Error in cut.default(ts, breaks = breaks) : 'x' must be numeric -- if the first column named differently than HEADER_TIME_STAMP

[martakarass]

I ran into Error in cut.default(ts, breaks = breaks) : 'x' must be numeric error if using a data frame where the first column -- the time component -- is named differently than "HEADER_TIME_STAMP". Note the documentation does not mention a need to name the first column -- the time component -- in a certain way; it only says df -- dataframe. Input multi-channel accelerometer signal. The first column should be the time component.

Below is an example of generating the error for raw accelerometry data sample included in adeptdata R package. These data were collected continuously for ~20 minutes with ActiGraph Link device at frequency 100 Hz.

Example when it works:

rm(list = ls())

# install.packages("adeptdata")
library(adeptdata)
library(MIMSunit)
library(dplyr)
library(lubridate)

# does work 
df <- adeptdata::acc_running %>% 
  filter(loc_id == "left_hip") %>%
  select(HEADER_TIME_STAMP = date_time, x, y, z) %>%
  mutate(HEADER_TIME_STAMP = lubridate::ymd_hms(HEADER_TIME_STAMP))

mims_out <- MIMSunit::mims_unit(df, epoch = "1 min", dynamic_range = c(-8, 8))
mims_out

     HEADER_TIME_STAMP MIMS_UNIT
1  2018-10-25 17:57:30 -0.010000
2  2018-10-25 17:58:00  2.851872
3  2018-10-25 17:59:00  3.398222
4  2018-10-25 18:00:00  3.546349
5  2018-10-25 18:01:00  3.948084
6  2018-10-25 18:02:00  3.733877
7  2018-10-25 18:03:00  3.495979
8  2018-10-25 18:04:00  0.000000
9  2018-10-25 18:05:00  3.564741
10 2018-10-25 18:06:00  5.340143
11 2018-10-25 18:07:00  3.285434
12 2018-10-25 18:08:00  3.234805
13 2018-10-25 18:09:00  3.635066
14 2018-10-25 18:10:00  2.391141
15 2018-10-25 18:11:00  1.296743
16 2018-10-25 18:12:00  4.239850
17 2018-10-25 18:13:00  2.843946
18 2018-10-25 18:14:00  3.699698
19 2018-10-25 18:15:00  3.670837
20 2018-10-25 18:16:00  3.494550
21 2018-10-25 18:17:00  1.699157
22 2018-10-25 18:18:00  2.959040
23 2018-10-25 18:19:00  4.022677
24 2018-10-25 18:20:00  4.234644
25 2018-10-25 18:21:00  2.658034
26 2018-10-25 18:22:00 -0.010000

• Example when it does not:

# does not work 
rm(df, mims_out)
df <- adeptdata::acc_running %>% 
  filter(loc_id == "left_hip") %>%
  select(date_time, x, y, z) %>%
  mutate(date_time = lubridate::ymd_hms(date_time))
mims_out <- MIMSunit::mims_unit(df, epoch = "1 min", dynamic_range = c(-8, 8))

===================================================================================Error in cut.default(ts, breaks = breaks) : 'x' must be numeric
In addition: Warning messages:
1: In regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
2: In regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
3: In regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
4: tz(): Don't know how to compute timezone for object of class NULL; returning "UTC". This warning will become an error in the next major version of lubridate. 

Session info

devtools::session_info()

─ Session info ───────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       macOS Catalina 10.15.7      
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/New_York            
 date     2021-04-12                  

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────
 package     * version  date       lib source        
 adeptdata   * 1.1      2021-03-24 [1] local         
 assertthat    0.2.1    2019-03-21 [1] CRAN (R 4.0.2)
 bitops        1.0-6    2013-08-17 [1] CRAN (R 4.0.2)
 cachem        1.0.4    2021-02-13 [1] CRAN (R 4.0.2)
 callr         3.5.1    2020-10-13 [1] CRAN (R 4.0.2)
 caTools       1.18.1   2021-01-11 [1] CRAN (R 4.0.2)
 cellranger    1.1.0    2016-07-27 [1] CRAN (R 4.0.2)
 cli           2.3.0    2021-01-31 [1] CRAN (R 4.0.3)
 crayon        1.4.1    2021-02-08 [1] CRAN (R 4.0.2)
 DBI           1.1.1    2021-01-15 [1] CRAN (R 4.0.2)
 desc          1.2.0    2018-05-01 [1] CRAN (R 4.0.2)
 devtools      2.3.2    2020-09-18 [1] CRAN (R 4.0.2)
 digest        0.6.27   2020-10-24 [1] CRAN (R 4.0.2)
 dplyr       * 1.0.4    2021-02-02 [1] CRAN (R 4.0.2)
 ellipsis      0.3.1    2020-05-15 [1] CRAN (R 4.0.2)
 fansi         0.4.2    2021-01-15 [1] CRAN (R 4.0.2)
 fastmap       1.1.0    2021-01-25 [1] CRAN (R 4.0.2)
 fs            1.5.0    2020-07-31 [1] CRAN (R 4.0.2)
 generics      0.1.0    2020-10-31 [1] CRAN (R 4.0.2)
 glue          1.4.2    2020-08-27 [1] CRAN (R 4.0.2)
 htmltools     0.5.1.1  2021-01-22 [1] CRAN (R 4.0.2)
 httpuv        1.5.5    2021-01-13 [1] CRAN (R 4.0.2)
 later         1.1.0.1  2020-06-05 [1] CRAN (R 4.0.2)
 lifecycle     1.0.0    2021-02-15 [1] CRAN (R 4.0.2)
 lubridate   * 1.7.9.2  2020-11-13 [1] CRAN (R 4.0.2)
 magrittr      2.0.1    2020-11-17 [1] CRAN (R 4.0.2)
 MASS          7.3-53.1 2021-02-12 [1] CRAN (R 4.0.2)
 memoise       2.0.0    2021-01-26 [1] CRAN (R 4.0.2)
 mime          0.10     2021-02-13 [1] CRAN (R 4.0.2)
 MIMSunit    * 0.9.2    2020-08-01 [1] CRAN (R 4.0.2)
 pillar        1.5.0    2021-02-22 [1] CRAN (R 4.0.3)
 pkgbuild      1.2.0    2020-12-15 [1] CRAN (R 4.0.2)
 pkgconfig     2.0.3    2019-09-22 [1] CRAN (R 4.0.2)
 pkgload       1.1.0    2020-05-29 [1] CRAN (R 4.0.2)
 plyr          1.8.6    2020-03-03 [1] CRAN (R 4.0.2)
 prettyunits   1.1.1    2020-01-24 [1] CRAN (R 4.0.2)
 processx      3.4.5    2020-11-30 [1] CRAN (R 4.0.2)
 promises      1.2.0.1  2021-02-11 [1] CRAN (R 4.0.2)
 ps            1.5.0    2020-12-05 [1] CRAN (R 4.0.2)
 purrr         0.3.4    2020-04-17 [1] CRAN (R 4.0.2)
 R6            2.5.0    2020-10-28 [1] CRAN (R 4.0.2)
 Rcpp          1.0.6    2021-01-15 [1] CRAN (R 4.0.2)
 readxl        1.3.1    2019-03-13 [1] CRAN (R 4.0.2)
 remotes       2.2.0    2020-07-21 [1] CRAN (R 4.0.2)
 rlang         0.4.10   2020-12-30 [1] CRAN (R 4.0.2)
 rprojroot     2.0.2    2020-11-15 [1] CRAN (R 4.0.2)
 sessioninfo   1.1.1    2018-11-05 [1] CRAN (R 4.0.2)
 shiny         1.6.0    2021-01-25 [1] CRAN (R 4.0.2)
 signal        0.7-6    2015-07-30 [1] CRAN (R 4.0.2)
 stringi       1.5.3    2020-09-09 [1] CRAN (R 4.0.2)
 stringr       1.4.0    2019-02-10 [1] CRAN (R 4.0.2)
 testthat      3.0.2    2021-02-14 [1] CRAN (R 4.0.2)
 tibble        3.0.6    2021-01-29 [1] CRAN (R 4.0.2)
 tidyselect    1.1.0    2020-05-11 [1] CRAN (R 4.0.2)
 usethis       2.0.1    2021-02-10 [1] CRAN (R 4.0.2)
 utf8          1.1.4    2018-05-24 [1] CRAN (R 4.0.2)
 vctrs         0.3.6    2020-12-17 [1] CRAN (R 4.0.2)
 withr         2.4.1    2021-01-26 [1] CRAN (R 4.0.2)
 xtable        1.8-4    2019-04-21 [1] CRAN (R 4.0.2)

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

[qutang]

Thanks for reporting. I spotted the bug in the code. I'll update the codes to fix it. For now, just make sure you used "HEADER_TIME_STAMP" as the column name.

Thanks.