phenopix (version 2.4.5)

get.options: Returns default options for function autoFilter.

Description

Returns default options for function autoFilter.

Usage

get.options()

Author

Gianluca Filippa <[e-mail]>

Details

Returns default options for function autoFilter. It can be assigned, changed and used within the function autoFilter. In night filter the user can change the threshold of GCC value below which records are discarded. In blue filter the user can change the threshold on daily standard deviation in blue channel above which records are discarded. In mad filter the user can change the z parameter. Increasing z means discarding more data. In max filter the user can change w, i.e. the time window (in days) on which the moving maximum quantile is computed, and qt, the quantile that is used (default 0.9). In spline filter the user can change stdup and stddown, upper and lower standard deviation thresholds, respectively and loop_spline, the number of spline iteractions. See examples for details.

Examples

if (FALSE) {
data(bartlett2009)
## with raw.dn ==TRUE and column position for chromatic coordinates
filtered.data <- autoFilter(bartlett2009, dn=c(5:7), 
	filter=c('night', 'spline', 'max'),
    filter.options=NULL, raw.dn=TRUE)
my.options <- get.options()
## change time window for max filter
my.options$max.filter$w <- 5
filtered.data2 <- autoFilter(bartlett2009, dn=c(5:7), 
	filter=c('night', 'spline', 'max'),
    filter.options=my.options, raw.dn=TRUE)
plot(filtered.data$max.filtered)
lines(filtered.data2$max.filtered, col='red')
}