as.week: Convert dates object in 'disease week' for plotting epidemic...
In epitools: Epidemiology Tools

Description Usage Arguments Details Value Author(s) References See Also Examples

Convert dates into "disease week" with values of 1 to 53 for plotting epidemic curves

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as.week(x, format = "%Y-%m-%d", 
        min.date, max.date, before = 7, after = 7,
        origin = as.Date("1970-01-01"), sunday = TRUE)

`x`	character vector of dates
`format`	date format of `x`; default is of form "2004-08-10"
`min.date`	[optional] minimum calendar date for plotting x-axis of an epidemic curve; should be of the form of "2004-08-10"; if no date is specified, then several days are subtracted from the minimum date in `x` as specified by the `before` option
`max.date`	[optional] maximum calendar date for plotting x-axis of an epidemic curve plot; should be f the form of "2004-08-10"; if no date is specified, then several days are added to the maximum date in `x` as specified by the `after` option
`before`	if `min.date` is not specified, then these number of days are subtracted from the minimum date in `x` for plotting minimum calendar date for epidemic curve
`after`	if `max.date` is not specified, then these number of days are added to the maximum date in `x` for plotting maximum calendar date for epidemic curve
`origin`	allows user to specify an alternative origin for Julian dates that are generated by this function (default = "1970-01-01")
`sunday`	First day of the week is Sunday (default = TRUE); setting to FALSE makes Monday the first day of the week

In public health, reportable diseases are often reported by 'disease week' (either week of reporting or week of symptom onset). In R, weeks are numbered from 0 to 53 in the same year. The first day of week 1 starts with either the first Sunday or Monday of the year. Days before week 1 are numbered as 0s.

In contrast to R, the as.week function generates weeks numbered from 1 to 53. The week before week 1 takes on the value (52 or 53) from the last week of the previous year. The as.week functions facilitates working with multiple years and generating epidemic curves.

Returns a list of the following:

`$dates`	input dates are converted to standard calendar date format
`$firstday`	first day of the week is reported
`$week`	week of the year (1-53); note that week 52 or 53 can represent both last week of a year but also the first few days at the beginning of the year
`$stratum`	the Julian date for the mid-week day of the `$week` value
`$stratum2`	the Julian date for the mid-week day of the `$week` value converted to a factor with levels determined by the Julian dates (`$cstratum`) used to plot the epidemic curve
`$stratum3`	the mid-week day of the `$week` value converted to standard calendar dates
`$cweek`	the week of the year used for plotting the x-axis of an epidemic curve
`$cstratum`	the Julian date for the mid-week day of the `$cweek` value used for plotting the x-axis of an epidemic curve
`$cstratum2`	the standard calendar date for the mid-week day of the `$cweek` value used for plotting the x-axis of an epidemic curve
`$cmday`	the day of the mon (1-31) for the calendar dates used for plotting the x-axis of an epidemic curve
`$cmonth`	the months (Jan, Feb, Mar, ...) for the calendar dates used for plotting the x-axis of an epidemic curve
`$cyear`	the years (e.g., 1996, 2001, ...) for the calendar dates used for plotting the x-axis of an epidemic curve

Tomas Aragon, aragon@berkeley.edu, http://www.phdata.science

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epitools: as.month, epicurve.dates

as.Date, strptime, DateTimeClasses

dates <- c("1/1/04", "1/2/04", "1/3/04", "1/4/04", "1/5/04",
"1/6/04", "1/7/04", "1/8/04", "1/9/04", "1/10/04", NA, "1/12/04",
"1/14/04", "3/5/04", "5/5/04", "7/6/04", "8/18/04", "12/13/05",
"1/5/05", "4/6/05", "7/23/05", "10/3/05")
aw <- as.week(dates, format = "%m/%d/%y")
aw

aw2 <- as.week(dates, format = "%m/%d/%y", sunday= FALSE)
aw2

aw3 <- as.week(dates, format = "%m/%d/%y", min.date="2003-01-01")
aw3