Analysis: Methods and Case Studies", +author = "BW Silverman and JO Ramsay", +note = "Other: Due for publication in June 2002", +year = "2002", +language = "English", +publisher = "Springer, New York, NY", +address = "United States", +}