as.week {epitools} R Documentation

## Convert dates object in 'disease week' for plotting epidemic curves

### Description

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

### Usage

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

### Arguments

 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

### Details

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.

### Value

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

### Author(s)

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

### References

none

epitools: as.month, epicurve.dates

### Examples

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

[Package epitools version 0.5-10.1 Index]