[R] How to use R0 package?

Luigi Marongiu m@rong|u@|u|g| @end|ng |rom gm@||@com
Fri May 22 14:31:48 CEST 2020 

In theory, it works
```
> R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=117,
                methods="EG",pop.size=pop, nsim=N)
>R0
Reproduction number estimate using  Exponential Growth  method.
R :  0.7425278[ 0.7409297 , 0.7441229 ]
```
but I am not happy because 1. I have to use numbers instead of
variables and 2. numbers instead of dates (which are instead reported in
the examples...).
Even if I force to an integer, I still get an error:
```
> R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=length(x1),
+                 methods="EG",pop.size=pop, nsim=N)
Error in integrity.checks(epid, t, GT, begin, end, date.first.obs,
time.step,  :
  If both 'begin'= 1  and 'end'= 117  are provided, they must be of the
same class (dates, character strings or integers).
> int
Error: object 'int' not found
> R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=as.integer(length(x1)),
+                 methods="EG",pop.size=pop, nsim=N)
Error in integrity.checks(epid, t, GT, begin, end, date.first.obs,
time.step,  :
  If both 'begin'= 1  and 'end'= 117  are provided, they must be of the
same class (dates, character strings or integers).
```



On Fri, May 22, 2020 at 1:51 PM Eric Berger <ericjberger using gmail.com> wrote:

> Hi Luigi,
> how about begin=1L (to force it to be integer).
> Also please keep the correspondence on the help list.
>
> Best,
> Eric
>
> On Fri, May 22, 2020 at 2:40 PM Luigi Marongiu <marongiu.luigi using gmail.com>
> wrote:
> >
> > Same error:
> > ```
> > > R0 = estimate.R(x1, t=d1, GT=mGT, begin=1, end=length(x1),
> >                 methods="EG",pop.size=pop, nsim=N)
> >  Error in integrity.checks(epid, t, GT, begin, end, date.first.obs,
> time.step,  :
> >   If both 'begin'= 1  and 'end'= 117  are provided, they must be of the
> same class (dates, character strings or integers).
> > > str(length(x1))
> >  int 117
> > ```
> >
> >
> > On Fri, May 22, 2020 at 12:35 PM Eric Berger <ericjberger using gmail.com>
> wrote:
> >>
> >> 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]]
> >> >
> >> > ______________________________________________
> >> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> > https://stat.ethz.ch/mailman/listinfo/r-help
> >> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> > --
> > Best regards,
> > Luigi
>


-- 
Best regards,
Luigi

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