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Stack Overflow Developer Survey 2017
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3 days ago by msurbey
The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates | bioRxiv
Divergence time estimation --- the calibration of a phylogeny to geological time --- is a integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more. While the incompleteness of the fossil record is a common concern, issues of data limitation and model inadequacy are viable (if underexplored) alternative explanations. In this vein, Beaulieu et al. (2015) convincingly demonstrated how methods of divergence time inference can be misled by both (i) extreme state-dependent molecular substitution rate heterogeneity and (ii) biased sampling of representative major lineages. While these (essentially model-violation) results are robust (and probably common in empirical data sets), we note a further alternative: that the configuration of the statistical inference problem alone precluded the reconstruction of the paleontological timeframe for the crown age of angiosperms. We demonstrate, through sampling from the joint prior (formed by combining the tree (diversification) prior with the various calibration densities specified for fossil-calibrated nodes), that with no data present at all, an Early Cretaceous crown angiosperms is rejected (i.e., has essentially zero probability). More worrisome, however, is that for the 24 nodes calibrated by fossils, almost all have indistinguishable marginal prior and posterior age distributions, indicating an absence of relevant information in the data. Given that these calibrated nodes are strategically placed in disparate regions of the tree, they essentially anchor the tree scaffold, and so the posterior inference for the tree as a whole is largely determined by the pseudo-data present in the (often arbitrary) calibration densities. We recommend, as for any Bayesian analysis, that marginal prior and posterior distributions be carefully compared, especially for parameters of direct interest. Finally, we note that the results presented here do not refute the biological modelling concerns identified by Beaulieu et al. (2015). Both sets of issues remain apposite to the goals of accurate divergence time estimation, and only by considering them in tandem can we move forward more confidently.
cladistics  statistics  modeling  paleontology  inference  rather-interesting  modeling-is-not-mathematics 
3 days ago by Vaguery
Stack Overflow Developer Survey 2017
Get insights on the world’s developers from the largest and most comprehensive survey ever. Demographics. Technologies. Salaries. Career satisfaction.
2017  statistics  stackoverflow  salary 
3 days ago by dreikanter
iPad Optics | Asymco
If we look further we see that the iPad is still a much loved and much used product. Data from the Pew Internet Survey shows that tablet ownership among US adults increased from 45% in April 2015 to 48% in April 2016 and 51% in November 2016. The rise has been steady. Although this counts tablets, the iPad had 85% share of the U.S. market for tablets priced above $200 so it’s a fair assumption that the iPad audience is growing. Similar data exists for the UK.
tablets  iPad  penetration  sales  review  statistics  Asymco  2017 
3 days ago by inspiral
‘Bad luck’ with random DNA errors is responsible for two-thirds of cancer mutations, study says - LA Times
In research published Thursday in the journal Science, geneticist Bert Vogelstein and biostatistician Cristian Tomasetti demonstrate that most cancer risk stems not from bad genes, environmental toxins or poor lifestyle choices, but from simple random mutations.

Every time a normal cell divides, about three mutations occur. The body has ingenious DNA-repair mechanisms to limit the damage, and not all mutations occur in parts of the genome that are active. So sometimes our luck is good, Vogelstein said.
health  research  cancer  biology  statistics 
3 days ago by jefframnani
survminer 0.3.0 | R-bloggers
I’m very pleased to announce that survminer 0.3.0 is now available on CRAN. survminer makes it easy to create elegant and informative survival curves. It includes also functions for summarizing and inspecting graphically the Cox proportional hazards model assumptions.
R  statistics 
3 days ago by campion1581

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