Submit to CRAN
zkamvar opened this issue · comments
This is a tracking issue for CRAN submission.
- spell check
- build with winbuilder
- fix errors on epitrix
- fix errors in projections
epitrix errors:
This appears to be a problem that can easily be fixed by updating the documentation.
> ## Ebola estimates of the SI distribution from the first 9 months of
> ## West-African Ebola oubtreak
>
> mu <- 15.3 # days
> sigma <- 9.3 # days
> param <- gamma_mucv2shapescale(mu, sigma / mu)
>
> if (require(distcrete)) {
+ w <- distcrete("gamma", interval = 1,
+ shape = param$shape,
+ scale = param$scale, w = 0)
+
+ r2R0(c(-1, -0.001, 0, 0.001, 1), w)
+
+
+ ## Use simulated Ebola outbreak and 'incidence' to get a log-linear
+ ## model of daily incidence.
+
+ if (require(outbreaks) && require(incidence)) {
+ i <- incidence(ebola_sim$linelist$date_of_onset)
+ plot(i)
+ f <- fit(i[1:100])
+ f
+ plot(i[1:150], fit = f)
+
+ R0 <- lm2R0_sample(f$lm, w) <======== FIX ME!!!!
+ hist(R0, col = "grey", border = "white", main = "Distribution of R0")
+ summary(R0)
+ }
+ }
Warning in fit(i[1:100]) :
22 dates with incidence of 0 ignored for fitting
Error: $ operator is invalid for atomic vectors
Execution halted
Projections errors
This appears to be a problem with the get_dates() method in incidence over-writing the get_dates() method from projections when incidence is loaded afterwards and is F R U S T R A T I N G
I've addressed the projections error in reconhub/projections#8 and the epitrix error in reconhub/epitrix#5