Update CA documentation, vignettes, and improve package examples - #8

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RaeesaGaney91 merged 64 commits into
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Jul 21, 2026
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Update CA documentation, vignettes, and improve package examples#8
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@RaeesaGaney91RaeesaGaney91 commented Jul 21, 2026

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sugnetand others added 28 commits September 18, 2025 09:35
@sugnet
fixed correlation PCA
2e15333
@sugnet
p>n for correlation PCA fixed
baf542f
@Xaleed
Loss function based on LnjTinyNew.f. Note that this loss function doe…
c4a7209
…s not fully match the one described in the paper: Spline-based Nonlinear Biplots; the code includes a penalty term (consistent with the FORTRAN implementation), which is not in the paper.
@Xaleed
Created a temporary folder for testing examples; this can be removed …
f28901b
…before merging. The folder is added to .Rbuildignore so it does not affect the package.
@Xaleed
Add the temporary example folder to .Rbuildignore.
ef49228
@Xaleed
Remove temporary example file
864326b
@Xaleed
Example is extended to multivariate responses
300a679
@Xaleed
Some minor corrections to the biplot.spline.axis function to improve …
7a8510f
…its alignment with the Fortran implementation.
@Xaleed
Example: calling from Fortran
17833eb
@Xaleed
Full Translation from Fortran to Rcpp
35d7965
@Xaleed
Replace R's optim() with a fully manual Nelder–Mead optimization algo…
8676905
…rithm implemented in Rcpp
@Xaleed
All Fortran code has been removed.
6e7811a
@Xaleed
The spline graph function has been updated from fortran to Rcpp.
4764fab
@Xaleed
Ready to install
e3892bb
@Xaleed
Differences with orignal code (fortran):
7cd669b
//Optimize alfunc by computing Z directly from BVEC and combining loops
//- Eliminated intermediate B matrix creation by computing Z = M %*% B directly from BVEC vector
//- Combined three separate loops (exind, prediction, loss calculation) into single pass
//- Removed fortran-unused utility functions matm() and exind()
//- Reduces memory allocations and improves cache locality
//- Maintains identical mathematical behavior with better performance
@Xaleed
fixed all the randomness in this code (using seed), so you should se…
54e2ee8
…e a similar result for Rcpp and Fortran.
@Xaleed
I fixed all the randomness in this code (using seed), so you should s…
fcf6391
…ee a similar result for Rcpp and Fortran.
@sugnet
minor errors fixed
4d6d576
@Xaleed
remove unused code and comments
417f598
@Xaleed
add tests/temp/ directory to .Rbuildignore
53cac74
@Xaleed
remove unused Fortran utility functions to improve performance and me…
8659fa6
…mory usage
@Xaleed
add documentation for biplot.spline.axis function.
7d9f78a
@Xaleed
Merge pull request#3from MuViSU/KMbranch
d8784a5
Replacement Loss function and Nelder-Mead based on FORTRAN with new version based on Rcpp (KMbranch)
@Xaleed
refactor biplot.spline.axis documentation and remove unused Rd file
aff16c6
@Xaleed
Merge pull request#4from MuViSU/KMbranch
4eff64b
refactor biplot.spline.axis documentation and remove unused Rd file
@MuViSU
Create CNAME
2eae081
@MuViSU
Delete CNAME
3ef9aaf
@MuViSU
Create CNAME
4db8ccf
@RaeesaGaney91
RaeesaGaney91 merged commit dcf2769 into RGbranchJul 21, 2026
3 checks passed
@RaeesaGaney91

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@RaeesaGaney91@jnienk@MuViSU@sugnet@Xaleed
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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Skip to content
Update CA documentation, vignettes, and improve package examples - #8
Merged
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Jul 21, 2026
Merged
Update CA documentation, vignettes, and improve package examples#8
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Conversation
@RaeesaGaney91
@RaeesaGaney91RaeesaGaney91
commented
Jul 21, 2026

Copy link


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Collaborator
 No description provided. 
sugnetand others
added 28 commits
September 18, 2025 09:35
@sugnet
fixed correlation PCA
2e15333
@sugnet
p>n for correlation PCA fixed
baf542f
@Xaleed
Loss function based on LnjTinyNew.f. Note that this loss function doe…
c4a7209
…s not fully match the one described in the paper: Spline-based Nonlinear Biplots; the code includes a penalty term (consistent with the FORTRAN implementation), which is not in the paper.
@Xaleed
Created a temporary folder for testing examples; this can be removed …
f28901b
…before merging. The folder is added to .Rbuildignore so it does not affect the package.
@Xaleed
Add the temporary example folder to .Rbuildignore.
ef49228
@Xaleed
Remove temporary example file
864326b
@Xaleed
Example is extended to multivariate responses
300a679
@Xaleed
Some minor corrections to the biplot.spline.axis function to improve …
7a8510f
…its alignment with the Fortran implementation.
@Xaleed
Example: calling from Fortran
17833eb
@Xaleed
Full Translation from Fortran to Rcpp
35d7965
@Xaleed
Replace R's optim() with a fully manual Nelder–Mead optimization algo…
8676905
…rithm implemented in Rcpp
@Xaleed
All Fortran code has been removed.
6e7811a
@Xaleed
The spline graph function has been updated from fortran to Rcpp.
4764fab
@Xaleed
Ready to install
e3892bb
@Xaleed
Differences with orignal code (fortran):
7cd669b
//Optimize alfunc by computing Z directly from BVEC and combining loops
//- Eliminated intermediate B matrix creation by computing Z = M %*% B directly from BVEC vector
//- Combined three separate loops (exind, prediction, loss calculation) into single pass
//- Removed fortran-unused utility functions matm() and exind()
//- Reduces memory allocations and improves cache locality
//- Maintains identical mathematical behavior with better performance
@Xaleed
 fixed all the randomness in this code (using seed), so you should se…
54e2ee8
…e a similar result for Rcpp and Fortran.
@Xaleed
I fixed all the randomness in this code (using seed), so you should s…
fcf6391
…ee a similar result for Rcpp and Fortran.
@sugnet
minor errors fixed
4d6d576
@Xaleed
remove unused code and comments
417f598
@Xaleed
add tests/temp/ directory to .Rbuildignore
53cac74
@Xaleed
remove unused Fortran utility functions to improve performance and me…
8659fa6
…mory usage
@Xaleed
add documentation for biplot.spline.axis function.
7d9f78a
@Xaleed
Merge pull request#3from MuViSU/KMbranch
d8784a5
Replacement Loss function and Nelder-Mead based on FORTRAN with new version based on Rcpp (KMbranch)
@Xaleed
refactor biplot.spline.axis documentation and remove unused Rd file
aff16c6
@Xaleed
Merge pull request#4from MuViSU/KMbranch
4eff64b
refactor biplot.spline.axis documentation and remove unused Rd file
@MuViSU
Create CNAME
2eae081
@MuViSU
Delete CNAME
3ef9aaf
@MuViSU
Create CNAME
4db8ccf
@RaeesaGaney91
RaeesaGaney91
merged commit dcf2769
into
RGbranchJul 21, 2026

3 checks passed

@RaeesaGaney91
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Jul 21, 2026

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5 participants

@RaeesaGaney91@jnienk@MuViSU@sugnet@Xaleed

, 'i');
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var __m = "*";
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Skip to content
Update CA documentation, vignettes, and improve package examples - #8
Merged
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Jul 21, 2026
Merged
Update CA documentation, vignettes, and improve package examples#8
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Conversation
@RaeesaGaney91
@RaeesaGaney91RaeesaGaney91
commented
Jul 21, 2026

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Collaborator
 No description provided. 
sugnetand others
added 28 commits
September 18, 2025 09:35
@sugnet
fixed correlation PCA
2e15333
@sugnet
p>n for correlation PCA fixed
baf542f
@Xaleed
Loss function based on LnjTinyNew.f. Note that this loss function doe…
c4a7209
…s not fully match the one described in the paper: Spline-based Nonlinear Biplots; the code includes a penalty term (consistent with the FORTRAN implementation), which is not in the paper.
@Xaleed
Created a temporary folder for testing examples; this can be removed …
f28901b
…before merging. The folder is added to .Rbuildignore so it does not affect the package.
@Xaleed
Add the temporary example folder to .Rbuildignore.
ef49228
@Xaleed
Remove temporary example file
864326b
@Xaleed
Example is extended to multivariate responses
300a679
@Xaleed
Some minor corrections to the biplot.spline.axis function to improve …
7a8510f
…its alignment with the Fortran implementation.
@Xaleed
Example: calling from Fortran
17833eb
@Xaleed
Full Translation from Fortran to Rcpp
35d7965
@Xaleed
Replace R's optim() with a fully manual Nelder–Mead optimization algo…
8676905
…rithm implemented in Rcpp
@Xaleed
All Fortran code has been removed.
6e7811a
@Xaleed
The spline graph function has been updated from fortran to Rcpp.
4764fab
@Xaleed
Ready to install
e3892bb
@Xaleed
Differences with orignal code (fortran):
7cd669b
//Optimize alfunc by computing Z directly from BVEC and combining loops
//- Eliminated intermediate B matrix creation by computing Z = M %*% B directly from BVEC vector
//- Combined three separate loops (exind, prediction, loss calculation) into single pass
//- Removed fortran-unused utility functions matm() and exind()
//- Reduces memory allocations and improves cache locality
//- Maintains identical mathematical behavior with better performance
@Xaleed
 fixed all the randomness in this code (using seed), so you should se…
54e2ee8
…e a similar result for Rcpp and Fortran.
@Xaleed
I fixed all the randomness in this code (using seed), so you should s…
fcf6391
…ee a similar result for Rcpp and Fortran.
@sugnet
minor errors fixed
4d6d576
@Xaleed
remove unused code and comments
417f598
@Xaleed
add tests/temp/ directory to .Rbuildignore
53cac74
@Xaleed
remove unused Fortran utility functions to improve performance and me…
8659fa6
…mory usage
@Xaleed
add documentation for biplot.spline.axis function.
7d9f78a
@Xaleed
Merge pull request#3from MuViSU/KMbranch
d8784a5
Replacement Loss function and Nelder-Mead based on FORTRAN with new version based on Rcpp (KMbranch)
@Xaleed
refactor biplot.spline.axis documentation and remove unused Rd file
aff16c6
@Xaleed
Merge pull request#4from MuViSU/KMbranch
4eff64b
refactor biplot.spline.axis documentation and remove unused Rd file
@MuViSU
Create CNAME
2eae081
@MuViSU
Delete CNAME
3ef9aaf
@MuViSU
Create CNAME
4db8ccf
@RaeesaGaney91
RaeesaGaney91
merged commit dcf2769
into
RGbranchJul 21, 2026

3 checks passed

@RaeesaGaney91
RaeesaGaney91
commented
Jul 21, 2026

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Merge complete
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5 participants

@RaeesaGaney91@jnienk@MuViSU@sugnet@Xaleed

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
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(function(){
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var __re = new RegExp('^' + ".*" + '

Skip to content
Update CA documentation, vignettes, and improve package examples - #8
Merged
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Jul 21, 2026
Merged
Update CA documentation, vignettes, and improve package examples#8
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Conversation
@RaeesaGaney91
@RaeesaGaney91RaeesaGaney91
commented
Jul 21, 2026

Copy link


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Collaborator
 No description provided. 
sugnetand others
added 28 commits
September 18, 2025 09:35
@sugnet
fixed correlation PCA
2e15333
@sugnet
p>n for correlation PCA fixed
baf542f
@Xaleed
Loss function based on LnjTinyNew.f. Note that this loss function doe…
c4a7209
…s not fully match the one described in the paper: Spline-based Nonlinear Biplots; the code includes a penalty term (consistent with the FORTRAN implementation), which is not in the paper.
@Xaleed
Created a temporary folder for testing examples; this can be removed …
f28901b
…before merging. The folder is added to .Rbuildignore so it does not affect the package.
@Xaleed
Add the temporary example folder to .Rbuildignore.
ef49228
@Xaleed
Remove temporary example file
864326b
@Xaleed
Example is extended to multivariate responses
300a679
@Xaleed
Some minor corrections to the biplot.spline.axis function to improve …
7a8510f
…its alignment with the Fortran implementation.
@Xaleed
Example: calling from Fortran
17833eb
@Xaleed
Full Translation from Fortran to Rcpp
35d7965
@Xaleed
Replace R's optim() with a fully manual Nelder–Mead optimization algo…
8676905
…rithm implemented in Rcpp
@Xaleed
All Fortran code has been removed.
6e7811a
@Xaleed
The spline graph function has been updated from fortran to Rcpp.
4764fab
@Xaleed
Ready to install
e3892bb
@Xaleed
Differences with orignal code (fortran):
7cd669b
//Optimize alfunc by computing Z directly from BVEC and combining loops
//- Eliminated intermediate B matrix creation by computing Z = M %*% B directly from BVEC vector
//- Combined three separate loops (exind, prediction, loss calculation) into single pass
//- Removed fortran-unused utility functions matm() and exind()
//- Reduces memory allocations and improves cache locality
//- Maintains identical mathematical behavior with better performance
@Xaleed
 fixed all the randomness in this code (using seed), so you should se…
54e2ee8
…e a similar result for Rcpp and Fortran.
@Xaleed
I fixed all the randomness in this code (using seed), so you should s…
fcf6391
…ee a similar result for Rcpp and Fortran.
@sugnet
minor errors fixed
4d6d576
@Xaleed
remove unused code and comments
417f598
@Xaleed
add tests/temp/ directory to .Rbuildignore
53cac74
@Xaleed
remove unused Fortran utility functions to improve performance and me…
8659fa6
…mory usage
@Xaleed
add documentation for biplot.spline.axis function.
7d9f78a
@Xaleed
Merge pull request#3from MuViSU/KMbranch
d8784a5
Replacement Loss function and Nelder-Mead based on FORTRAN with new version based on Rcpp (KMbranch)
@Xaleed
refactor biplot.spline.axis documentation and remove unused Rd file
aff16c6
@Xaleed
Merge pull request#4from MuViSU/KMbranch
4eff64b
refactor biplot.spline.axis documentation and remove unused Rd file
@MuViSU
Create CNAME
2eae081
@MuViSU
Delete CNAME
3ef9aaf
@MuViSU
Create CNAME
4db8ccf
@RaeesaGaney91
RaeesaGaney91
merged commit dcf2769
into
RGbranchJul 21, 2026

3 checks passed

@RaeesaGaney91
RaeesaGaney91
commented
Jul 21, 2026

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Merge complete
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5 participants

@RaeesaGaney91@jnienk@MuViSU@sugnet@Xaleed

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
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Skip to content
Update CA documentation, vignettes, and improve package examples - #8
Merged
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Jul 21, 2026
Merged
Update CA documentation, vignettes, and improve package examples#8
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Conversation
@RaeesaGaney91
@RaeesaGaney91RaeesaGaney91
commented
Jul 21, 2026

Copy link


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Collaborator
 No description provided. 
sugnetand others
added 28 commits
September 18, 2025 09:35
@sugnet
fixed correlation PCA
2e15333
@sugnet
p>n for correlation PCA fixed
baf542f
@Xaleed
Loss function based on LnjTinyNew.f. Note that this loss function doe…
c4a7209
…s not fully match the one described in the paper: Spline-based Nonlinear Biplots; the code includes a penalty term (consistent with the FORTRAN implementation), which is not in the paper.
@Xaleed
Created a temporary folder for testing examples; this can be removed …
f28901b
…before merging. The folder is added to .Rbuildignore so it does not affect the package.
@Xaleed
Add the temporary example folder to .Rbuildignore.
ef49228
@Xaleed
Remove temporary example file
864326b
@Xaleed
Example is extended to multivariate responses
300a679
@Xaleed
Some minor corrections to the biplot.spline.axis function to improve …
7a8510f
…its alignment with the Fortran implementation.
@Xaleed
Example: calling from Fortran
17833eb
@Xaleed
Full Translation from Fortran to Rcpp
35d7965
@Xaleed
Replace R's optim() with a fully manual Nelder–Mead optimization algo…
8676905
…rithm implemented in Rcpp
@Xaleed
All Fortran code has been removed.
6e7811a
@Xaleed
The spline graph function has been updated from fortran to Rcpp.
4764fab
@Xaleed
Ready to install
e3892bb
@Xaleed
Differences with orignal code (fortran):
7cd669b
//Optimize alfunc by computing Z directly from BVEC and combining loops
//- Eliminated intermediate B matrix creation by computing Z = M %*% B directly from BVEC vector
//- Combined three separate loops (exind, prediction, loss calculation) into single pass
//- Removed fortran-unused utility functions matm() and exind()
//- Reduces memory allocations and improves cache locality
//- Maintains identical mathematical behavior with better performance
@Xaleed
 fixed all the randomness in this code (using seed), so you should se…
54e2ee8
…e a similar result for Rcpp and Fortran.
@Xaleed
I fixed all the randomness in this code (using seed), so you should s…
fcf6391
…ee a similar result for Rcpp and Fortran.
@sugnet
minor errors fixed
4d6d576
@Xaleed
remove unused code and comments
417f598
@Xaleed
add tests/temp/ directory to .Rbuildignore
53cac74
@Xaleed
remove unused Fortran utility functions to improve performance and me…
8659fa6
…mory usage
@Xaleed
add documentation for biplot.spline.axis function.
7d9f78a
@Xaleed
Merge pull request#3from MuViSU/KMbranch
d8784a5
Replacement Loss function and Nelder-Mead based on FORTRAN with new version based on Rcpp (KMbranch)
@Xaleed
refactor biplot.spline.axis documentation and remove unused Rd file
aff16c6
@Xaleed
Merge pull request#4from MuViSU/KMbranch
4eff64b
refactor biplot.spline.axis documentation and remove unused Rd file
@MuViSU
Create CNAME
2eae081
@MuViSU
Delete CNAME
3ef9aaf
@MuViSU
Create CNAME
4db8ccf
@RaeesaGaney91
RaeesaGaney91
merged commit dcf2769
into
RGbranchJul 21, 2026

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Update CA documentation, vignettes, and improve package examples - #8
Merged
RaeesaGaney91 merged 64 commits into
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main
Jul 21, 2026
Merged
Update CA documentation, vignettes, and improve package examples#8
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
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@RaeesaGaney91RaeesaGaney91
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Jul 21, 2026

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 No description provided. 
sugnetand others
added 28 commits
September 18, 2025 09:35
@sugnet
fixed correlation PCA
2e15333
@sugnet
p>n for correlation PCA fixed
baf542f
@Xaleed
Loss function based on LnjTinyNew.f. Note that this loss function doe…
c4a7209
…s not fully match the one described in the paper: Spline-based Nonlinear Biplots; the code includes a penalty term (consistent with the FORTRAN implementation), which is not in the paper.
@Xaleed
Created a temporary folder for testing examples; this can be removed …
f28901b
…before merging. The folder is added to .Rbuildignore so it does not affect the package.
@Xaleed
Add the temporary example folder to .Rbuildignore.
ef49228
@Xaleed
Remove temporary example file
864326b
@Xaleed
Example is extended to multivariate responses
300a679
@Xaleed
Some minor corrections to the biplot.spline.axis function to improve …
7a8510f
…its alignment with the Fortran implementation.
@Xaleed
Example: calling from Fortran
17833eb
@Xaleed
Full Translation from Fortran to Rcpp
35d7965
@Xaleed
Replace R's optim() with a fully manual Nelder–Mead optimization algo…
8676905
…rithm implemented in Rcpp
@Xaleed
All Fortran code has been removed.
6e7811a
@Xaleed
The spline graph function has been updated from fortran to Rcpp.
4764fab
@Xaleed
Ready to install
e3892bb
@Xaleed
Differences with orignal code (fortran):
7cd669b
//Optimize alfunc by computing Z directly from BVEC and combining loops
//- Eliminated intermediate B matrix creation by computing Z = M %*% B directly from BVEC vector
//- Combined three separate loops (exind, prediction, loss calculation) into single pass
//- Removed fortran-unused utility functions matm() and exind()
//- Reduces memory allocations and improves cache locality
//- Maintains identical mathematical behavior with better performance
@Xaleed
 fixed all the randomness in this code (using seed), so you should se…
54e2ee8
…e a similar result for Rcpp and Fortran.
@Xaleed
I fixed all the randomness in this code (using seed), so you should s…
fcf6391
…ee a similar result for Rcpp and Fortran.
@sugnet
minor errors fixed
4d6d576
@Xaleed
remove unused code and comments
417f598
@Xaleed
add tests/temp/ directory to .Rbuildignore
53cac74
@Xaleed
remove unused Fortran utility functions to improve performance and me…
8659fa6
…mory usage
@Xaleed
add documentation for biplot.spline.axis function.
7d9f78a
@Xaleed
Merge pull request#3from MuViSU/KMbranch
d8784a5
Replacement Loss function and Nelder-Mead based on FORTRAN with new version based on Rcpp (KMbranch)
@Xaleed
refactor biplot.spline.axis documentation and remove unused Rd file
aff16c6
@Xaleed
Merge pull request#4from MuViSU/KMbranch
4eff64b
refactor biplot.spline.axis documentation and remove unused Rd file
@MuViSU
Create CNAME
2eae081
@MuViSU
Delete CNAME
3ef9aaf
@MuViSU
Create CNAME
4db8ccf
@RaeesaGaney91
RaeesaGaney91
merged commit dcf2769
into
RGbranchJul 21, 2026

3 checks passed

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@RaeesaGaney91@jnienk@MuViSU@sugnet@Xaleed

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Update CA documentation, vignettes, and improve package examples - #8
Merged
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Jul 21, 2026
Merged
Update CA documentation, vignettes, and improve package examples#8
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Conversation
@RaeesaGaney91
@RaeesaGaney91RaeesaGaney91
commented
Jul 21, 2026

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Collaborator
 No description provided. 
sugnetand others
added 28 commits
September 18, 2025 09:35
@sugnet
fixed correlation PCA
2e15333
@sugnet
p>n for correlation PCA fixed
baf542f
@Xaleed
Loss function based on LnjTinyNew.f. Note that this loss function doe…
c4a7209
…s not fully match the one described in the paper: Spline-based Nonlinear Biplots; the code includes a penalty term (consistent with the FORTRAN implementation), which is not in the paper.
@Xaleed
Created a temporary folder for testing examples; this can be removed …
f28901b
…before merging. The folder is added to .Rbuildignore so it does not affect the package.
@Xaleed
Add the temporary example folder to .Rbuildignore.
ef49228
@Xaleed
Remove temporary example file
864326b
@Xaleed
Example is extended to multivariate responses
300a679
@Xaleed
Some minor corrections to the biplot.spline.axis function to improve …
7a8510f
…its alignment with the Fortran implementation.
@Xaleed
Example: calling from Fortran
17833eb
@Xaleed
Full Translation from Fortran to Rcpp
35d7965
@Xaleed
Replace R's optim() with a fully manual Nelder–Mead optimization algo…
8676905
…rithm implemented in Rcpp
@Xaleed
All Fortran code has been removed.
6e7811a
@Xaleed
The spline graph function has been updated from fortran to Rcpp.
4764fab
@Xaleed
Ready to install
e3892bb
@Xaleed
Differences with orignal code (fortran):
7cd669b
//Optimize alfunc by computing Z directly from BVEC and combining loops
//- Eliminated intermediate B matrix creation by computing Z = M %*% B directly from BVEC vector
//- Combined three separate loops (exind, prediction, loss calculation) into single pass
//- Removed fortran-unused utility functions matm() and exind()
//- Reduces memory allocations and improves cache locality
//- Maintains identical mathematical behavior with better performance
@Xaleed
 fixed all the randomness in this code (using seed), so you should se…
54e2ee8
…e a similar result for Rcpp and Fortran.
@Xaleed
I fixed all the randomness in this code (using seed), so you should s…
fcf6391
…ee a similar result for Rcpp and Fortran.
@sugnet
minor errors fixed
4d6d576
@Xaleed
remove unused code and comments
417f598
@Xaleed
add tests/temp/ directory to .Rbuildignore
53cac74
@Xaleed
remove unused Fortran utility functions to improve performance and me…
8659fa6
…mory usage
@Xaleed
add documentation for biplot.spline.axis function.
7d9f78a
@Xaleed
Merge pull request#3from MuViSU/KMbranch
d8784a5
Replacement Loss function and Nelder-Mead based on FORTRAN with new version based on Rcpp (KMbranch)
@Xaleed
refactor biplot.spline.axis documentation and remove unused Rd file
aff16c6
@Xaleed
Merge pull request#4from MuViSU/KMbranch
4eff64b
refactor biplot.spline.axis documentation and remove unused Rd file
@MuViSU
Create CNAME
2eae081
@MuViSU
Delete CNAME
3ef9aaf
@MuViSU
Create CNAME
4db8ccf
@RaeesaGaney91
RaeesaGaney91
merged commit dcf2769
into
RGbranchJul 21, 2026

3 checks passed

@RaeesaGaney91
RaeesaGaney91
commented
Jul 21, 2026

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Merge complete
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5 participants

@RaeesaGaney91@jnienk@MuViSU@sugnet@Xaleed

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
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})();

Skip to content
Update CA documentation, vignettes, and improve package examples - #8
Merged
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Jul 21, 2026
Merged
Update CA documentation, vignettes, and improve package examples#8
RaeesaGaney91 merged 64 commits into
RGbranchfrom 
main
Conversation
@RaeesaGaney91
@RaeesaGaney91RaeesaGaney91
commented
Jul 21, 2026

Copy link


Copy Markdown

Collaborator
 No description provided. 
sugnetand others
added 28 commits
September 18, 2025 09:35
@sugnet
fixed correlation PCA
2e15333
@sugnet
p>n for correlation PCA fixed
baf542f
@Xaleed
Loss function based on LnjTinyNew.f. Note that this loss function doe…
c4a7209
…s not fully match the one described in the paper: Spline-based Nonlinear Biplots; the code includes a penalty term (consistent with the FORTRAN implementation), which is not in the paper.
@Xaleed
Created a temporary folder for testing examples; this can be removed …
f28901b
…before merging. The folder is added to .Rbuildignore so it does not affect the package.
@Xaleed
Add the temporary example folder to .Rbuildignore.
ef49228
@Xaleed
Remove temporary example file
864326b
@Xaleed
Example is extended to multivariate responses
300a679
@Xaleed
Some minor corrections to the biplot.spline.axis function to improve …
7a8510f
…its alignment with the Fortran implementation.
@Xaleed
Example: calling from Fortran
17833eb
@Xaleed
Full Translation from Fortran to Rcpp
35d7965
@Xaleed
Replace R's optim() with a fully manual Nelder–Mead optimization algo…
8676905
…rithm implemented in Rcpp
@Xaleed
All Fortran code has been removed.
6e7811a
@Xaleed
The spline graph function has been updated from fortran to Rcpp.
4764fab
@Xaleed
Ready to install
e3892bb
@Xaleed
Differences with orignal code (fortran):
7cd669b
//Optimize alfunc by computing Z directly from BVEC and combining loops
//- Eliminated intermediate B matrix creation by computing Z = M %*% B directly from BVEC vector
//- Combined three separate loops (exind, prediction, loss calculation) into single pass
//- Removed fortran-unused utility functions matm() and exind()
//- Reduces memory allocations and improves cache locality
//- Maintains identical mathematical behavior with better performance
@Xaleed
 fixed all the randomness in this code (using seed), so you should se…
54e2ee8
…e a similar result for Rcpp and Fortran.
@Xaleed
I fixed all the randomness in this code (using seed), so you should s…
fcf6391
…ee a similar result for Rcpp and Fortran.
@sugnet
minor errors fixed
4d6d576
@Xaleed
remove unused code and comments
417f598
@Xaleed
add tests/temp/ directory to .Rbuildignore
53cac74
@Xaleed
remove unused Fortran utility functions to improve performance and me…
8659fa6
…mory usage
@Xaleed
add documentation for biplot.spline.axis function.
7d9f78a
@Xaleed
Merge pull request#3from MuViSU/KMbranch
d8784a5
Replacement Loss function and Nelder-Mead based on FORTRAN with new version based on Rcpp (KMbranch)
@Xaleed
refactor biplot.spline.axis documentation and remove unused Rd file
aff16c6
@Xaleed
Merge pull request#4from MuViSU/KMbranch
4eff64b
refactor biplot.spline.axis documentation and remove unused Rd file
@MuViSU
Create CNAME
2eae081
@MuViSU
Delete CNAME
3ef9aaf
@MuViSU
Create CNAME
4db8ccf
@RaeesaGaney91
RaeesaGaney91
merged commit dcf2769
into
RGbranchJul 21, 2026

3 checks passed

@RaeesaGaney91
RaeesaGaney91
commented
Jul 21, 2026

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CollaboratorAuthor
Merge complete
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5 participants

@RaeesaGaney91@jnienk@MuViSU@sugnet@Xaleed