replace article urls in CutPoints by doi urls and mask all reference

_pkgdown.yml

@@ -109,6 +109,48 @@ news:
     href: https://www.accelting.com/updates/ggir-release-2-5-0/
 
 search:
-  exclude: ['news/index.html', 'articles/GGIR.html']
+  exclude: ['news/index.html', 'articles/GGIR.html', 
+  'articles/cosinorAnalyses.html', 'articles/appendRecords.html', 'articles/applyCosinorAnalyses.html',
+  'articles/applyExtFunction.html', 'articles/CalcSleepRegularityIndex.html', 
+  'articles/checkMilestoneFolders.html', 'articles/check_log.html', 
+  'articles/check_myfun.html', 'articles/check_params.html', 'articles/convertEpochData.html',
+  'articles/correctOlderMilestoneData.html', 'articles/cosinorAnalyses.html',
+  'articles/createConfigFile.html', 'articles/create_test_acc_csv.html', 
+  'articles/create_test_sleeplog_csv.html', 'articles/data.calibrate.html', 
+  'articles/data.getmeta.html', 'articles/data.inspectfile.html', 'articles/data.metalong.html', 
+  'articles/data.ts.html', 'articles/datadir2fnames.html', 'articles/detect_nonwear_clipping.html', 
+  'articles/extractID.html', 'articles/extract_params.html', 'articles/g.abr.day.names.html', 
+  'articles/g.analyse.avday.html', 'articles/g.analyse.html', 'articles/g.analyse.perday.html', 
+  'articles/g.analyse.perfile.html', 'articles/g.applymetrics.html', 'articles/g.calibrate.html', 
+  'articles/g.conv.actlog.html', 'articles/g.convert.part2.long.html', 'articles/g.create.sp.mat.html', 
+  'articles/g.detecmidnight.html', 'articles/g.dotorcomma.html', 'articles/g.extractheadervars.html', 
+  'articles/g.fragmentation.html', 'articles/g.getbout.html', 'articles/g.getM5L5.html', 
+  'articles/g.getmeta.html', 'articles/g.getstarttime.html', 'articles/g.impute.html', 
+  'articles/g.imputeTimegaps.html', 'articles/g.inspectfile.html', 'articles/g.intensitygradient.html', 
+  'articles/g.IVIS.html', 'articles/g.loadlog.html', 'articles/g.part1.html', 'articles/g.part2.html', 
+  'articles/g.part3.html', 'articles/g.part4.html', 'articles/g.part4_extradctid.html', 
+  'articles/g.part5.addfirstwake.html', 'articles/g.part5.addsib.html', 'articles/g.part5.analyseRest.html', 
+  'articles/g.part5.classifyNaps.html', 'articles/g.part5.definedays.html', 
+  'articles/g.part5.fixmissingnight.html', 'articles/g.part5.handle_lux_extremes.html', 
+  'articles/g.part5.html', 'articles/g.part5.lux_persegment.html', 
+  'articles/g.part5.ontsetwaketiming.html', 'articles/g.part5.savetimeseries.html', 
+  'articles/g.part5.wakesleepwindows.html', 'articles/g.part5_analyseSegment.html', 
+  'articles/g.part5_initialise_ts.html', 'articles/g.part6.html', 'articles/g.plot.html', 
+  'articles/g.plot5.html', 'articles/g.readaccfile.html', 'articles/g.readtemp_movisens.html', 
+  'articles/g.report.part2.html', 'articles/g.report.part4.html', 'articles/g.report.part5.html', 
+  'articles/g.report.part5_dictionary.html', 'articles/g.report.part6.html', 
+  'articles/g.shell.GGIR.html', 'articles/g.sib.det.html', 'articles/g.sib.plot.html', 
+  'articles/g.sib.sum.html', 'articles/g.sibreport.html', 'articles/g.weardec.html', 
+  'articles/getfolderstructure.html', 'articles/get_nw_clip_block_params.html', 
+  'articles/get_starttime_weekday_truncdata.html', 'articles/GGIR-package.html', 
+  'articles/GGIR.html', 'articles/HASIB.html', 'articles/HASPT.html', 'articles/identify_levels.html', 
+  'articles/index.html', 'articles/is.ISO8601.html', 'articles/isfilelist.html', 'articles/ismovisens.html', 
+  'articles/iso8601chartime2POSIX.html', 'articles/is_this_a_dst_night.html', 
+  'articles/load_params.html', 'articles/parametersVignette.html', 'articles/part6AlignIndividuals.html', 
+  'articles/part6PairwiseAggregation.html', 'articles/POSIXtime2iso8601.html', 
+  'articles/read.myacc.csv.html', 'articles/ShellDoc2Vignette.html', 
+  'articles/tidyup_df.html', 'articles/updateBlocksize.html']
+
+
 
 

docs/pkgdown.yml

@@ -29,7 +29,7 @@ articles:
   HouseHoldCoanalysis: HouseHoldCoanalysis.html
   readmyacccsv: readmyacccsv.html
   TutorialDaySegmentAnalyses: TutorialDaySegmentAnalyses.html
-last_built: 2024-09-03T08:15Z
+last_built: 2024-09-03T09:17Z
 urls:
   reference: https://wadpac.github.io/GGIR/reference
   article: https://wadpac.github.io/GGIR/articles

vignettes/CutPoints.Rmd

@@ -40,7 +40,7 @@ described by Neishabouri (see GGIR argument `do.neishabouricounts`) which reflec
 the indicator of accumulated body movement over time, referred to as counts, 
 calculated by the ActiLife software from the ActiGraph accelerometer brand.
 Cut-points for counts corresponding to the ActiGraph brand have been recurrently 
-proposed in the literature, for example, see this [systematic review](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231536/)
+proposed in the literature, for example, see this [systematic review](https://doi.org/10.1007%2Fs40279-017-0716-0)
 with a stratification by age group. Note that cut-points for ActiGraph counts proposed before
 the introduction of multiday raw data collection are most likely
 hardware-based calculations which may not perfectly align with ActiGraph
@@ -232,7 +232,7 @@ activity intensity classification with cut-points.
 +-------------------+--------------------+---------------+-----------------------------------+------------------+
 
 \*These publications used acceleration metrics that sum their values per epoch rather than average them per epoch like GGIR does. So, to use their cut-point in GGIR, we provide a scaled version of the cut-points presented in the paper as: `(CutPointFromPaper_in_gmins/(sampleRateFromPaper * EpochLengthInSecondsPaper)) * 1000`
-^†^ In this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858250/), there are cut-point based on data sampled at 30 Hz and 100 Hz. When scaling the cut-points as specified in (\*), the resulting thresholds are virtually the same (the ones presented in this table).
+^†^ In this [publication](https://doi.org/10.1371%2Fjournal.pone.0109913), there are cut-point based on data sampled at 30 Hz and 100 Hz. When scaling the cut-points as specified in (\*), the resulting thresholds are virtually the same (the ones presented in this table).
 
 ## Cut-points for older adults
 
@@ -356,20 +356,20 @@ why cut-points still have value in GGIR see:
 
 # References
 
--   Aittasalo 2015: <https://bmcsportsscimedrehabil.biomedcentral.com/articles/10.1186/s13102-015-0010-0>
+-   Aittasalo 2015: <https://doi.org/10.1186/s13102-015-0010-0>
 -   Bammann 2021: <https://doi.org/10.1371/journal.pone.0252615>
--   Dibben 2020: <https://bmcsportsscimedrehabil.biomedcentral.com/articles/10.1186/s13102-020-00196-7>
--   Dillon 2016: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858250/>
--   Esliger 2011: <https://journals.lww.com/acsm-msse/Fulltext/2011/06000/Validation_of_the_GENEA_Accelerometer.22.aspx>
--   Fraysse 2020: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7843957/>
--   Hildebrand 2014: <https://journals.lww.com/acsm-msse/Fulltext/2014/09000/Age_Group_Comparability_of_Raw_Accelerometer.17.aspx>
+-   Dibben 2020: <https://doi.org/10.1186/s13102-020-00196-7>
+-   Dillon 2016: <https://doi.org/10.1371%2Fjournal.pone.0109913>
+-   Esliger 2011: <https://doi.org/10.1249/mss.0b013e31820513be>
+-   Fraysse 2020: <https://doi.org/10.3389%2Ffspor.2020.579278>
+-   Hildebrand 2014: <https://doi.org/10.1249/mss.0000000000000289>
 -   Hildebrand 2016: <https://doi.org/10.1111/sms.12795>
--   Migueles 2021: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8150960/>
+-   Migueles 2021: <https://doi.org/10.3390%2Fs21103326>
 -   Phillips 2013: <https://doi.org/10.1016/j.jsams.2012.05.013>
 -   Sanders 2018: <https://doi.org/10.1080/02640414.2018.1555904>
--   Schaefer 2014: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960318/>
--   Roscoe 2017: <https://link.springer.com/article/10.1007/s00431-017-2948-2>
--   Vähä-Ypyä 2015: <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134813>
+-   Schaefer 2014: <https://doi.org/10.1249%2FMSS.0000000000000150>
+-   Roscoe 2017: <https://doi.org/10.1007/s00431-017-2948-2>
+-   Vähä-Ypyä 2015: <https://doi.org/10.1371/journal.pone.0134813>