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

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

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.1 (2023-06-16) #> os macOS Sonoma 14.4.1 #> system x86_64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz America/New_York #> date 2024-05-14 #> pandoc 3.1.11.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> agcounts * 0.6.6 2024-04-10 [1] local #> bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0) #> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0) #> blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0) #> bslib 0.6.1 2023-11-28 [1] CRAN (R 4.3.0) #> cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.0) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0) #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) #> data.table 1.14.10 2023-12-08 [1] CRAN (R 4.3.0) #> DBI 1.2.1 2024-01-12 [1] CRAN (R 4.3.0) #> digest 0.6.34 2024-01-11 [1] CRAN (R 4.3.0) #> dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0) #> evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.0) #> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.0) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) #> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) #> GGIR 3.0-3 2024-01-11 [1] CRAN (R 4.3.0) #> ggplot2 3.5.0 2024-02-23 [1] CRAN (R 4.3.2) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.0) #> gsignal 0.3-5 2022-05-15 [1] CRAN (R 4.3.0) #> gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0) #> hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0) #> htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.0) #> htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.0) #> httpuv 1.6.13 2023-12-06 [1] CRAN (R 4.3.0) #> jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0) #> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.0) #> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.0) #> later 1.3.2 2023-12-06 [1] CRAN (R 4.3.0) #> lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.0) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.0) #> lubridate 1.9.3 2023-09-27 [1] CRAN (R 4.3.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) #> Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.0) #> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0) #> mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) #> png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0) #> promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0) #> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.3.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0) #> R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.3.2) #> R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.3.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.0) #> reactable 0.4.4 2023-03-12 [1] CRAN (R 4.3.0) #> read.gt3x 1.2.0 2022-06-30 [1] CRAN (R 4.3.0) #> readr * 2.1.5 2024-01-10 [1] CRAN (R 4.3.0) #> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.3.0) #> reticulate 1.35.0 2024-01-31 [1] CRAN (R 4.3.2) #> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.0) #> rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.0) #> RSQLite 2.3.5 2024-01-21 [1] CRAN (R 4.3.0) #> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.2) #> sass 0.4.8 2023-12-06 [1] CRAN (R 4.3.0) #> scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) #> shiny 1.8.0 2023-11-17 [1] CRAN (R 4.3.0) #> stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.0) #> stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.0) #> styler 1.10.2 2023-08-29 [1] CRAN (R 4.3.0) #> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0) #> timechange 0.3.0 2024-01-18 [1] CRAN (R 4.3.0) #> tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.3.0) #> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.0) #> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.0) #> vroom 1.6.5 2023-12-05 [1] CRAN (R 4.3.0) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.0) #> xfun 0.41 2023-11-01 [1] CRAN (R 4.3.0) #> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0) #> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.0) #> zoo 1.8-12 2023-04-13 [1] CRAN (R 4.3.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library #> #> ─ Python configuration ─────────────────────────────────────────────────────── #> python: /Users/johnmuschelli/miniconda3/bin/python3 #> libpython: /Users/johnmuschelli/miniconda3/lib/libpython3.11.dylib #> pythonhome: /Users/johnmuschelli/miniconda3:/Users/johnmuschelli/miniconda3 #> version: 3.11.4 (main, Jul 5 2023, 08:41:25) [Clang 14.0.6 ] #> numpy: /Users/johnmuschelli/miniconda3/lib/python3.11/site-packages/numpy #> numpy_version: 1.25.2 #> pygt3x: /Users/johnmuschelli/miniconda3/lib/python3.11/site-packages/pygt3x #> #> NOTE: Python version was forced by RETICULATE_PYTHON #> #> ────────────────────────────────────────────────────────────────────────────── ```

actigraph / agcounts

`NA/NaN/Inf in 'y'` induced by `gcalibrateC` #22