How to use R0 package?

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

How to use R0 package?

Luigi
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]]

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: 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 <[hidden email]> 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]]
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: How to use R0 package?

Luigi
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 <[hidden email]> 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 <[hidden email]>
> 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 <[hidden email]>
> 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 <
> [hidden email]> 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]]
> >> >
> >> > ______________________________________________
> >> > [hidden email] 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

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: How to use R0 package?

Eric Berger
class(length(x1))
"integer"

Your problem is thinking that begin=1 means you are passing begin as
an integer.
class(1)
"numeric"
class(1L)
"integer"

You should pass:  begin=1L, end=length(x1)

Best,
Eric

On Fri, May 22, 2020 at 3:31 PM Luigi Marongiu <[hidden email]> wrote:

>
> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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]]
>> >> >
>> >> > ______________________________________________
>> >> > [hidden email] 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

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: How to use R0 package?

Olivier Crouzet-2
In reply to this post by Luigi
Hi,

you should be able to convert your date variables to integers (usually
viewed as the elapse between 1970/01/01 and today) by using date
conversion to integers:

TODAY="2020-05-22"
as.Date(TODAY)
[1] "2020-05-22"
> as.integer(as.Date(TODAY))
[1] 18404

Doing the same with your reference dates should do the job.

Yours.
Olivier.


On Fri, 22 May 2020
14:31:48 +0200 Luigi Marongiu <[hidden email]> wrote:

> 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 <[hidden email]>
> 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
> > <[hidden email]> 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
> > > <[hidden email]>
> > 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 <
> > [hidden email]> 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]]
> > >> >
> > >> > ______________________________________________
> > >> > [hidden email] 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
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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.


--
  Olivier Crouzet, PhD
  http://olivier.ghostinthemachine.space
  /Maître de Conférences/
  @LLING - Laboratoire de Linguistique de Nantes
    UMR6310 CNRS / Université de Nantes
  /Guest Researcher/
  @UMCG (University Medical Center Groningen)
    ENT department
    Rijksuniversiteit Groningen

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: How to use R0 package?

Jeff Newmiller
In reply to this post by Luigi
This is getting off-topic here but R0 is a mathematical parameter unrelated to calendar dates. It arises when analyzing case counts (integers) as a function of the numerical measure of time since some non-trivial number of cases has occurred (conventionally this measure is in days)..

dta$days <- as.numeric( dta$date - startdate, units="days" )

On May 22, 2020 5:31:48 AM PDT, Luigi Marongiu <[hidden email]> wrote:

>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 <[hidden email]>
>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
><[hidden email]>
>> 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
><[hidden email]>
>> 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 <
>> [hidden email]> 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]]
>> >> >
>> >> > ______________________________________________
>> >> > [hidden email] 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
>>

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: How to use R0 package?

Jim Lemon-4
So what if you treat a nuisance as a feature and import your dates as
factors? as.numeric(dates) would have the correct structure or am I,
as usual, missing something?

Jim

On Sat, May 23, 2020 at 1:00 AM Jeff Newmiller <[hidden email]> wrote:

>
> This is getting off-topic here but R0 is a mathematical parameter unrelated to calendar dates. It arises when analyzing case counts (integers) as a function of the numerical measure of time since some non-trivial number of cases has occurred (conventionally this measure is in days)..
>
> dta$days <- as.numeric( dta$date - startdate, units="days" )
>
> On May 22, 2020 5:31:48 AM PDT, Luigi Marongiu <[hidden email]> wrote:
> >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 <[hidden email]>
> >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
> ><[hidden email]>
> >> 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
> ><[hidden email]>
> >> 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 <
> >> [hidden email]> 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]]
> >> >> >
> >> >> > ______________________________________________
> >> >> > [hidden email] 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
> >>
>
> --
> Sent from my phone. Please excuse my brevity.
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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.
Reply | Threaded
Open this post in threaded view
|

Re: How to use R0 package?

Jeff Newmiller
Because the dates might not be consecutive.  Or in ISO format.

On May 22, 2020 7:38:17 PM PDT, Jim Lemon <[hidden email]> wrote:

>So what if you treat a nuisance as a feature and import your dates as
>factors? as.numeric(dates) would have the correct structure or am I,
>as usual, missing something?
>
>Jim
>
>On Sat, May 23, 2020 at 1:00 AM Jeff Newmiller
><[hidden email]> wrote:
>>
>> This is getting off-topic here but R0 is a mathematical parameter
>unrelated to calendar dates. It arises when analyzing case counts
>(integers) as a function of the numerical measure of time since some
>non-trivial number of cases has occurred (conventionally this measure
>is in days)..
>>
>> dta$days <- as.numeric( dta$date - startdate, units="days" )
>>
>> On May 22, 2020 5:31:48 AM PDT, Luigi Marongiu
><[hidden email]> wrote:
>> >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 <[hidden email]>
>> >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
>> ><[hidden email]>
>> >> 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
>> ><[hidden email]>
>> >> 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 <
>> >> [hidden email]> 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]]
>> >> >> >
>> >> >> > ______________________________________________
>> >> >> > [hidden email] 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
>> >>
>>
>> --
>> Sent from my phone. Please excuse my brevity.
>>
>> ______________________________________________
>> [hidden email] 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.

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[hidden email] 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.