Dates

[annecori]

proposed changes to allow a Date column to be specified in I, which is then used for plotting
--> addresses issue #12

also, added errors when the estimation is performed to early or too late
--> addresses issue #15 and #19

finally, also allowed EstimateR and WT to take incidence objects (from class incidence from package incidence) as arguments
--> addresses issue #13

[jstockwin]

@annecori What am I doing wrong:

library(devtools)
install_github('annecori/EpiEstim', ref = "dates", force = TRUE)
library(EpiEstim)


I <- data.frame(c(0,1,2,2,3,3), c(1,0,0,0,0,0), as.Date(c("01-05-2017", "02-05-2017", "03-05-2017", "04-05-2017", "05-05-2017", "06-05-2017")))
colnames(I) <- c("local", "imported", "dates")

> str(I)
'data.frame':	6 obs. of  3 variables:
 $ local   : num  0 1 2 2 3 3
 $ imported: num  1 0 0 0 0 0
 $ dates   : Date, format: "0001-05-20" "0002-05-20" "0003-05-20" "0004-05-20" ...
> EstimateR(I, T.Start=1:5, T.End=2:6, method="ParametricSI")
Error in process_I(I) : I must contain only non negative integer values.

[jstockwin]

Okay so now it's working a bit better, but I'm still getting errors:

library(devtools)
install_github('annecori/EpiEstim', ref = "dates", force = TRUE)
library(EpiEstim)


I <- data.frame(c(0,1,2,2,3,3,4,3,4,5,2),
                c(1,0,0,0,0,0,0,0,0,0,0),
                as.Date(c("2017-05-01", "2017-05-02", "2017-05-03", "2017-05-04", "2017-05-05", "2017-05-06"
                          , "2017-05-07", "2017-05-08", "2017-05-09", "2017-05-10", "2017-05-11")))
colnames(I) <- c("local", "imported", "dates")

>EstimateR(I, T.Start=8:10, T.End=9:11, method="ParametricSI", Mean.SI=2, Std.SI=1, plot=TRUE)
Error: Invalid input: date_trans works with objects of class Date only
In addition: Warning message:
In EstimateR_func(I = I, T.Start = T.Start, T.End = T.End, method = method,  :
  You're estimating R too early in the epidemic to get the desired posterior CV.

[jstockwin]

I also get this sometimes:

Error in if (any(I < 0)) { : missing value where TRUE/FALSE needed
In addition: Warning message:
In Ops.factor(left, right) : ‘<’ not meaningful for factors

Perhaps you need to restrict the <0 check to only I$local and I$imported.

There seem to be a lot of code changes which are nothing to do with the dates, so it's quite hard to track down exactly what is going on, and I don't really have the time right now.

Hopefully those errors give you something to work on, though...

[annecori]

Thanks for your comments Jake, seems by creating weird dates you have indeed found a bug in some of my checking functions - I think I've fixed the issues related with your two first comments - for the third one if it still happens can you please provide some code?
thanks

[jstockwin]

@annecori The most recent snippet of code now runs properly. The others which didn't run now give a correct looking error.

I've not tested much outside what I've explicitly said about. In particular, nothing about the incidence objects, but it seems you've got an example of this so I assume you've checked that.

[jstockwin]

I've approved this but will leave it up to you to merge. If you want anything else tested let me know, but I'm pretty short on time.