NA/NaN/Inf in 'y' induced by gcalibrateC

[muschellij2]

NHANES File is located at https://figshare.com/articles/dataset/Accelerometer_file_that_s_failing_for_Resampling/25627848?file=46327363 and can be downloaded via: https://figshare.com/ndownloader/files/46327363,

url = "https://figshare.com/ndownloader/files/46327363"
file = tempfile(fileext = ".csv.gz")
download.file(url, file, quiet = FALSE)
library(agcounts)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(readr)


data = readr::read_csv(file,
                       col_types = 
                         readr::cols(
                           # HEADER_TIMESTAMP = col_datetime_with_frac_secs(),
                           HEADER_TIMESTAMP = vroom::col_datetime(),
                           X = vroom::col_double(),
                           Y = vroom::col_double(),
                           Z = vroom::col_double()
                         ))
probs = readr::problems(data)
stopifnot(nrow(probs) == 0)
readr::stop_for_problems(data)

head(data)
#> # A tibble: 6 × 4
#>   HEADER_TIMESTAMP         X     Y      Z
#>   <dttm>               <dbl> <dbl>  <dbl>
#> 1 2000-01-03 20:24:00 -0.032 0.053 -0.974
#> 2 2000-01-03 20:24:00 -0.032 0.053 -0.982
#> 3 2000-01-03 20:24:00 -0.032 0.047 -0.982
#> 4 2000-01-03 20:24:00 -0.032 0.053 -0.979
#> 5 2000-01-03 20:24:00 -0.032 0.053 -0.977
#> 6 2000-01-03 20:24:00 -0.032 0.053 -0.979
data = data %>%
  dplyr::rename(time = HEADER_TIMESTAMP)
# needed for fix of agcounts
# PR at https://github.com/bhelsel/agcounts/pull/32
data = as.data.frame(data)
attr(data, "sample_rate") = 80L
attr(data, "last_sample_time") = max(data$time)
xyz = c("X", "Y", "Z")

mat = as.matrix(data[, xyz])
# calibrated = agcalibrate(df, verbose = TRUE)
C <- agcounts:::gcalibrateC(dataset = mat, sf = 80L)
#> Loading chunk: 1 2
#> Error in (function (x, y, w, offset = NULL, method = "qr", tol = 1e-07, : NA/NaN/Inf in 'y'

^{Created on 2024-05-14 with reprex v2.1.0}

Session info

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[bhelsel]

It looks like this issue is linked to lines 321-323 in the GGIR g.calibrate.R file where the authors state that there are some NaN values in the sphere data for ActiGraph monitor brands. I'm not sure if this is the case with other device brands too, but I edited line 277 in the agcounts R package to exclude these NaN values.

The code now reads:

if(curr(i, j) != 0 {
 closestpoint(i, j) = curr(i, j) / sqrt(rsum[i]);
}