junruidi / actfrag Goto Github PK

Hi Junrui, I am finally able to get started with making your work available via GGIR.

In https://github.com/junruidi/ActFrag/blob/master/R/fragmentation.R
should the following documentation for Gini index

#' \item{Gini_r}{Gini index for active bout}
#' \item{Gini_a}{Gini index for sedentary bout}

be replaced by

#' \item{Gini_r}{Gini index for sedentary bout}
#' \item{Gini_a}{Gini index for active bout}

in that way it will be consistent with the naming of the other variables, where 'a' refers to active and 'r' to sedentary? or does the naming intentionally flip direction for the Gini index?

I have data where I have non-wear periods that are not at the end of the recording time.
I have elected to pre-screen the counts vector, and place NA values in the counts variable x where there is non-wear. Your function does not provide the same output as if there were 0s for NA values. I've compared running your function with NA's (row 2) vs. 0's (row 1) using the reproducible code below. I also tried pre-filtering my data for wear time before providing it to your function (row 3). These three methods produce different results. Which one is theoretically correct? Given your answer, I would recommend editing the function to make at least rows 1 and 2 consistent.

# simulate data
x <- c(sample(0:2, 600, prob = c(.75,.2,.05), replace = T), 
       rep(0,200),
       sample(0:2, 200, prob = c(.75,.2,.05), replace = T)) %>% 
  as.integer
wear <- c(rep(1,600), rep(0,200), rep(1,200))
x.NA <- x
x.NA[wear == 0] <- NA

# fragmentation metrics
bind_rows(
fragmentation(x, wear, thresh = 1, metrics = "all") %>% as.tibble,
fragmentation(x.NA, wear, thresh = 1, metrics = "all") %>% as.tibble,
fragmentation(x.NA[wear == 1], w = rep(1,800), thresh = 1, metrics = "all") %>% as.tibble
)