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Intro

Hi all, I'm working with hospital-based surveillance data. My peers and I are trained (loosely speaking) as frequentists. I'm mindful of the aphorism:

Statistics: A subject which most statisticians find difficult but which many physicians are experts on.

... and want to improve through practice.

Example

Here's a good example.

hospitalizations <- structure(list(timespan = structure(1:4, .Label = c("2002-2004", 
"2005-2007", "2008-2010", "2011-2013"), class = c("ordered", 
"factor")), c(65, 66, 52, 44), c(4417, 4361, 
4458, 4560)), class = "data.frame", row.names = c(NA, -4L), .Names = c("timespan", 
"count", "pop"))

Trend or No Trend?

In this particular case, I've been advised to rely on stats::prop.trend.test(), which exploits the sequencing of the observations, in preference to prop.test().

Less power: prop.test()

> with(hospitalizations, prop.test(count, pop))

    4-sample test for equality of proportions without continuity correction

data:  count out of pop
X-squared = 7.2, df = 3, p-value = 0.07
alternative hypothesis: two.sided
sample estimates:
  prop 1   prop 2   prop 3   prop 4 
0.014716 0.015134 0.011664 0.009649 

More power: prop.trend.test()

help(prop.trend.test) says:

Performs chi-squared test for trend in proportions, i.e., a test asymptotically optimal for local alternatives where the log odds vary in proportion with score. By default, score is chosen as the group numbers.

> with(hospitalizations, prop.trend.test(count, pop))

    Chi-squared Test for Trend in Proportions

data:  count out of pop ,
 using scores: 1 2 3 4
X-squared = 6.2, df = 1, p-value = 0.01

Doing it Differently

How should I start learning about ways to tackle this question, and related ones, using a different, complementary approach? I'm particularly interested in using this as a jumping-off point into simple Bayesian / MLE techniques.

  • For example, suppose I'm willing to start with a prior based on the first two observations, and then update my belief/model according to the next two. How would I implement that in R? Any recommendations for libraries, whitepapers, chapters, books, articles, posts, etc.? (Stan sounds fun.)

  • Or, suppose I want to generate a maximum-likelihood estimate of a slope and intercept. I don't know where to start. (I'm an R user, and like to learn from code-based examples.)

I recognize that this is a wide-open question, and you have other jobs to do. Please allow me to thank you in advance for your time and attention. Comments on this specific example (prop.trend.test() vs prop.test()) are also very welcome.

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