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sport of sacred spherical cowsAnother three hundred lines for <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> project since last round of work in June:<a href="https://hcommons.social/@beadsland/114788341947558989" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/114788341947558989</a>Work in July focused on:• streamline variants <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> alt-text generation • extensive refactoring across multiple annoplot and tiop modules • build out option for using GISAID for tree chart, in lieu of recent estimates • prototype dynamic offsets for flanking artistsWith other tasks including:• refine flattening of variants lineages • resume TODO tracking • tweak log messages in various methods • tweak title adornment overhang • tweak legend to better accommodate footnotes • address data import issues • tweak inclusion of ancestor variants on legend • conform throughout to non-specific reporting periods • add option for dropping most recent period • migrate hatchmask suppression for scrim periods • bugfixing of paragraph artist • copy editing and revisions of captions • tweak captions to better reflect runtime options • tweak emboss edge collision detection

sport of sacred spherical cowsAnother two hundred lines for <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> project since last round of work in May: <a href="https://hcommons.social/@beadsland/114634070336715545" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/114634070336715545</a>Work in June included:• refine, expand and refactor variant legend <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> footnotes • correct representation of negative growth in share • refactor and improve reversible dict • streamline handling of chained clusters • refactor, expand and debug footnote peaks methods • refine and refactor alt-text pruning cascade • refactoring in multiple additional submodules • tweaks to this devpie chart • fix errors import and inline presentation of GISAID data • fix error in dot-hatch trigger • tweak legend headers and family grouping • prepare for handling of CDC's announced change in reporting periods • resolve collisions for new clusters and common names • preserve legend entries for significant GISAID variants

sport of sacred spherical cowsTwo weeks ago, Mike Honey noted that there are three recombinants that have arrived on Doppelgänger spike proteins, namely XFJ, XFM, and XFP:<a href="https://aus.social/@mike_honey_/114611686572899925" rel="nofollow noopener" translate="no" target="_blank">https://aus.social/@mike_honey_/114611686572899925</a>Last week, Xu Zhu (HT D. Focosi) identified a superset of recombinants that have all arrived at a pairing of LF.7's NTD with RBD from elsewhere, namely: XFC, XFG, XFH, XFJ, XFM, XFN and XFP:<a href="https://x.com/dfocosi/status/1931351676880879856" rel="nofollow noopener" translate="no" target="_blank">https://x.com/dfocosi/status/1931351676880879856</a>Above variants chart <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> script is now updated to favor grouping by such emerging clusters preferentially over grouping by legacy ancestors.As a reminder, recombinants happen when more than one virus strain is actively replicating in the same organism.Here, that means two simultaneous infections, from different sources, finding a home in the same person. When <a href="https://hcommons.social/tags/PublicHealth" class="mention hashtag" rel="nofollow noopener" target="_blank">#PublicHealth</a> is a priority, this should be a rare occurrence.There are seven unique recombinants identified in this new cluster, alone.❖ <a href="https://hcommons.social/tags/ThisIsOurPolio" class="mention hashtag" rel="nofollow noopener" target="_blank">#ThisIsOurPolio</a> <a href="https://hcommons.social/tags/Covid" class="mention hashtag" rel="nofollow noopener" target="_blank">#Covid</a> <a href="https://hcommons.social/tags/Covid19" class="mention hashtag" rel="nofollow noopener" target="_blank">#Covid19</a> <a href="https://hcommons.social/tags/SARS2" class="mention hashtag" rel="nofollow noopener" target="_blank">#SARS2</a> <a href="https://hcommons.social/tags/variants" class="mention hashtag" rel="nofollow noopener" target="_blank">#variants</a> <a href="https://hcommons.social/tags/CovidIsNotOver" class="mention hashtag" rel="nofollow noopener" target="_blank">#CovidIsNotOver</a> <a href="https://hcommons.social/tags/CovidIsAirborne" class="mention hashtag" rel="nofollow noopener" target="_blank">#CovidIsAirborne</a> <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a>

sport of sacred spherical cowsHave a short list of refactorings and improvements still want to make to variants chart and <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> libraries in support of same...After which, will be able to move on to rebuilding legacy hospital capacity chart into a fuller suite of AnnoPlot mapping tools...With goal of using those tools to map out continental fire and smoke data...Assuming any such data is publicly available by the time am ready to embark on that project...All the while confident that, were we ever to get H5N1 pandemic data, the existing variants tooling would be ready for repurposing.

sport of sacred spherical cowsPut in an intensive week of work preparing <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> project variants chart for adequately representing the Nimbus strain, on the off chance that the CDC bothered to break same out in their data drop today.Only for <a href="https://hcommons.social/tags/CDC" class="mention hashtag" rel="nofollow noopener" target="_blank">#CDC</a> to punt on releasing any data this week, for reasons of an "issue with the software".K.<a href="https://hcommons.social/@beadsland/114639885219714547" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/114639885219714547</a>

sport of sacred spherical cowsAnother four hundred lines for <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> project since last round of work in March:<a href="https://hcommons.social/@beadsland/114475406737012154" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/114475406737012154</a>Work in May/early June included:• tweaks to this pie chart, chirp logging, annoplot legend classes and newspaper columns orphan control; • tweaks to variants <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a>: tree constructor process, alt-text pruning internals, legend subclass, tree constructor methods, name collisions and recombinant lineage assignments, family groupings and legend headers, variant mocking, title overhang, tile embossing, growth calculation, and captions, all including significant refactoring;• migration of bug to legend footer, and build out of prioritized legend footnotes for prominent lineages and recombinants, including recombinant chains, with calculation and approximation of historical peaks, and pruning for space constraints of both alt-text and footer proper.

sport of sacred spherical cowsAnother hundred lines for <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> project in March:<a href="https://hcommons.social/@beadsland/113977456216970296" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/113977456216970296</a>Work in March included:• accommodating less frequent updates to GISAID data • debug flattening in preparation for tilt • mixin for checking orientation and helper class for rotation and mirroring • rework and refactor tilt calculations for inline bubble charts • refactor degrees str method to helper class and consolidate older asdegrees util method

sport of sacred spherical cowsHoliday programming ticked over another hundred lines for <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> project since last update:<a href="https://hcommons.social/@beadsland/113842033121034976" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/113842033121034976</a>Variants was last <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> being updated. May be the end.Work in last month includes:• auto-generated alt-text for variants chart • rework of markdown utility module • runtime-option aware captions • prelim devpie alt-text generation • tweaks to variant bundling, cluster ancestry & recombinant assignment; also emboss hemming, GISAID import, and footnote plumbing.

sport of sacred spherical cowsGave myself some programming time as a holiday treat. Added ~300 lines to <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> project since last update:<a href="https://hcommons.social/@beadsland/113711696418854256" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/113711696418854256</a>In our post-data era, only variants <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> is still actively being updated.Work in last month includes:• tweaks to variant bundling, family grouping, cluster ancestry & recombinant assignment • footnote on legend • auto-generated alt-text for variants chart • rework of markdown utility module • tweaks to GISAID imports, bubbles & tile embossing

sport of sacred spherical cowsHave been only debug maintenance mode since our last update. No appreciable increase in <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> line count:<a href="https://hcommons.social/@beadsland/113586957042066086" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/113586957042066086</a>In our post-data era, only variants <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> is still actively being updated.Maintenance includes: further refining GISAID data imports, correct assignment of cluster lineages, including recombinant children of cluster variants, and conforming to upgraded python version.Unfortunately, ongoing fires in personal life means little time for <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> programming.

sport of sacred spherical cowsHave been only debug maintenance mode since our last update. No appreciable increase in <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> line count:<a href="https://hcommons.social/@beadsland/113456689508810628" rel="nofollow noopener" translate="no" target="_blank">https://hcommons.social/@beadsland/113456689508810628</a>In our post-data era, only variants <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> is still actively being updated.Maintenance includes: managing GISAID data imports, further refining legend criteria, revisions & corrections to naming tables, & properly pinning subvariants of clusters to progenitor lineages.Unfortunately, ongoing fires in personal life means little time for <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> programming.

sport of sacred spherical cowsOnce again, have only had opportunity to add hundred or so lines to <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> project since the last update:<a href="https://hcommons.social/@beadsland/113218241027273518" rel="nofollow noopener" target="_blank">https://hcommons.social/@beadsland/113218241027273518</a>In our post-data era, only variants <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> is still actively being updated.Maintenance includes: cosmetic tweaks to bubbles and embossing; tweaks to label order, bundle logic, and legend families; debugging cluster and recombinants parent tracing; & general refactoring.Unfortunately, ongoing fires in personal life means little time for <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> programming.

sport of sacred spherical cowsHave only had opportunity to add hundred or so lines to the <a href="https://hcommons.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> project since the last update:<a href="https://disabled.social/@beadsland/112897038827615226" rel="nofollow noopener" target="_blank">https://disabled.social/@beadsland/112897038827615226</a>Most of that was experimentation with pyrlang under bots/. (First step in developing language paradigm for a propinquity-based social media platform.)Other work incl debugging egregious cosmetic issues with bubble chart layout, tile embossing & legend labels in variants <a href="https://hcommons.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a>.Unfortunately, ongoing fires in personal life means little time for <a href="https://hcommons.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> programming.

"You do you" is Eu-gen-ics.K.That's ten hours straight of my working on nothing but <a href="https://disabled.social/tags/covid" class="mention hashtag" rel="nofollow noopener" target="_blank">#covid</a> variants <a href="https://disabled.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a>:<a href="https://disabled.social/@beadsland/112895801182229552" rel="nofollow noopener" translate="no" target="_blank">https://disabled.social/@beadsland/112895801182229552</a>…and dispelling tendentious unfounded conjectures linking traffic fatalities to <a href="https://disabled.social/tags/LongCovid" class="mention hashtag" rel="nofollow noopener" target="_blank">#LongCovid</a>:<a href="https://disabled.social/@beadsland/112896102358517759" rel="nofollow noopener" translate="no" target="_blank">https://disabled.social/@beadsland/112896102358517759</a>Admittedly, more than half of that consisted of somewhat sleep-deprived debugging how <a href="https://disabled.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> variants <a href="https://disabled.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a> assigns colors and assembles its legend.Nonetheless, might be time to eat something and prepare for sleep. Today's household chores will wait for tomorrow.

"You do you" is Eu-gen-ics.Only few dozen lines added to variants <a href="https://disabled.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> "rajdash" submodule—as <a href="https://disabled.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> dev stalled this week attending to family health emergency.That and a surprise household issue will consume available spoons next week.Final refinements of rajdash bolt-on to variants <a href="https://disabled.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a>, and thereafter HHS capacity replacement & CDC flu tracking dataviz, will hopefully see movement in June, followed by long overdue North American fire/smoke/AQI composite map, and longer overdue NHTSA & CDCWonder analyses.

"You do you" is Eu-gen-ics.Another ~200 lines added to <a href="https://disabled.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> & associated <a href="https://disabled.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> dev over the past week.Refinements of variants composite orchard-chart-and-packed-bubbles <a href="https://disabled.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a>, including HHS regional map replacement, will continue next week.After which, will explore ways to better present CDC's paltry flu tracking data, before figuring out how to adapt hospital capacity charts to new regime of CDC data withholding.Also, at some point, want to find time to create unified North America fire, smoke & AQI map.

"You do you" is Eu-gen-ics.After a several months hiatus from <a href="https://disabled.social/tags/AnnoPlot" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnnoPlot</a> and associated <a href="https://disabled.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataviz</a> dev, rolled out new variants chart features past two weeks.Chart now reconciles CDC's Nowcast estimates against NYITCOM summary of GISAID data, providing packed bubble charts within larger tiles for recent fortnight of Raj's chart. Also, caption now supports newspaper columns.Planning a few refinements to variants <a href="https://disabled.social/tags/datavis" class="mention hashtag" rel="nofollow noopener" target="_blank">#datavis</a>, before figuring out how best to adapt hospital capacity charts to new regime of CDC data withholding.

"You do you" is Eu-gen-ics.covid variants trends USpol

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