[R] How to use R0 package?

[Eric Berger]

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.luigi using 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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