add sample_posterior_R function

[zkamvar]

This will fix #70, but I've modified it so that it takes from a specific time window of R:

library("EpiEstim")
#> Registered S3 methods overwritten by 'ggplot2':
#>   method         from 
#>   [.quosures     rlang
#>   c.quosures     rlang
#>   print.quosures rlang
data("Flu2009")

res <- estimate_R(incid = Flu2009$incidence, 
                  method = "non_parametric_si",
                  config = make_config(list(si_distr = Flu2009$si_distr)))
#> Default config will estimate R on weekly sliding windows.
#>     To change this change the t_start and t_end arguments.

hist(sample_posterior_R(res, n = 5000, window = 1L), col = "grey",
     main = "5000 samples of R from the first weekly window",
     xlab = "R",
     xlim = c(0, 4))

hist(sample_posterior_R(res, n = 5000, window = 10L), col = "grey",
     main = "5000 samples of R from the tenth weekly window",
     xlab = "R",
     xlim = c(0, 4))

win_col <- ifelse(seq(nrow(res$R)) %in% c(1, 10), "red", "black")
plot(res, "R") + ggplot2::geom_point(color = win_col)

^{Created on 2019-06-06 by the reprex package (v0.3.0)}

[jstockwin]

From a code-style perspective this LGTM. This does not include a review of the mathematics of the actual function, though :)

Does EpiEstimApp require any changes from this?

[zkamvar]

Does EpiEstimApp require any changes from this?

No, the app shouldn't require any change from this. It is an extra feature.

[codecov-io]

Codecov Report

Merging #76 into master will increase coverage by 0.72%.
The diff coverage is 100%.

@@            Coverage Diff            @@
##           master     #76      +/-   ##
=========================================
+ Coverage   49.07%   49.8%   +0.72%     
=========================================
  Files          12      13       +1     
  Lines        1243    1251       +8     
=========================================
+ Hits          610     623      +13     
+ Misses        633     628       -5

Impacted Files	Coverage Δ
R/sample_posterior_R.R	100% <100%> (ø)
R/make_config.R	100% <0%> (+14.28%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 6d12c57...4519a8d. Read the comment docs.

[zkamvar]

@annecori, Can you take a look at this and see if it works for you?

[zkamvar]

bumping @annecori to see if this function makes sense to her.

[annecori]

looks great thanks @zkamvar, I've only added a small comment explaining the set.seed call in the example, hope that's ok