Error in some analyses of Activity accelerometers with GGIR package
Marcos Echevarría Polo
> library(GGIR)
> GGIR(mode=c(1,2,3,4,5),
+ datadir="entrada",
+ outputdir="salida",
+ do.report=c(2,4,5),
+ #=====================
+ # Part 2
+ #=====================
+ strategy = 1,
+ hrs.del.start = 0, hrs.del.end = 0,
+ maxdur = 16, includedaycrit = 16,
+ qwindow=c(0,24),
+ mvpathreshold =c(100),
+ excludefirstlast = FALSE,
+ includenightcrit = 16,
+ qlevels = c(c(960/1440),c(1320/1440),c(1380/1440),c(1410/1440),c(1425/1440),c(1430/1440),c(1435/1440),c(1438/1440)),
+ #=====================
+ # Part 3 + 4
+ #=====================
+ def.noc.sleep = 1,
+ outliers.only = TRUE,
+ criterror = 4,
+ do.visual = TRUE,
+ #=====================
+ # Part 5
+ #=====================
+ threshold.lig = c(30), threshold.mod = c(100), threshold.vig = c(400),
+ boutcriter = 0.8, boutcriter.in = 0.9, boutcriter.lig = 0.8,
+ boutcriter.mvpa = 0.8, boutdur.in = c(1,10,30), boutdur.lig = c(1,10),
+ boutdur.mvpa = c(1),
+ includedaycrit.part5 = 2/3,
+ #=====================
+ # Visual report
+ #=====================
+ timewindow = c("WW"),
+ visualreport=TRUE)
Checking that user has write access permission for directory specified by argument outputdir: Yes
GGIR version: 3.0.0
Do not forget to cite GGIR in your publications via a version number and
Migueles et al. 2019 JMPB. doi: 10.1123/jmpb.2018-0063.
See also: https://cran.r-project.org/package=GGIR/vignettes/GGIR.html#citing-ggir
To make your research reproducible and interpretable always report:
(1) Accelerometer brand and product name
(2) How you configured the accelerometer
(3) Study protocol and wear instructions given to the participants
(4) GGIR version
(5) How GGIR was used: Share the config.csv file or your R script.
(6) How you post-processed / cleaned GGIR output
(7) How reported outcomes relate to the specific variable names in GGIR
_________________________________________________________________________________________________________________________
Part 1
Checking that user has read access permission for all files in data directory: Yes
1
P1 file 1
Investigate calibration of the sensors with function g.calibrate:
Loading chunk: 1 2 3 4 5 6 7
Extract signal features (metrics) with the g.getmeta function:
Loading chunk: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Save .RData-file with: calibration report, file inspection report and all signal features...
_________________________________________________________________________________________________________________________
Part 2
1 measurement starts at midnight or there is no midnight
_________________________________________________________________________________________________________________________
Part 3
1
_________________________________________________________________________________________________________________________
Part 4
1Error in if (is.na(defaultSptOnset) == TRUE) { :
argument is of length zero
> setwd("/Users/marcosechevarriapolo/Desktop")
> library(GGIR)
> GGIR(mode=c(1,2,3,4,5),
+ datadir="entrada",
+ outputdir="salida",
+ do.report=c(2,4,5),
+ #=====================
+ # Part 2
+ #=====================
+ strategy = 1,
+ hrs.del.start = 0, hrs.del.end = 0,
+ maxdur = 16, includedaycrit = 16,
+ qwindow=c(0,24),
+ mvpathreshold =c(100),
+ excludefirstlast = FALSE,
+ includenightcrit = 16,
+ qlevels = c(c(960/1440),c(1320/1440),c(1380/1440),c(1410/1440),c(1425/1440),c(1430/1440),c(1435/1440),c(1438/1440)),
+ #=====================
+ # Part 3 + 4
+ #=====================
+ def.noc.sleep = 1,
+ outliers.only = TRUE,
+ criterror = 4,
+ do.visual = TRUE,
+ #=====================
+ # Part 5
+ #=====================
+ threshold.lig = c(30), threshold.mod = c(100), threshold.vig = c(400),
+ boutcriter = 0.8, boutcriter.in = 0.9, boutcriter.lig = 0.8,
+ boutcriter.mvpa = 0.8, boutdur.in = c(1,10,30), boutdur.lig = c(1,10),
+ boutdur.mvpa = c(1),
+ includedaycrit.part5 = 2/3,
+ #=====================
+ # Visual report
+ #=====================
+ timewindow = c("WW"),
+ visualreport=TRUE)
Checking that user has write access permission for directory specified by argument outputdir: Yes
GGIR version: 3.0.0
Do not forget to cite GGIR in your publications via a version number and
Migueles et al. 2019 JMPB. doi: 10.1123/jmpb.2018-0063.
See also: https://cran.r-project.org/package=GGIR/vignettes/GGIR.html#citing-ggir
To make your research reproducible and interpretable always report:
(1) Accelerometer brand and product name
(2) How you configured the accelerometer
(3) Study protocol and wear instructions given to the participants
(4) GGIR version
(5) How GGIR was used: Share the config.csv file or your R script.
(6) How you post-processed / cleaned GGIR output
(7) How reported outcomes relate to the specific variable names in GGIR
____________________________________________________________________________
Part 1
Checking that user has read access permission for all files in data directory: Yes
1
P1 file 1
Investigate calibration of the sensors with function g.calibrate:
Loading chunk: 1 2
Extract signal features (metrics) with the g.getmeta function:
Loading chunk: 1
Save .RData-file with: calibration report, file inspection report and all signal features...
______________________________________________________________________
Part 2
1
_______________________________________________________________________
Part 3
1 P3 file NAFilename not recognizedError in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file 'salida/output_entrada/meta/basic/meta_NA', probable reason 'No such file or directory'
What should I do??
Thanks for all.
