How to use R0 package?

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
<jdnewmil at dcn.davis.ca.us> 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

<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

        [[alternative HTML version deleted]]

see

code.

--
Best regards,
Luigi

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