Where alpha diversity focuses on community variation within acommunity (sample), beta diversity quantifies (dis-)similaritesbetween communities (samples). Some of the most popular beta diversitymeasures in microbiome research include Bray-Curtis index (forcompositional data), Jaccard index (for presence / absence data,ignoring abundance information), Aitchison distance (Euclideandistance for clr transformed abundances, aiming to avoid thecompositionality bias), and the Unifrac distances (that take intoaccount the phylogenetic tree information). Only some of the commonlyused beta diversity measures are actual distances; this is amathematically well-defined concept and many ecological beta diversitymeasures, such as Bray-Curtis index, are not proper distances.Therefore, the term dissimilarity or beta diversity is commonly used.
Alpha diversity, also sometimes interchangeably used with theterm species diversity, summarizes the distribution of speciesabundances in a given sample into a single number that depends onspecies richness and evenness. Diversity indices measure the overallcommunity heterogeneity. A number of ecological diversity measures areavailable. The Hill coefficient combines many standard indices into asingle equation that provides observed richness, inverse Simpson, andShannon diversity, and generalized diversity as special cases. Ingeneral, diversity increases together with increasing richness andevenness. Sometimes richness, phylogenetic diversity, evenness, dominance,and rarity are considered to be variants of alpha diversity.
Dominance indices are in general negatively correlated withdiversity, and sometimes used in ecological literature. Highdominance is obtained when one or few species have a high share ofthe total species abundance in the community.
Richness gives the number of features present within a community and can be calculated with estimateRichness. Each of the estimate diversity/richness/evenness/dominance functions adds the calculated measure(s) to the colData of the SummarizedExperiment under the given column name. Here, we calculate observed features as a measure of richness.
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Hohndel noted that Kernel Summit pictures tend to contain only white males, buthe thinks we are making some progress on making the kernel community morerepresentative of the world we live in; \"is it improving\", he asked.Torvalds said that he thinks it is improving, but that the Kernel Summit isthe \"worst possible example\" because it mostly represents those who havebeen involved for 10-15 years. In the early days, Linux was mostlydeveloped in western Europe and the US, which makes the diversity at thesummit rather low.
Beyond geographic diversity, the number of women in the open sourcesoftware world is low, though Torvalds is not clear on why that is. It isgetting better through efforts by companies like Intel and organizationslike the Linux Foundation to help women get more involved so that thecommunity won't be so \"one-sided\". He noted that there were few Japanesekernel developers when the first Japan Linux Symposiums started, but thathas now changed. Japan (and Asia in general) are much better representedthese days.
I personally think that the reason the single-hierarchy method works is that it is an analogue of the physical world, where an object has one definite location. We've spent our lives learning about a world where the knife is in the drawer, in the kitchen, on the ground floor, in the house at number 42, on Sycamore street... Cultural diversity Posted May 31, 2013 10:37 UTC (Fri) by NAR (guest, #1313) [Link]
I might be flamed to death, but I can't stop showing this group picture from a midwifery conference. Has anybody ever heard complaints about the lack of gender-diversity in that profession I mean even the name of the profession is blatantly sexist... Cultural diversity Posted May 31, 2013 11:16 UTC (Fri) by xanni (subscriber, #361) [Link]
Real or virtual, men write 99.99% of the kernel code, not (as we can see from the history so far) - women. To me, trying to change this artificially seems to be a waste of time. Let the nature run it's course, i'd say. Cultural diversity Posted May 31, 2013 13:24 UTC (Fri) by mpr22 (subscriber, #60784) [Link]
However, if you can't make that connection then I'd suggest you hold forth on the topic less, because you're remarkably poorly informed. Cultural diversity Posted Jun 2, 2013 16:25 UTC (Sun) by smitty_one_each (subscriber, #28989) [Link]
If you insist on a straw-manning a request for evidence in this manner, then I may not be the one in need of help.>However, if you can't make that connection then I'd suggest you hold forth on the topic less, because you're remarkably poorly informed.Strawman *and* a \"'Shut up!' he explained.\" Good times.k8to, this is but one data point, so I'll resist forming the opinion that you're one who argues in bad faith. Cultural diversity Posted Jun 3, 2013 0:55 UTC (Mon) by k8to (subscriber, #15413) [Link]
Even midwives! Go back several centuries and the job was the province of \"amateur\" women. As it became professionalised, it became almost totally male. Now it's back to almost totally women.It's a historical accident most kernel developers are men. And one only has to read of the experience of women in the field to learn that many women who would like to be kernel developers are driven out by blatant sexism. (Two kinds, imho. The MCPs who assume that \"women can't be any good\" or who simply assume that any woman can be treated as a sex object - the repeated complaints about sexual assaults bear that out. And the other guys who insist on treating women as if they were blokes. Common courtesy says you treat people as individuals, and you respect them for who and what they are, you don't try and force them into your idea of the \"ideal\".) That said, there's no reason why we couldn't attract more women - IF WE RESPECT THEM AS *PEOPLE* - and they could bring a lot to the development.Cheers,Wol Cultural diversity Posted May 31, 2013 15:51 UTC (Fri) by vonbrand (guest, #4458) [Link]
I personally don't care who made the patch/contribution so long it makes sense. Recently Sarah Sharp caught a bug in a driver i wrote long time ago. It was a bug alright and i fixed it as soon as i could. With the appropriate \"thank you\" note in the commit message. See, i didn't mention she's female.\"Twice the manpower\" is a good thing when you need to dig a trench. I kind of doubt it is so when it comes to software development, or any other highly specialized field. If somebody wants to see more females at the Linux conferences i'd suggest different approach, not making them kernel developers first. ;-) Cultural diversity Posted May 31, 2013 20:00 UTC (Fri) by hummassa (subscriber, #307) [Link]
They are deeply discouraged by patriarchalist thinking and discourse like yours.They are deeply discouraged when, at age three, boys are given miniature remote control cars and building sets as gifts and girls are given barbie dolls.They are deeply discouraged when they see that the popular girls in high school tend to \"feminine\" classes and activities.I could go on and on. You are refusing to see that yes, we should especially encourage girls with maths and hard sciences and computers and programming and kernel programming because they are not being encouraged enough. And you are hiding behind the \"girls are not as good at math as boys\" fallacious argument. Cultural diversity Posted May 31, 2013 20:07 UTC (Fri) by raven667 (guest, #5198) [Link]
Or the corollary Bugblatter Beast of Trall argument; if it doesn't obviously happen to me then I can't see it happens to someone else. Cultural diversity Posted May 31, 2013 20:45 UTC (Fri) by RobSeace (subscriber, #4435) [Link]
So, the solution involves a complete overhaul of all of society I genuinely wish you luck with that!But, I think the point was that the problem is not something that can really be solved by a bunch of male kernel developers... As cool as they may be, I don't think they have the power to dictate to parents all over the world to stop treating their daughters and sons differently, or order the popular girls in high school how to behave... The best they can realistically do is be accepting of any women who wish to contribute... And, of course they should do so! But, that's not really going to do anything to change how women have been socialized into thinking about what sorts of things they wish to do... They're not going to all suddenly say, \"Oh, the kernel developers are welcoming women, now Well, I'm going to take up C programming immediately!\"... They still have to deal with all of the rest of society pressuring them to behave like \"proper ladies\"...> And you are hiding behind the \"girls are not as good at math as boys\"> fallacious argument.I didn't get that impression at all from what he said... It was more like \"girls choose not to do math as much as boys for whatever reason\"... Cultural diversity Posted Jun 1, 2013 0:44 UTC (Sat) by hummassa (subscriber, #307) [Link]
Any solution to our social problems do... ;-)> I genuinely wish you luck with that!I seriously and genuinely appreciate it.> The best they can realistically do is be accepting of any women who wish to contribute... And, of course they should do so! But, that's not really going to do anything to change how women have been socialized into thinking about what sorts of things they wish to do...Ok, that last part is where my opinion diverge. If they are accepting, or better yet, encouraging, of women in the CSs, in some decades there will be enough female role models so youngsters can emulate. At the present time, a 13-yo boy has Gates, Jobs, Shuttleworth, Torvalds, Joy, Cerf, etc. to look up to, if he decides he likes computing and computers as a means of living. But who would a girl emulateTHAT is the way one generation has \"suffragettes\", the next has women voters, the following one has women candidates, and eventually you get a women head of government (like we have down here right now, and Germany, and Chile, and the UK had in the 80s, etc. etc.) Cultural diversity Posted Jun 1, 2013 13:03 UTC (Sat) by RobSeace (subscriber, #4435) [Link] 153554b96e