| Date | Topic | Details |
|---|---|---|
2023-07-27 |
TBD | |
2023-07-20 |
Debugging in R | see also HackMD, linked in links.md |
2023-07-13 |
Optimising predictive models to prioritise viral discovery in zoonotic resevoirs | |
2023-07-06 |
COVID-19 data analysis using Bayesian models and nonparametric geostatistical models | JF may lead |
2023-06-15 |
Multiple models for outbreak decision support in the face of uncertainty | SW may lead |
2023-06-08 |
Caroline Mburu talk | in the public Zoom |
2023-06-01 |
How should lab meetings be organized? |
- People like the idea of doing more software workshops, not necessarily every week, perhaps following up on last summer's workshops.
- MR suggested that people should "sign up" for a week and organize, without necessarily leading, a topic for that week.
- MJ will help JD reorganize the lab repo.
- DE dropped remarks about Faculty Opinions (formerly Faculty of 1000)
in
misc/FacultyOpinions.md.
- News article: https://evidenceandpolicyblog.co.uk/2023/04/12/when-should-scientists-rock-the-boat-advising-government-in-a-pandemic/ .
- Original paper: Atkinson, Paul, Hayley Mableson, Sally Sheard, Anne-Marie Martindale, Tom Solomon, Aleksandra Borek, and Caitlin Pilbeam. 2022. “How Did UK Policymaking in the COVID-19 Response Use Science? Evidence from Scientific Advisers.” Evidence & Policy 18 (4): 633–50. https://ora.ox.ac.uk/objects/uuid:a7244d17-bade-46d3-ab16-21352025e74c/files/rvm40xs076
macpan 2 practice talk; Emma Coates meets lab
Mellor, Jonathon, Rachel Christie, Christopher E. Overton, Robert S. Paton, Rhianna Leslie, Maria Tang, Sarah Deeny, and Thomas Ward. 2023. “Forecasting Influenza Hospital Admissions within English Sub-Regions Using Hierarchical Generalised Additive Models.” arXiv. https://doi.org/10.48550/arXiv.2302.11904.
Some thing (things) from this list: Chen et al. is a recent review of use of FDEs in epidemic models, but really doesn't say much at all about interpretation. Podlubny is weird; maybe interesting but not, I think, useful. My guess is that Du et al. might be the best choice.
- Chen, Yuli, Fawang Liu, Qiang Yu, and Tianzeng Li. “Review of Fractional Epidemic Models.” Applied Mathematical Modelling 97 (September 2021): 281–307. https://doi.org/10.1016/j.apm.2021.03.044 .
- Du, Maolin, Zaihua Wang, and Haiyan Hu. “Measuring Memory with the Order of Fractional Derivative.” Scientific Reports 3, no. 1 (December 5, 2013): 3431. https://doi.org/10.1038/srep03431 .
- Podlubny, Igor. “Geometric and Physical Interpretation of Fractional Integration and Fractional Differentiation.” arXiv, October 22, 2001. http://arxiv.org/abs/math/0110241 .
This also looks useful as a very basic intro/start to getting some intuition:
- Panda the Red. 2019. “What Is Fractional Calculus?” Medium. October 7, 2019. https://www.cantorsparadise.com/fractional-calculus-48192f4e9c9f.
Various guides to Random Forests (that might all say similar things):
- Chapter 8 of Introduction to Statistical Learning
- Understanding Random Forests
- Random Forest with simple vacation destination example
- Random Forests for Complete Beginners
- An Introduction to Random Forest Algorithm for beginners
- Breiman 2001. “Statistical Modeling: The Two Cultures.” Statistical Science 16 (3): 199–215.
Feel free to optionally also look at one of:
- McCormick 2021 "The "given Data" Paradigm Undermines Both Cultures"
- Miller 2021 Breiman's Two Cultures: {{You}} Don't Have to Choose Sides
- Gelman 2021 Reflections on Breiman's Two Cultures of Statistical Modeling
- Raper 2020 Leo Breiman's "Two Cultures"
- Levin 1992, The Problem of Pattern and Scale in Ecology
- Meetings and papers
- Zulip
- Ridge Regularization: An Essential Concept in Data Science
Short reports and informal discussion
- Reading the paper Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 (Particularly interested in the materials and methods section- Agronah).
Accounting for uncertainty during a pandemic, Zelner et al.
Ackley et al. "Compartmental Model Diagrams as Causal Representations in Relation to DAGs"
Agenda item: technical workshops this spring or summer?
D’Agostino McGowan, Lucy, Kyra H. Grantz, and Eleanor Murray. Quantifying Uncertainty in Mechanistic Models of Infectious Disease.. American Journal of Epidemiology 190, no. 7 (July 1, 2021): 1377–85.
David J. Hand. Measuring classifier performance: a coherent alternative to the area under the ROC curve; hmeasure package on CRAN; web page on the H-measure
- Bicko presentation
David J. Hand. Measuring classifier performance: a coherent alternative to the area under the ROC curve; hmeasure package on CRAN; web page on the H-measure
- Simulation considerations (see notes here, comments/edits welcome)
- Excess deaths analysis by The Economist
Ben Bolker will present and lead a discussion about reproducible workflow and collaboration tools. For background, please review this document; I will be working on an updated version of the brain dump here.
- Short reports
- Discussion about COVID and academic policies
- Steve Walker will go through his presentation on refactoring McMasterPandemic
informal meeting
Volz, Erik M, Sergei L Kosakovsky Pond, Melissa J Ward, Andrew J Leigh Brown, and Simon D W Frost. “Phylodynamics of Infectious Disease Epidemics.” Genetics 183, no. 4 (December 1, 2009): 1421–30. https://doi.org/10.1534/genetics.109.106021.
Discussion of web site generation and backups
- https://docs.google.com/document/d/1uXw_sY26PIbBiF5GDmRmFAltPGaM9XlxAIovBaJtP9k/edit?usp=sharing
- https://github.com/bbolker/website/
- https://ms.mcmaster.ca/~bolker/
Tanaka, Y. “Extinction of Populations by Inbreeding Depression under Stochastic Environments.” Population Ecology 42, no. 1 (2000): 55–62. https://doi.org/10.1007/s101440050009.
Presentation on citation and web machinery
- The recording is password protected for some reason; you may have it in your email under data-driven CV
Tredennick, Hooker, Ellner, Adler. A practical guide to selecting models for exploration, inference, and prediction in ecology
Short reports
More about model calibration; we can use this paper as a point of departure
Reading week---no meetings or coffee
We'll discuss Markov chain Monte Carlo; read the reference below to get started
Ravenzwaaij, Don van, Pete Cassey, and Scott D. Brown. “A Simple Introduction to Markov Chain Monte–Carlo Sampling.” Psychonomic Bulletin & Review 25, no. 1 (February 1, 2018): 143–54. https://doi.org/10.3758/s13423-016-1015-8.
(This isn't perfect, but is a good start.)
Also see section 7.3 here (also not perfect!)
Visualizations:
See also BMB notes: markdown, bibtex, html
Vianey Leos Barajas: physical coffee at 2:30.
Physics of spread:
Informal and planning
Heather Krause - Equity in Data video
SARS-CoV-2 viral load in nasopharyngeal swabs is not an independent predictor of unfavorable outcome Scientific Reports volume 11:12931 (2021). This is an interesting study of COVID outcomes, but we will also talk about statistical practice:
- What does the titular claim "not an independent predictor" mean?
- Is it statistically justifiable?
- What are the goals for this study?
Wymant, Chris, Luca Ferretti, Daphne Tsallis, Marcos Charalambides, Lucie Abeler-Dörner, David Bonsall, Robert Hinch, et al. “The Epidemiological Impact of the NHS COVID-19 App.” Nature 594, no. 7863 (June 2021): 408–12. https://doi.org/10.1038/s41586-021-03606-z .
- short report from Maya about her agent-based version of the MacPan model
- practice talk for the CAIMS annual meeting by Irena
Reading: Grange, Zoë L., Tracey Goldstein, Christine K. Johnson, Simon Anthony, Kirsten Gilardi, Peter Daszak, Kevin J. Olival, et al. “Ranking the Risk of Animal-to-Human Spillover for Newly Discovered Viruses.” Proceedings of the National Academy of Sciences 118, no. 15 (April 13, 2021).
Discussion of Rogers et al. 2021: "High-frequency screening combined with diagnostic testing for control of SARS-CoV-2 in high-density settings: an economic evaluation of resources allocation for public health benefit" - led by Irena
Discussion of modelling papers being reviewed for NCCMT
Schielzeth, Holger. “Simple Means to Improve the Interpretability of Regression Coefficients: Interpretation of Regression Coefficients.” Methods in Ecology and Evolution 1, no. 2 (February 10, 2010): 103–13. https://doi.org/10.1111/j.2041-210X.2010.00012.x.
We will be discussing packages/tools for stochastic simulation. Please take a look at this paper: feel free to skip sections 3.2, 3.3, 6.2 unless you're feeling very energetic.
Allen, Linda J. S. “A Primer on Stochastic Epidemic Models: Formulation, Numerical Simulation, and Analysis.” Infectious Disease Modelling 2, no. 2 (May 1, 2017): 128–42. https://doi.org/10.1016/j.idm.2017.03.001.
R packages/resources:
- adaptivetau, GillespieSSA2 (continuous-time, discrete-state)
- odin (mostly ODEs, but capability for discrete-time, discrete- or continuous-state)
- Differential Equations task view (includes a section on stochastic diff eqs)
- [IA]BMs: simecol, SpaDES (spatial), RNetLogo, ibm (simple IBMs in Rcpp); blog post on IBMs from scratch
Presentation by Daniel Park about inferring pathogen interactions.
Ideas for potential McMaster return-to-campus survey
Carlson, Colin J., Sarah N. Bevins, and Boris V. Schmid. “Plague Risk in the Western United States over Seven Decades of Environmental Change.” BioRxiv, February 27, 2021, 2021.02.26.433096.
Dushoff, J. and Park, S. W. PRSB. Speed and strength of an epidemic intervention
The debate about vaccine priorities
- Popular article from SFU. See also preprint link at the bottom.
- Controversial peer-reviewed paper from PNAS
See if you can form an opinion about whether and why these two perspectives are in contradiction.
Practice talk by Zachary Levine.
Add info or slides if you like
- Oidtman et al (2021) "Trade-offs between individual and ensemble forecasts of an emerging infectious disease"
- Twitter summary
- Irena will lead:
- This looks like a really nice "lessons learned" paper about modeling an emergent infectious disease, and it's not COVID! The case study is actually Zika virus, which means there's more hindsight to learn from.
- The preprint is hot off the press (posted 1 March), but from Twitter, it sounds like it's already been reviewed. I wonder if the preprint was only posted recently because it's been accepted by a high tier journal...
Fox, Spencer J., Pratyush Potu, Michael Lachmann, Ravi Srinivasan, and Lauren Ancel Meyers. “The COVID-19 Herd Immunity Threshold Is Not Low: A Re-Analysis of European Data from Spring of 2020.” MedRxiv, December 3, 2020, 2020.12.01.20242289.
| Thing | Source |
|---|---|
| Reading | Ellner SP, Snyder RE, Adler PB, Hooker G. An expanded modern coexistence theory for empirical applications. Ecology Letters. 2018;22:3-18. Sections prior to "General Theory" on page 10 are recommended, and following any references to the supplement is probably a good idea. Further reading is at your leisure. |
| If short on time or motivation to read... | A recent talk by Ellner on an extension of the 2018 work to spatial models, prefaced by an overview of the paper. |
| Background on modern coexistence theory (MCT) | Chesson, P. Multispecies competition in variable environments. Theoretical Population Biology. 1994;45:227-276. Up to page 233. |
| Background on coexistence mechanisms | Chesson, P. Mechanisms of maintenance of species diversity. Annual Review of Ecology and Systematics. 2000;30:343-366. |
Norton et al. (2019). Marginal Effects—Quantifying the Effect of Changes in Risk Factors in Logistic Regression Models.
Muff et al. (2016). Marginal or conditional regression models for correlated non‐normal data?
- Martin
- Bolker
Vehtari et al (2020). Bayesian Analysis. "Rank-Normalization, Folding, and Localization: An Improved Rhat for Assessing Convergence of MCMC"
Juul et al (2020). Nature Physics. "Fixed-time descriptive statistics underestimate extremes of epidemic curve ensembles"
Zulip and other topics
McCarthy et al. (Jianhong Wu group): Quantifying the shift in social contact patterns in response to non-pharmaceutical interventions
- Elsevier link (requires free account)
- wuContact.pdf in our private Dropbox folder, email JD
- Supp now added to folder
- Fields talk on 17 Nov 2020
Main reading: Sections 7.1, 7.2 and 7.4 of Ben's EMD book in our private Dropbox folder, email JD
Short reports and agenda items (including Cygu-led discussion of pcox)
- Snyder and Ellner 2018 Pluck or Luck: Does Trait Variation or Chance Drive Variation in Lifetime Reproductive Success? Am Nat
Please read one of the following papers:
- Brett and Rohani: "Transmission dynamics reveal the impracticality of COVID-19 herd immunity strategies" https://www.pnas.org/content/early/2020/09/21/2008087117
- Rice, Wynne, Martin, and Ackland. “Effect of School Closures on Mortality from Coronavirus Disease 2019: Old and New Predictions.” BMJ 371 (October 7, 2020). https://doi.org/10.1136/bmj.m3588.
These are approximately "pro-lockdown" and "anti-lockdown" stances.
-
Short reports:
- Matthew; Fady; Ben
Seasonality of Covid transmission
Main reading: Misconceptions about weather and seasonality must not misguide COVID-19 response. Carlson et al. _Nature Communications)
Additional readings (medRxiv): Neher et al.; Huang et al.
- Queenie
- Zach
- Friday at 13:30 on zoom (you will need a link or password from your email to join)
Short reports from Mikael and Geetha
Informal meeting.
- Cambridge University logo info: https://www.cl.cam.ac.uk/local/typography/#identifier (you could write to
Richard.Clayton@cl.cam.ac.ukif you really want the short, hand-crafted version)
- Replication of Hastings and Powell 1991, "Chaos in a three-species food chain" (implemented in Julia)
Autoregressive methods
- Main reading: to lag or not to lag
- Count response lecture notes
- Modeling multivariate binary time series
- Hierarchical logit function from MCMCpack
Informal meeting; any notes?
Bedford et al "Fitting stochastic epidemic models to gene genealogies using linear noise approximation"
- Park: Practical tools for phylodynamics. LNA to save time cf. filters.
- Dushoff: I like the term "gene genealogies"
Main reading
- Meng, Xiao-Li. “Statistical Paradises and Paradoxes in Big Data (I): Law of Large Populations, Big Data Paradox, and the 2016 US Presidential Election.” Annals of Applied Statistics 12, no. 2 (June 2018): 685–726. (apparently inaccessible even via Mac!), Direct pdf link
Follow up
- An interesting twitter thread that is apparently about our main reading from the heterogeneity meeting
Agenda item
- short-report schedule
Heesterbeek et al 2015 "Modeling infectious disease dynamics in the complex landscape of global health" Science, 347(6227) (Main reading)
Testing and fatality rates
- Primary reading: Grewelle and DeLeo IFR
- Campbell, deValpine et al: estimating IFR in the presence of testing bias
MacPan shiny
- To play in advance, try
run_shiny(TRUE)to open it in a browser, orrun_shiny(FALSE)to run in an RStudio window.
Presentation from Ash
- more reports
Reports??
- Send me email!!
TMB (Template model builder)
-
Reading: Friston dark matter
-
Agenda item: epigrowthfit project
This topic was triggered by this twitter thread (scroll up for main thread). There are at least three interesting-looking pubs cited here (Gomes, Britton, Bansal). Gomes is the main reading for this week, so spend some time on that and move on to the others if you have time and interes.
Please also add notes or resources about this topic!
We will talk about adjusting for reporting delays when analyzing epidemics.
Please read:
Please also add notes or resources about this topic!
Impact of climate and public health interventions … Jüni, al. Fisman, al. CMAJ
2020 27 March. Elizabeth O'Meara, thesis discussion
2020 13 March. Kucharski et al (2020) "Early dynamics of transmission and control of COVID-19: a mathematical modelling study"
Mizumoto and Chowell (2020) "Transmission potential of the novel coronavirus (COVID-19) onboard the diamond Princess Cruises ship"
Whitty 2015 What makes an academic paper useful for health policy?
- Bolker: relevant to our nCoV work etc. ...
- More on Bacon's "idols of the cave" here and here and (if you can read Latin) here
- Informal planning meeting
Morrisey et al "Multiple Regression Is Not Multiple Regressions: The Meaning of Multiple Regression and the Non-Problem of Collinearity"
- Dushoff: simple, good for stats foundations
Kim, Dong Wook, et al "Deep learning-based survival prediction of oral cancer patients"
- Cygu: Compared two ML methods to regular Cox. This paper could be useful to Steve's project.
- Read a paper, and come prepared to talk (efficiently) about why it would or would not be good for the group to read or discuss
- Measles and the canonical path to elimination (Graham et al., Science)
- O'Meara and/or Earn
- Stewart et al (2019) "Information gerrymandering and undemocratic decisions" Nature 573, 117–121
- Bolker
- Long Introductions
- Planning topics
5 Jul A discussion with Chai Molina about “public bads” – including greenhouse emissions and hospital infections
-
A big gap for some reason
-
12 Apr: Read paper on seasonal influenza forecasting challenge in the US. This is a good overview of what the community of epidemic modelling does and how forecasts are compared. Reich et al. (2019): "A collaborative multiyear, multimodel assessment of seasonal influenza forecasting in the United States". Link to paper in PNAS.
-
29 Mar: Very long reports from Ben and Jordan
-
15 Mar:
- recent Gelman blog post saying power analysis: https://statmodeling.stat.columbia.edu/2019/03/04/yes-design-analysis-no-power-no-sample-size-calculations/
- Gelman, Andrew, and John Carlin. “Beyond Power Calculations Assessing Type S (Sign) and Type M (Magnitude) Errors.” Perspectives on Psychological Science 9, no. 6 (November 1, 2014): 641–51. https://doi.org/10.1177/1745691614551642
- BMB brain dump/opinions
-
1 Mar RR: Earn and Li
-
22 READING week
-
15 Feb Paper (email ballot)
-
8 Feb Ridiculous reports: Dushoff, Champredon
-
1 Feb: Doebeli et al (2017) Towards a mechanistic foundation of evolutionary theory
- Kain
-
25 January Steve C. to give a presentation about neural nets (25 January)
-
17 January. Planning
-
11 January. Informal
-
Thu 6 Dec: Forum: Living dangerously with big fancy models (see Forum section) a discussion of Heisey et al. Linking process to pattern: …
-
Readings:
- Intro (short)
- Waller: Bridging gaps between statistical and mathematical modeling in ecology
- One other piece of your choosing from the Forum section
-
Thu 29 Nov: Cheng et al. 2018 on arxiv, Polynomial Regression as an Alternative to Neural Nets
- Szamosi
-
Thu 22 Nov: Daniel practice talk
-
Thu 15 Nov: Short reports.
-
Thu 8 Nov: Somers 2018, The Scientific Paper is Obsolete (The Atlantic)
- Paul Romero on Mma vs Jupyter
- Joel Grus doesn't like notebooks: see here, here, ...
-
Thu 1 Nov: Informal
-
Thu 25 Oct: Morgan Kain practice talk
-
Thu 18 Oct: Hefley et al, Ecology, The basis function approach for modeling autocorrelation in ecological data
-
???
-
26 Sep: Ellner 2018 Generation Time in Structured Populations
- Dushoff-led discussion
-
19 September: "Transient phenomena in ecology" Hastings et al 2018, Science Vol. 361, Issue 6406, eaat6412 (Review)
- Earn-led discussion
-
11 September: informal meeting
-
Mon 27 Aug Statistical Modeling: The Two Cultures, Leo Breiman
-
Mon 20 Aug: Dormann et al 2018 Model averaging in ecology: a review of Bayesian, information‐theoretic, and tactical approaches for predictive inference
-
Mon 23 July:
- Morgan has two agenda item: General paper identity crisis + weights in a spatio-temporal GAM (weighting by citizen effort in measuring bird communities)
-
Mon 16 July: Informal meeting
- DJDE will bring >3 matched juggling balls
- BMB will be away, so please pick something boring to read
-
Tues 10 July: Informal meeting
-
date?: Adler et al. 2018 Weak interspecific interactions in a sagebrush steppe? Conflicting evidence from observations and experiments
- Park
-
Mon 11 Jun: Informal meeting
-
Mon 18 Jun: Sah et al 2018 Optimizing the impact of low-efficacy influenza vaccines PNAS (early online edition)
- Dushoff
-
Mon 4 Jun: Informal meeting
-
Mon 28 May: No meeting
-
Wed 23 May: Simonsen et al 2016 Infectious disease surveillance in the big data era: Towards faster and locally relevant systems Journal of Infectious Diseases (2016) 214 S380-S385
-
Wed 16 May: Are Age-Structured Models Appropriate for Catch-Effort Data? Ludwig and Walters 1985
-
Wed 2 May: Ludwig, Hilborn, and Walters, Uncertainty, Resource Exploitation, and Conservation: Lessons from History, Science (Vol. 260, No. 5104, Apr. 2, 1993)
-
16 April: Visitor Mark Lewis
-
7 Jul: Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo
-
May 26 (?) A report from Morgan on his daphnia experiment
-
May 5
-
CRISPR/phage predator/prey dynamics. Nice modeling exercise, but didn't seem relevant to our interests.
-
Frog crystals
-
-
28 April Ethics stuff related to JD current work, new from Lipsitch: Vaccine testing for emerging infections (JME online first)
-
21 April Leggett virulence
-
11 Apr spatially explicit capture-recapture analysis: Borchers et al 2014 J Am Stat Assoc ("As it involves a distance-based detection function, SECR (spatially explicit capture-recapture) is closer to DS (distance sampling) than [it] is [to] traditional CR (capture-recapture) ...")
- Other (less useful I think) readings:
- Stevenson et al 2014 Meth Ecol Evol "A general framework for animal density estimation from acoustic detections across a fixed microphone array"
- Earlier paper (not dealing with time-of-arrival etc.) Efford et al 2009 Ecology "Population density estimated from locations of individuals on a passive detector array"
- Borchers and Fewster 2016 Statistical Science "Spatial Capture–Recapture Models"
- Other (less useful I think) readings:
-
4 Apr Antonovics review from the PTRSB Theme issue on ecology and evolution of parasite transmission
-
Mar 28: problems with detection of causality by cross-convergent mapping ("does influenza cause humidity?"): Baskerville and Cobey PNAS
- Read related articles (Sugihara's and theirs in PLoS ONE) if you have time
-
Mar 14: Two papers (split your time between them as you like):
-
Mar 7: Scale-dependent parameter estimation
- Cornulier ISEC presentation
- A possible background paper – BB says don't get bogged down in it.
- A weird contribution by al. et JD: is it OK to snoop if you don't find anything?
-
Feb 28: Read from the GUSTA ME website for 45 minutes, focusing on:
-
Dissimilarity based methods
-
constrained analyses
-
indirect gradient analysis
-
Some other resources:
- Learn the basics of PCoA. Can anyone suggest a reading?
- This isn't a full solution: it doesn't help with the inference/why we would do one or the other, but it does explain the geometry pretty nicely ... PCA and PCoA explained, from Bob Carpenter
- Mike suggests we cover all the variants: (PCA, PCoA, CPC (common principal components), Factor analysis, CVA (canonical variate analysis), Non-negative matrix factorization) (the CANOCO web page lists: DCA, CA, CCA, DCCA, PCA, and RDA ...)
- There's also NMDS, which is very popular among microbiome people. (JCSz) That link says something I don't understand about NMDS:
- "NMDS requires a distance matrix, or a matrix of dissimilarities. Raw Euclidean distances are not ideal for this purpose: they’re sensitive to total abundances, so may treat sites with a similar number of species as more similar, even though the identities of the species are different." This shouldn't be true, should it? If each species gets its own axis...
- Learn the basics of PCoA. Can anyone suggest a reading?
-
BB proposed inviting Steve Walker to talk to us if he has time.
-
-
Jan 9: How to construct R-packages BB's slides
-
- from Katriona Shea's lab: "Results illustrate how control actions change across both the base metric used to measure management success and across the statistic used to rank control actions according to said metric. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making."
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All Hallows' Eve Retention of Adult Patients on Antiretroviral Therapy in Low- and Middle-Income Countries: Systematic Review and Meta-analysis 2008-2013
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Oct 24: Callahan et al. (2016): DADA2: High-resolution sample inference from Illumina amplicon data
- JCSz: stuff with McMurdie's name on it can sometimes be sloppy, so I'm interested in people's opinions on this method.
- So what did you-all think of this one anyway?
-
Oct 17: Wilson et al (2016 arxiv): Good Enough Practices in Scientific Computing
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Sep 26: Delva et al (2016): Connecting the dots: network data and models in HIV epidemiology.
-
- for what it's worth these methods are available in an R package ...
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Sep 15: Skyline plots
- Pybus et al Genetics 155: 1429–1437 (Original paper, July 2000)
- Drummond et al 2005doi:10.1093/molbev/msi103 (Cool Bayesian stuff)