diff --git a/inst/guide/user_guide_en.Rmd b/inst/guide/user_guide_en.Rmd index 3e80860b..eb14248f 100644 --- a/inst/guide/user_guide_en.Rmd +++ b/inst/guide/user_guide_en.Rmd @@ -139,12 +139,12 @@ Once these new variables added to the initial dataset, the app summarizes the re * `peak_steps_5min`: step accumulation per minute averaged over the best 5 continuous or discontinuous minutes. * `peak_steps_1min`: step accumulation per minute over the best minute (same result as for `max_steps_1min`). * `ig`: intensity gradient. -* `M1/3`: the count value (in counts/epoch duration) above which the most active 8h are accumulated over the day -* `M120`: the count value (in counts/epoch duration) above which the most active 120 minutes are accumulated over the day -* `M60`: the count value (in counts/epoch duration) above which the most active 60 minutes are accumulated over the day -* `M30`: the count value (in counts/epoch duration) above which the most active 30 minutes are accumulated over the day -* `M15`: the count value (in counts/epoch duration) above which the most active 15 minutes are accumulated over the day -* `M5`: the count value (in counts/epoch duration) above which the most active 5 minutes are accumulated over the day +* `M1/3`: the count value (in counts/epoch duration) at and above which the most active 8h are accumulated over the day +* `M120`: the count value (in counts/epoch duration) at and above which the most active 120 minutes are accumulated over the day +* `M60`: the count value (in counts/epoch duration) at and above which the most active 60 minutes are accumulated over the day +* `M30`: the count value (in counts/epoch duration) at and above which the most active 30 minutes are accumulated over the day +* `M15`: the count value (in counts/epoch duration) at and above which the most active 15 minutes are accumulated over the day +* `M5`: the count value (in counts/epoch duration) at and above which the most active 5 minutes are accumulated over the day To compute PAL, total energy expenditure (TEE) related to the period of the day the user wanted to analyse is divided by BMR that is computed to also correspond to the period of the day the user wanted to analyse. TEE is obtained by summing the kilocalories measured during wear time epochs and the kilocalories related to BMR expended during nonwear time epochs (it is assumed that the periods where the device was not worn corresponded to sleeping periods, during which energy expenditure is near of BMR), and by multiplying this sum by 10/9 to take into account the thermic effect of food. In principle, PAL should be computed using the whole day, not a given period of the day. Of course, such calculations may conduct to underestimate TEE and PAL if the device was removed during prolonged periods of physical activity, unless the user manually adds physical activity information into the dedicated boxes of the app as explained above. Moreover, even if the device was correctly worn, the estimate of PAL is very approximate since both BMR and kilocalories are estimated using methods that may not be accurate at the individual level. diff --git a/inst/guide/user_guide_en.aux b/inst/guide/user_guide_en.aux index 83724be2..7e13b020 100644 --- a/inst/guide/user_guide_en.aux +++ b/inst/guide/user_guide_en.aux @@ -1,16 +1,5 @@ \relax \providecommand\hyper@newdestlabel[2]{} -\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} -\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined -\global\let\oldnewlabel\newlabel -\gdef\newlabel#1#2{\newlabelxx{#1}#2} -\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} -\AtEndDocument{\ifx\hyper@anchor\@undefined -\let\newlabel\oldnewlabel -\fi} -\fi} -\global\let\hyper@last\relax -\gdef\HyperFirstAtBeginDocument#1{#1} \providecommand*\HyPL@Entry[1]{} \HyPL@Entry{0<>} \@writefile{toc}{\contentsline {chapter}{\numberline {1}Information}{5}{chapter.1}\protected@file@percent } @@ -37,8 +26,7 @@ {1}{118.52275pt}} \@writefile{lot}{\contentsline {table}{\numberline {3.1}{Equations\ for\ estimating\ basal\ metabolic\ rate}}{10}{table.3.1}\protected@file@percent } \newlabel{tab:METsEquations}{{3.1}{10}{Equations\ for\ estimating\ basal\ metabolic\ rate}{table.3.1}{}} -\@writefile{lot}{\contentsline {table}{\numberline {3.1}{Equations\ for\ estimating\ basal\ metabolic\ rate}}{11}{table.3.1}\protected@file@percent } -\newlabel{tab:METsEquations}{{3.1}{11}{Equations\ for\ estimating\ basal\ metabolic\ rate}{table.3.1}{}} +\newlabel{tab:METsEquations}{{3.1}{11}{Configuration for metrics computation}{table.3.1}{}} \@writefile{toc}{\contentsline {chapter}{\numberline {4}Results and export}{15}{chapter.4}\protected@file@percent } \@writefile{lof}{\addvspace {10\p@ }} \@writefile{lot}{\addvspace {10\p@ }} diff --git a/inst/guide/user_guide_en.log b/inst/guide/user_guide_en.log index e125416c..a235385e 100644 --- a/inst/guide/user_guide_en.log +++ b/inst/guide/user_guide_en.log @@ -1,36 +1,37 @@ -This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex 2023.1.13) 3 FEB 2023 18:24 +This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex 2023.11.29) 26 APR 2024 17:31 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **user_guide_en.tex (./user_guide_en.tex -LaTeX2e <2022-11-01> patch level 1 -L3 programming layer <2022-12-17> (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/book.cls -Document Class: book 2022/07/02 v1.4n Standard LaTeX document class +LaTeX2e <2023-11-01> +L3 programming layer <2023-11-09> +(c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/book.cls +Document Class: book 2023/05/17 v1.4n Standard LaTeX document class (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/bk10.clo -File: bk10.clo 2022/07/02 v1.4n Standard LaTeX file (size option) +File: bk10.clo 2023/05/17 v1.4n Standard LaTeX file (size option) ) -\c@part=\count181 -\c@chapter=\count182 -\c@section=\count183 -\c@subsection=\count184 -\c@subsubsection=\count185 -\c@paragraph=\count186 -\c@subparagraph=\count187 -\c@figure=\count188 -\c@table=\count189 +\c@part=\count182 +\c@chapter=\count183 +\c@section=\count184 +\c@subsection=\count185 +\c@subsubsection=\count186 +\c@paragraph=\count187 +\c@subparagraph=\count188 +\c@figure=\count189 +\c@table=\count190 \abovecaptionskip=\skip48 \belowcaptionskip=\skip49 \bibindent=\dimen140 ) (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/amsmath/amsmath.sty -Package: amsmath 2022/04/08 v2.17n AMS math features +Package: amsmath 2023/05/13 v2.17o AMS math features \@mathmargin=\skip50 For additional information on amsmath, use the `?' option. 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[15] [16] [17 ] [18] (./user_guide_en.aux) + *********** +LaTeX2e <2023-11-01> +L3 programming layer <2023-11-09> + *********** LaTeX Warning: There were multiply-defined labels. -Package rerunfilecheck Info: File `user_guide_en.out' has not changed. -(rerunfilecheck) Checksum: 6DE870DDAFBF3A5BAE2BD804E0C71FBE;1209. ) Here is how much of TeX's memory you used: - 17695 strings out of 478757 - 328700 string characters out of 5847534 - 1869973 words of memory out of 5000000 - 37472 multiletter control sequences out of 15000+600000 - 518754 words of font info for 87 fonts, out of 8000000 for 9000 + 17784 strings out of 476909 + 327171 string characters out of 5803306 + 1944189 words of memory out of 5000000 + 39416 multiletter control sequences out of 15000+600000 + 564536 words of font info for 91 fonts, out of 8000000 for 9000 14 hyphenation exceptions out of 8191 - 86i,11n,121p,2820b,437s stack positions out of 10000i,1000n,20000p,200000b,200000s + 90i,11n,120p,2820b,442s stack positions out of 10000i,1000n,20000p,200000b,200000s Output written on user_guide_en.pdf (18 pages). diff --git a/inst/guide/user_guide_en.pdf b/inst/guide/user_guide_en.pdf index 33aa4ed8..5008e21f 100644 Binary files a/inst/guide/user_guide_en.pdf and b/inst/guide/user_guide_en.pdf differ diff --git a/inst/guide/user_guide_fr.Rmd b/inst/guide/user_guide_fr.Rmd index a8518b72..89378f63 100644 --- a/inst/guide/user_guide_fr.Rmd +++ b/inst/guide/user_guide_fr.Rmd @@ -144,12 +144,12 @@ Une fois ces nouvelles variables ajoutées au jeu de données initial, l'applica * `peak_steps_5min`: accumulation de pas par minute moyennée sur les 5 meilleures minutes, consécutives ou non. * `peak_steps_1min`: accumulation de pas par minute sur la meilleure minute (même résultat que pour `max_steps_1min`). * `ig`: gradient d'intensité. -* `M1/3`: la valeur de count (en counts/période d'échantillonnage) au-delà de laquelle les 8 heures les plus actives sont accumulées au cours de la journée -* `M120`: la valeur de count (en counts/période d'échantillonnage) au-delà de laquelle les 120 minutes les plus actives sont accumulées au cours de la journée -* `M60`: la valeur de count (en counts/période d'échantillonnage) au-delà de laquelle les 60 minutes les plus actives sont accumulées au cours de la journée -* `M30`: la valeur de count (en counts/période d'échantillonnage) au-delà de laquelle les 30 minutes les plus actives sont accumulées au cours de la journée -* `M15`: la valeur de count (en counts/période d'échantillonnage) au-delà de laquelle les 15 minutes les plus actives sont accumulées au cours de la journée -* `M5`: la valeur de count (en counts/période d'échantillonnage) au-delà de laquelle les 5 minutes les plus actives sont accumulées au cours de la journée +* `M1/3`: la valeur de count (en counts/période d'échantillonnage) à et au-delà de laquelle les 8 heures les plus actives sont accumulées au cours de la journée +* `M120`: la valeur de count (en counts/période d'échantillonnage) à et au-delà de laquelle les 120 minutes les plus actives sont accumulées au cours de la journée +* `M60`: la valeur de count (en counts/période d'échantillonnage) à et au-delà de laquelle les 60 minutes les plus actives sont accumulées au cours de la journée +* `M30`: la valeur de count (en counts/période d'échantillonnage) à et au-delà de laquelle les 30 minutes les plus actives sont accumulées au cours de la journée +* `M15`: la valeur de count (en counts/période d'échantillonnage) à et au-delà de laquelle les 15 minutes les plus actives sont accumulées au cours de la journée +* `M5`: la valeur de count (en counts/période d'échantillonnage) à et au-delà de laquelle les 5 minutes les plus actives sont accumulées au cours de la journée Pour calculer le NAP, la dépense énergétique totale (DET) liée à la période de la journée que l'utilisateur souhaitait analyser est divisée par le MB, qui lui est calculé pour correspondre aussi à la période de la journée à analyser. La DET est obtenue en faisant la somme des kilocalories mesurées durant le temps de port et des kilocalories liées au MB dépensées durant les périodes de non-port (il est supposé que les périodes lors desquelles l'appareil n'était pas porté correspondaient à des périodes de sommeil, durant lesquelles la dépense énergétique est proche du MB), et en multipliant cette somme par 10/9 afin de prendre en compte l'effet thermique des aliments. En principe, le NAP devrait être calculé en utilisant l'ensemble de la journée, pas une période donnée de la journée. Bien sûr, de tels calculs peuvent conduire à sous-estimer la DET et le NAP si l'appareil était enlevé pendant des périodes prolongées d'activité physique, à moins que l'utilisateur ajoute manuellement des périodes d'activité physique dans les espaces de l'application prévus à cet effet comme expliqué plus haut. De plus, même si l'appareil était correctement porté, l'estimation du NAP reste très approximative étant donné qu'à la fois le MB et les kilocalories liées au temps de port étaient estimées à partir de méthodes qui peuvent ne pas être exactes au niveau individuel. diff --git a/inst/guide/user_guide_fr.log b/inst/guide/user_guide_fr.log index 148a6f00..50186981 100644 --- a/inst/guide/user_guide_fr.log +++ b/inst/guide/user_guide_fr.log @@ -1,36 +1,37 @@ -This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex 2023.1.13) 3 FEB 2023 18:25 +This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex 2023.11.29) 26 APR 2024 17:32 entering extended mode restricted \write18 enabled. %&-line parsing enabled. **user_guide_fr.tex (./user_guide_fr.tex -LaTeX2e <2022-11-01> patch level 1 -L3 programming layer <2022-12-17> (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/book.cls -Document Class: book 2022/07/02 v1.4n Standard LaTeX document class +LaTeX2e <2023-11-01> +L3 programming layer <2023-11-09> +(c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/book.cls +Document Class: book 2023/05/17 v1.4n Standard LaTeX document class (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/base/bk10.clo -File: bk10.clo 2022/07/02 v1.4n Standard LaTeX file (size option) +File: bk10.clo 2023/05/17 v1.4n Standard LaTeX file (size option) ) -\c@part=\count181 -\c@chapter=\count182 -\c@section=\count183 -\c@subsection=\count184 -\c@subsubsection=\count185 -\c@paragraph=\count186 -\c@subparagraph=\count187 -\c@figure=\count188 -\c@table=\count189 +\c@part=\count182 +\c@chapter=\count183 +\c@section=\count184 +\c@subsection=\count185 +\c@subsubsection=\count186 +\c@paragraph=\count187 +\c@subparagraph=\count188 +\c@figure=\count189 +\c@table=\count190 \abovecaptionskip=\skip48 \belowcaptionskip=\skip49 \bibindent=\dimen140 ) (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/amsmath/amsmath.sty -Package: amsmath 2022/04/08 v2.17n AMS math features +Package: amsmath 2023/05/13 v2.17o AMS math features \@mathmargin=\skip50 For additional information on amsmath, use the `?' option. 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LaTeX Info: Redefining \addtolength on input line 81. -\calc@Ccount=\count300 +\calc@Ccount=\count301 \calc@Cskip=\skip61 ) (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/etoolbox/etoolbox.sty Package: etoolbox 2020/10/05 v2.5k e-TeX tools for LaTeX (JAW) -\etb@tempcnta=\count301 +\etb@tempcnta=\count302 ) (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/latex/mdwtools/footnote.sty Package: footnote 1997/01/28 1.13 Save footnotes around boxes \fn@notes=\box61 @@ -297,25 +298,23 @@ Package graphics Info: Driver file: xetex.def on input line 107. \csllabelwidth=\skip63 \cslentryspacingunit=\skip64 (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/generic/babel/babel.sty -Package: babel 2022/12/26 3.84 The Babel package -\babel@savecnt=\count302 +Package: babel 2023/11/11 v3.97 The Babel package +\babel@savecnt=\count303 \U@D=\dimen182 \l@unhyphenated=\language4 (c:/Users/pydemullenheim/AppData/Roaming/TinyTeX/texmf-dist/tex/generic/babel/xebabel.def) \bbl@readstream=\read2 -\bbl@dirlevel=\count303 +\bbl@dirlevel=\count304 Package babel Info: You haven't specified a language as a class or package -(babel) option. 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[3] [4 @@ -908,7 +906,7 @@ Package fancyhdr Warning: \headheight is too small (12.0pt): ] Section 3. -Underfull \hbox (badness 3108) in paragraph at lines 180--181 +Underfull \hbox (badness 3108) in paragraph at lines 183--184 []\TU/lmr/m/n/10 L’équation \TU/lmtt/m/n/10 Santos-Lozano et al. (2013) [Older adults] \TU/lmr/m/n/10 ([]Santos-Lozano et al., [] @@ -919,19 +917,21 @@ Section 4. ] [16] [17 ] [18] (./user_guide_fr.aux) + *********** +LaTeX2e <2023-11-01> +L3 programming layer <2023-11-09> + *********** LaTeX Warning: There were multiply-defined labels. -Package rerunfilecheck Info: File `user_guide_fr.out' has not changed. -(rerunfilecheck) Checksum: 7E0432D8B7FC2F82B1CB54FCC3BD0092;1428. ) Here is how much of TeX's memory you used: - 18796 strings out of 478757 - 348893 string characters out of 5847534 - 1869973 words of memory out of 5000000 - 38558 multiletter control sequences out of 15000+600000 - 518754 words of font info for 87 fonts, out of 8000000 for 9000 + 18958 strings out of 476909 + 349169 string characters out of 5803306 + 1944189 words of memory out of 5000000 + 40576 multiletter control sequences out of 15000+600000 + 564536 words of font info for 91 fonts, out of 8000000 for 9000 14 hyphenation exceptions out of 8191 - 86i,12n,121p,3291b,451s stack positions out of 10000i,1000n,20000p,200000b,200000s + 90i,12n,120p,3291b,473s stack positions out of 10000i,1000n,20000p,200000b,200000s Output written on user_guide_fr.pdf (18 pages). diff --git a/inst/guide/user_guide_fr.pdf b/inst/guide/user_guide_fr.pdf index ff9b99b5..55ae9897 100644 Binary files a/inst/guide/user_guide_fr.pdf and b/inst/guide/user_guide_fr.pdf differ diff --git a/inst/report/report_en_long.Rmd b/inst/report/report_en_long.Rmd index 4d2fe402..f569451e 100644 --- a/inst/report/report_en_long.Rmd +++ b/inst/report/report_en_long.Rmd @@ -580,7 +580,7 @@ reactable::reactable( ) ``` -### Radar view based on means of valid days +### Radar view based on the means of the valid days ```{r, fig.align = "center", out.width='50%', out.height='50%', fig.width=8, fig.height=8} cor_factor <- 60 / params$epoch diff --git a/inst/report/report_en_short.Rmd b/inst/report/report_en_short.Rmd index 362db570..a576be3c 100644 --- a/inst/report/report_en_short.Rmd +++ b/inst/report/report_en_short.Rmd @@ -233,7 +233,7 @@ create_flextable_summary( ) ``` -### Radar view based on means of valid days +### Radar view based on the means of the valid days ```{r, fig.align = "center", out.width='50%', out.height='50%', fig.width=8, fig.height=8} cor_factor <- 60 / params$epoch