Website #310
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Website #310
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I'm making this a PR mainly to get us started. I assume there will be some changes to the code before we can merge. |
Literally the output of `usethis::use_github_action("pkgdown")`
This is just for testing the online deployment and should be removed after merge (or just before).
wleoncio
approved these changes
Sep 8, 2023
osorensen
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Oct 4, 2023
* Removed duplicated output element (#291) * Removed duplicated output element * Updated package version and NEWS * Should fix #292 (#293) * Updated NEWS and increment version * Updated citation info in README * Should fix #299 (#300) * Should fix #299 * Added missing documentation objects and changed the name of one argument * Fixed another documentation issue * Removed deprecated SMC functions (#303) * Updated build version number * Increment version number to 1.3.2.9002 * Removed deprecated SMC functions (#301) * Updated NEWS (#301) * Logz issue 158 (#304) * Added exact partition function option * Updated tests * Updated SMC Mallows examples * Styling * More linting * Updated linter workflow Some linter were deprecated, ignored line on vignette needed update * Trying to please CodeFactor * Incremented version number and added entry to NEWS.md --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Added BugReport URL (#308) * Added URL for bug reports * Increment version number to 1.3.2.9004 * Small typo correction and documentation update * Website (#310) * Website * De-duplicating vignettes * Adding GH Action for pkgdown (#290) Literally the output of `usethis::use_github_action("pkgdown")` * Triggering `gh-pages` when pushing to PR #310 (tests) This is just for testing the online deployment and should be removed after merge (or just before). --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Small changes (#311) * Small changes * Fixed gh-pages bases for deployment (#290) The PR branch was left over. More importantly, the file listed "main" instead of "master". --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Corrected small typo in documentation * Cleaner unit test output (#314) * Increment version number to 1.3.2.9006 * Capturing output of test unit * Dirichlet concentration parameter is now actually being used (#315) * forwarded psi argument to run_mcmc * Incremented version and updated news.md * ready for cran submission * CRAN wanted a trailing slash in the URL to the website, since it becomes added automatically if one follows the URL --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
osorensen
added a commit
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Oct 5, 2023
* Removed duplicated output element (#291) * Removed duplicated output element * Updated package version and NEWS * Should fix #292 (#293) * Updated NEWS and increment version * Updated citation info in README * Should fix #299 (#300) * Should fix #299 * Added missing documentation objects and changed the name of one argument * Fixed another documentation issue * Removed deprecated SMC functions (#303) * Updated build version number * Increment version number to 1.3.2.9002 * Removed deprecated SMC functions (#301) * Updated NEWS (#301) * Logz issue 158 (#304) * Added exact partition function option * Updated tests * Updated SMC Mallows examples * Styling * More linting * Updated linter workflow Some linter were deprecated, ignored line on vignette needed update * Trying to please CodeFactor * Incremented version number and added entry to NEWS.md --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Added BugReport URL (#308) * Added URL for bug reports * Increment version number to 1.3.2.9004 * Small typo correction and documentation update * Website (#310) * Website * De-duplicating vignettes * Adding GH Action for pkgdown (#290) Literally the output of `usethis::use_github_action("pkgdown")` * Triggering `gh-pages` when pushing to PR #310 (tests) This is just for testing the online deployment and should be removed after merge (or just before). --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Small changes (#311) * Small changes * Fixed gh-pages bases for deployment (#290) The PR branch was left over. More importantly, the file listed "main" instead of "master". --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Corrected small typo in documentation * Cleaner unit test output (#314) * Increment version number to 1.3.2.9006 * Capturing output of test unit * Dirichlet concentration parameter is now actually being used (#315) * forwarded psi argument to run_mcmc * Incremented version and updated news.md * ready for cran submission * CRAN wanted a trailing slash in the URL to the website, since it becomes added automatically if one follows the URL * Internalized a bunch of SMC functions and made families #312 * incrementing development versions * updating news.md * linting * fixed most of the thigns * incremented dev version * Fixed lint issues --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
osorensen
added a commit
that referenced
this pull request
Oct 5, 2023
* Removed duplicated output element (#291) * Removed duplicated output element * Updated package version and NEWS * Should fix #292 (#293) * Updated NEWS and increment version * Updated citation info in README * Should fix #299 (#300) * Should fix #299 * Added missing documentation objects and changed the name of one argument * Fixed another documentation issue * Removed deprecated SMC functions (#303) * Updated build version number * Increment version number to 1.3.2.9002 * Removed deprecated SMC functions (#301) * Updated NEWS (#301) * Logz issue 158 (#304) * Added exact partition function option * Updated tests * Updated SMC Mallows examples * Styling * More linting * Updated linter workflow Some linter were deprecated, ignored line on vignette needed update * Trying to please CodeFactor * Incremented version number and added entry to NEWS.md --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Added BugReport URL (#308) * Added URL for bug reports * Increment version number to 1.3.2.9004 * Small typo correction and documentation update * Website (#310) * Website * De-duplicating vignettes * Adding GH Action for pkgdown (#290) Literally the output of `usethis::use_github_action("pkgdown")` * Triggering `gh-pages` when pushing to PR #310 (tests) This is just for testing the online deployment and should be removed after merge (or just before). --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Small changes (#311) * Small changes * Fixed gh-pages bases for deployment (#290) The PR branch was left over. More importantly, the file listed "main" instead of "master". --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Corrected small typo in documentation * Cleaner unit test output (#314) * Increment version number to 1.3.2.9006 * Capturing output of test unit * Dirichlet concentration parameter is now actually being used (#315) * forwarded psi argument to run_mcmc * Incremented version and updated news.md * ready for cran submission * CRAN wanted a trailing slash in the URL to the website, since it becomes added automatically if one follows the URL * Internalized a bunch of SMC functions and made families #312 * incrementing development versions * updating news.md * linting * fixed most of the thigns * incremented dev version * Fixed lint issues * removing tagging of Anja as author since she is listed in DESCRIPTION * lots of work in order to clean up compute_consensus * linting --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
osorensen
added a commit
that referenced
this pull request
Oct 12, 2023
* Removed duplicated output element (#291) * Removed duplicated output element * Updated package version and NEWS * Should fix #292 (#293) * Updated NEWS and increment version * Updated citation info in README * Should fix #299 (#300) * Should fix #299 * Added missing documentation objects and changed the name of one argument * Fixed another documentation issue * Removed deprecated SMC functions (#303) * Updated build version number * Increment version number to 1.3.2.9002 * Removed deprecated SMC functions (#301) * Updated NEWS (#301) * Logz issue 158 (#304) * Added exact partition function option * Updated tests * Updated SMC Mallows examples * Styling * More linting * Updated linter workflow Some linter were deprecated, ignored line on vignette needed update * Trying to please CodeFactor * Incremented version number and added entry to NEWS.md --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Added BugReport URL (#308) * Added URL for bug reports * Increment version number to 1.3.2.9004 * Small typo correction and documentation update * Website (#310) * Website * De-duplicating vignettes * Adding GH Action for pkgdown (#290) Literally the output of `usethis::use_github_action("pkgdown")` * Triggering `gh-pages` when pushing to PR #310 (tests) This is just for testing the online deployment and should be removed after merge (or just before). --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Small changes (#311) * Small changes * Fixed gh-pages bases for deployment (#290) The PR branch was left over. More importantly, the file listed "main" instead of "master". --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Corrected small typo in documentation * Cleaner unit test output (#314) * Increment version number to 1.3.2.9006 * Capturing output of test unit * Dirichlet concentration parameter is now actually being used (#315) * forwarded psi argument to run_mcmc * Incremented version and updated news.md * ready for cran submission * CRAN wanted a trailing slash in the URL to the website, since it becomes added automatically if one follows the URL * Internalized a bunch of SMC functions and made families #312 * incrementing development versions * updating news.md * linting * fixed most of the thigns * incremented dev version * Fixed lint issues * removing tagging of Anja as author since she is listed in DESCRIPTION * lots of work in order to clean up compute_consensus * linting * got rid of annoying row names in posterior interval dataframe * made a version with parallel chains that is actually working * close to a working version with parallel chains * first iteration * styling and updating style rules * attempt at refactoring * getting there * styling * fixing initial value hickup * styling * Parallel issue 307 (#320) * made a version with parallel chains that is actually working * close to a working version with parallel chains * first iteration * styling and updating style rules * attempt at refactoring * getting there * styling * fixing initial value hickup * styling --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
osorensen
added a commit
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Oct 13, 2023
#324) * Removed duplicated output element (#291) * Removed duplicated output element * Updated package version and NEWS * Should fix #292 (#293) * Updated NEWS and increment version * Updated citation info in README * Should fix #299 (#300) * Should fix #299 * Added missing documentation objects and changed the name of one argument * Fixed another documentation issue * Removed deprecated SMC functions (#303) * Updated build version number * Increment version number to 1.3.2.9002 * Removed deprecated SMC functions (#301) * Updated NEWS (#301) * Logz issue 158 (#304) * Added exact partition function option * Updated tests * Updated SMC Mallows examples * Styling * More linting * Updated linter workflow Some linter were deprecated, ignored line on vignette needed update * Trying to please CodeFactor * Incremented version number and added entry to NEWS.md --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Added BugReport URL (#308) * Added URL for bug reports * Increment version number to 1.3.2.9004 * Small typo correction and documentation update * Website (#310) * Website * De-duplicating vignettes * Adding GH Action for pkgdown (#290) Literally the output of `usethis::use_github_action("pkgdown")` * Triggering `gh-pages` when pushing to PR #310 (tests) This is just for testing the online deployment and should be removed after merge (or just before). --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Small changes (#311) * Small changes * Fixed gh-pages bases for deployment (#290) The PR branch was left over. More importantly, the file listed "main" instead of "master". --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Corrected small typo in documentation * Cleaner unit test output (#314) * Increment version number to 1.3.2.9006 * Capturing output of test unit * Dirichlet concentration parameter is now actually being used (#315) * forwarded psi argument to run_mcmc * Incremented version and updated news.md * ready for cran submission * CRAN wanted a trailing slash in the URL to the website, since it becomes added automatically if one follows the URL * Internalized a bunch of SMC functions and made families #312 * incrementing development versions * updating news.md * linting * fixed most of the thigns * incremented dev version * Fixed lint issues * removing tagging of Anja as author since she is listed in DESCRIPTION * lots of work in order to clean up compute_consensus * linting * got rid of annoying row names in posterior interval dataframe * made a version with parallel chains that is actually working * close to a working version with parallel chains * first iteration * styling and updating style rules * attempt at refactoring * getting there * styling * fixing initial value hickup * styling * Parallel issue 307 (#320) * made a version with parallel chains that is actually working * close to a working version with parallel chains * first iteration * styling and updating style rules * attempt at refactoring * getting there * styling * fixing initial value hickup * styling * correcting typos in vignette --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
osorensen
added a commit
that referenced
this pull request
Oct 20, 2023
* Removed duplicated output element (#291) * Removed duplicated output element * Updated package version and NEWS * Should fix #292 (#293) * Updated NEWS and increment version * Updated citation info in README * Should fix #299 (#300) * Should fix #299 * Added missing documentation objects and changed the name of one argument * Fixed another documentation issue * Removed deprecated SMC functions (#303) * Updated build version number * Increment version number to 1.3.2.9002 * Removed deprecated SMC functions (#301) * Updated NEWS (#301) * Logz issue 158 (#304) * Added exact partition function option * Updated tests * Updated SMC Mallows examples * Styling * More linting * Updated linter workflow Some linter were deprecated, ignored line on vignette needed update * Trying to please CodeFactor * Incremented version number and added entry to NEWS.md --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Added BugReport URL (#308) * Added URL for bug reports * Increment version number to 1.3.2.9004 * Small typo correction and documentation update * Website (#310) * Website * De-duplicating vignettes * Adding GH Action for pkgdown (#290) Literally the output of `usethis::use_github_action("pkgdown")` * Triggering `gh-pages` when pushing to PR #310 (tests) This is just for testing the online deployment and should be removed after merge (or just before). --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Small changes (#311) * Small changes * Fixed gh-pages bases for deployment (#290) The PR branch was left over. More importantly, the file listed "main" instead of "master". --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no> * Corrected small typo in documentation * Cleaner unit test output (#314) * Increment version number to 1.3.2.9006 * Capturing output of test unit * Dirichlet concentration parameter is now actually being used (#315) * forwarded psi argument to run_mcmc * Incremented version and updated news.md * ready for cran submission * CRAN wanted a trailing slash in the URL to the website, since it becomes added automatically if one follows the URL * Internalized a bunch of SMC functions and made families #312 * incrementing development versions * updating news.md * linting * fixed most of the thigns * incremented dev version * Fixed lint issues * removing tagging of Anja as author since she is listed in DESCRIPTION * lots of work in order to clean up compute_consensus * linting * got rid of annoying row names in posterior interval dataframe * made a version with parallel chains that is actually working * close to a working version with parallel chains * first iteration * styling and updating style rules * attempt at refactoring * getting there * styling * fixing initial value hickup * styling * Parallel issue 307 (#320) * made a version with parallel chains that is actually working * close to a working version with parallel chains * first iteration * styling and updating style rules * attempt at refactoring * getting there * styling * fixing initial value hickup * styling * correcting typos in vignette * Removed unused argument from augment_pairwise() #325 * Updated news * incremented version --------- Co-authored-by: Waldir Leoncio <w.l.netto@medisin.uio.no>
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This should set up a website, cf. #290. The online tricky part is that the introductory vignette is a pdf paper, so it won't render properly. I've followed the advise from this issue, but not completely happy with it.
I've generated the website locally and there it looks good. I've also enabled GitHub Pages, so each time we push to the master branch, the site will be re-built.