Hi Luigi,
I am not familiar with the R0 package but I took a quick look.
The example in the documentation sets begin and end to integers.
Try setting begin = 1, end = 121 and see if that works.
HTH,
Eric
On Fri, May 22, 2020 at 1:17 PM Luigi Marongiu <marongiu.lu...@gmail.com> wrote:
>
> Hello,
> I am trying ot get the R0 from the incidence data from China for the
> COVID-19. I set the following:
> ```
> library("R0")
> x1 <- c(259, 457, 688, 769, 1771, 1459, 1737, 1981, 2099, 2589,
> 2825, 3235, 3884, 3694, 3143,
> 3385, 2652, 2973, 2467, 2015, 14108, 5090, 2641, 2008,
> 2048, 1888, 1749, 391, 889, 823,
> 648, 214, 508, 406, 433, 327, 427, 573, 202, 125,
> 119, 139, 143, 99, 44,
> 40, 19, 24, 15, 8, 11, 20, 0, 16, 13,
> 13, 34, 39, 46, 39,
> 78, 47, 67, 55, 54, 45, 0, 79, 36, 35,
> 31, 19, 30, 39, 32,
> 0, 63, 42, 46, 99, 108, 89, 46, 46, 26,
> 325, 27, 16, 12, 11,
> 30, 10, 6, 12, 11, 3, 6, 22, 4, 12,
> 1, 3, 3, 1, 2,
> 2, 1, 1, 14, 17, 1, 7, 3, 4, 8,
> 6, 7)
> d1 = c("2020-01-23", "2020-01-24", "2020-01-25", "2020-01-26",
> "2020-01-27", "2020-01-28", "2020-01-29",
> "2020-01-30", "2020-01-31", "2020-02-01", "2020-02-02",
> "2020-02-03", "2020-02-04", "2020-02-05",
> "2020-02-06", "2020-02-07", "2020-02-08", "2020-02-09",
> "2020-02-10", "2020-02-11", "2020-02-12",
> "2020-02-13", "2020-02-14", "2020-02-15", "2020-02-16",
> "2020-02-17", "2020-02-18", "2020-02-19",
> "2020-02-20", "2020-02-21", "2020-02-22", "2020-02-23",
> "2020-02-24", "2020-02-25", "2020-02-26",
> "2020-02-27", "2020-02-28", "2020-02-29", "2020-03-01",
> "2020-03-02", "2020-03-03", "2020-03-04",
> "2020-03-05", "2020-03-06", "2020-03-07", "2020-03-08",
> "2020-03-09", "2020-03-10", "2020-03-11",
> "2020-03-12", "2020-03-13", "2020-03-14", "2020-03-15",
> "2020-03-16", "2020-03-17", "2020-03-18",
> "2020-03-19", "2020-03-20", "2020-03-21", "2020-03-22",
> "2020-03-23", "2020-03-24", "2020-03-25",
> "2020-03-26", "2020-03-27", "2020-03-28", "2020-03-29",
> "2020-03-30", "2020-03-31", "2020-04-01",
> "2020-04-02", "2020-04-03", "2020-04-04", "2020-04-05",
> "2020-04-06", "2020-04-07", "2020-04-08",
> "2020-04-09", "2020-04-10", "2020-04-11", "2020-04-12",
> "2020-04-13", "2020-04-14", "2020-04-15",
> "2020-04-16", "2020-04-17", "2020-04-18", "2020-04-19",
> "2020-04-20", "2020-04-21", "2020-04-22",
> "2020-04-23", "2020-04-24", "2020-04-25", "2020-04-26", "2020-04-27"
> ,"2020-04-28", "2020-04-29",
> "2020-04-30", "2020-05-01", "2020-05-02", "2020-05-03",
> "2020-05-04", "2020-05-05", "2020-05-06",
> "2020-05-07", "2020-05-08", "2020-05-09", "2020-05-10",
> "2020-05-11", "2020-05-12", "2020-05-13",
> "2020-05-14", "2020-05-15", "2020-05-16", "2020-05-17", "2020-05-18")
> names(x1) <- d1
> pop = 1438443864
> Ts_mean = 5.16
> Ts_sd = 1.49
> N=10000
> TODAY = Sys.Date()
> mGT = generation.time("gamma", c(Ts_mean, Ts_sd))
> R0 = estimate.R(x1, t=d1, GT=mGT, begin=as.Date(d1[1]), end=TODAY,
> methods="EG",pop.size=pop, nsim=N)
> ```
> but when I run I get:
> ```
> Error in if (end.nb <= begin.nb) stop("'begin' and 'end' are not
> consistent.") :
> argument is of length zero
> > as.Date(d1[1])
> [1] "2020-01-23"
> > TODAY
> [1] "2020-05-22"
> > str(TODAY)
> Date[1:1], format: "2020-05-22"
> > str(as.Date(d1[1]))
> Date[1:1], format: "2020-01-23"
> ```
> Since I provided both start and end in the same format, I don't understand
> the error.
> Any tips?
> Thank you
> --
> Best regards,
> Luigi
>
> [[alternative HTML version deleted]]
>
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