How to use R0 package?
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 <marongiu.luigi at gmail.com> 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 <ericjberger at 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 at 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 at 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 at 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
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-- Best regards, Luigi
-- Best regards, Luigi