cultivating & crashing

an organic collection of notes, observations, and thoughts

First sighting of WinBUGS in the wild

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2984379/

Bayesian analysis in the NYTimes

The Odds, Continually Updated

I had read the story of the fisherman who was found, but had no idea Bayesian statistics was the hero.

Multiple imputation

Multiple imputation is my new favourite thing. I still need to figure out how Stata manages (pretends?) to do it, or if it’s just executing an approximation of the Bayesian process of iteratively drawing samples from distributions of alpha and the beta(s) in the model. To be continued.

Huir y enfrentar

Cuando sentís algo de lo cual querés huir, respirá. Y aceptalo. Sumergíte en la sensación, que te lo alivia. No te escondas, porque te termina trastornando.

Garlic, butter, mussels

I used this recipe (with different quantities) to put on linguine. My grandmother would hit me if she heard me, but I think it’s necessary to overcook linguine in order to properly roll them on your fork, as al dente they’re too stiff.

3 pounds fresh mussels, scrubbed and debearded
10 tablespoons (1 1/4 sticks) butter
3/4 cup finely chopped shallots
6 large garlic cloves, minced
4 tablespoons chopped fresh parsley
2 tablespoons fresh lemon juice
1 teaspoon grated lemon peel

Place mussels in heavy large Dutch oven, cover and cook over high heat until mussels open, shaking pan occasionally, about 5 minutes. Drain mussels, reserving liquid. Transfer mussels to bowl; discard any that do not open. Tent bowl with foil.

Melt butter in same Dutch oven over medium-high heat. Add shallots and garlic and sauté until tender, about 3 minutes. Add 3 tablespoons parsley, lemon juice, lemon peel and reserved liquid from mussels and bring to boil. Season to taste with pepper. Drizzle garlic butter over mussels. Sprinkle with 1 tablespoon parsley.

Ultimate procrastination tip

In order to stop procrastinating, do nothing. If you’re putting off something, stop everything and sit in your miserable unease. I think this works because doing nothing at all is close to some strange form of torture that few can tolerate (see: meditation), and actually sitting down to work on what you’re supposed to be working on becomes preferable.

I want a god

I want a god
as my accomplice
a god
who hurts
to the last
bone and
bites the air
in pain
a jobless god
a striking god
a hungry god
a fugitive god
an exiled god
an enraged god
a god
who longs
from jail
for a change
in the order
of things
I want a
more godlike
god

Francisco X. Alarcón

Compassion hurts

Compassion hurts. When you feel connected to everything, you also feel responsible for everything. And you cannot turn away. Your destiny is bound with the destinies of others. You must either learn to carry the Universe or be crushed by it. You must grow strong enough to love the world, yet empty enough to sit down at the same table with its worst horrors.

Andrew Boyd

Null hypothesis testing: methodus non grato

The journal Basic and Applied Social Psychology just announced that it will no longer publish p-values, test statistics, confidence intervals, or any other null hypothesis testing procedures. This is pretty extreme, and equally exciting. From the little that I understand, Bayesian analysis is slowly but surely gaining ground against frequentist analysis, and this is one more (rather large) step in that direction.

Read the article here.

How old is epidemiology?

Seminar by Alfredo Morabia

1. 17th century move toward centralized states, organization of Europe after 30 year war

2. Crisis of Western ideas
Francis Bacon
– biases
– tabulating data
– determinants of longevity including heredity, height and weight, age, diet, behaviour, exercise, housing, medical treatment

Descartes
– only trust “evidence”
– study one determinant at a time
– ignore interactions

Jan Baptista Van Helmont
– “Dawn or the New Rise of Medicine”
– iatrochemistry
– anti Galenist medicine: believed in diseases, separate from the individual, with external causes
– did not believe in blood letting (Van Helmont contest) “how many funerals each of us will have funerals” idea of fraction that will get better will be greater than your fraction that will get better was opposed to all mine will be cured and none of yours will

this is Renaissance thinking; will be implemented in the Enlightenment

3. Data!
Bills of Mortality (death certificates) in England

Bubonic plague – disruption of society and absolutist states
idea: plague has astrological cause or is transmitted by miasms

person would diagnose and count plague deaths, then publish them weekly
idea was to have a retreat outside of London when there was an outbreak
solution to the crisis every time there was an outbreak, based on weekly death counts, then add other causes of death, then births

4. Emergence of political arithmetic and capitalism
birth of epi is related to birth of capitalism

only merchants could deal with numbers, or intellectuals

William Petty “political arithmetic”

John Graunt: Natural and Politcal Observations made on Bills of Mortality (1662)

births and deaths = gains and losses. the same skills for tracking small margins of business was applied to deaths.

5. Royal Society of London (1661)
– centralized intellectual activity and skills
– “Nvllivs in Verba” no words or no speculation, only observation

Graunt is the convergence of these things
“The Table of Casualties” shows there is regularity of health phenomena
Was able to say that plague came from outside London, which was not the same for stable diseases
as a result, more quarantine enforced, and the plague stops affecting London

The Table of Casualties

Huygen’s adaptation of Graunt’s lifetable – median survival age
why asked this? how much should ask from people buying life insurance!

So how old is epidemiology? 1662 Graunt’s observation, our Big Bang. So 353 years in 2015!

Graunt_Observations

Marz. read the book, asks how to educate everyone in the world, as Morabia says we should. Need to promote “epidemiological literacy”. No one understands epi spontaneously; it requires learning to understand interpretation. That’s why epi should be taught in high school, and become part of general culture.
asks 16 year olds : what do you know about health?
marijuana does x. Can get STIs. HOW DO YOU KNOW?
Ah! That’s the question.

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