|

In activAnalyzer: A 'Shiny' App to Analyze Accelerometer-Measured Daily Physical Behavior Data

knitr::opts_chunk$set(echo = TRUE, message=FALSE, warning=FALSE, echo = FALSE)
library(magrittr)
library(ggplot2)
library(patchwork)

sex <- ifelse(params$sex == "male", "masculin", 
              ifelse(params$sex == "female", "féminin",
                     "non défini"))
position <- ifelse(params$position == "hip", "hanche", 
              ifelse(params$position == "wrist", "poignet",
                     ifelse(params$position == "thigh", "cuisse",
                            ifelse(params$position == "ankle", "cheville", "NA"))))

side <- ifelse(params$side == "right", "droit", 
              ifelse(params$side == "left", "gauche",
                     "non défini"))

axis_weartime <- ifelse(params$axis_weartime == "vertical axis", "l'axe vertical", 
              ifelse(params$axis_weartime == "vector magnitude", "le vecteur magnitude",
                     "non défini"))

axis_mvpa <- ifelse(params$axis_mvpa == "vertical axis", "axe vertical", 
              ifelse(params$axis_mvpa == "vector magnitude", "vecteur magnitude",
                     "non défini"))

options("scipen"=100, "digits"=4)

Informations

Patient : r params$patient_surname r params$patient_name | Date : r Sys.Date() | Évaluateur : r params$assessor_surname r params$assessor_name

Age : r params$age ans | Sexe : r sex | Masse : r params$weight kg | Période de mesure : r format(params$start_date, "%d/%m/%Y %H:%M:%S") au r format(params$end_date, "%d/%m/%Y %H:%M:%S")

Appareil : r params$device | Position : r position | Côté : r side | Fréquence d'échantillonnage : r params$sampling_rate Hz | Filtre : r params$filter

'Epoch' : r params$epoch s | Temps de non-port : Basé sur r axis_weartime, intervalle de r params$frame_size min avec zéro count pour la détection du temps de non-port, intervalle de r params$allowanceFrame_size min avec counts différents de 0 autorisé durant une période de non-port, intervalle de r params$streamFrame_size min avec zéro count autour de la période d'activité détectée pour confirmer le non-port

Période journalière considérée pour compter le temps de port : de r params$start_day_analysis à r params$end_day_analysis

Nombre minimum d'heures avec temps de port pour valider un jour: r params$minimum_wear_time_for_analysis heures

Résumé

diff_raw <-
  ggplot(data = data.frame(x = 0.1, y = 0.6, label = params$cppac_diff_raw), aes(x, y, label = paste0(label, " / 40"))) +
  geom_text(size = 17, color = "white", fontface = "bold", hjust = 0) +
  coord_cartesian(xlim = c(0, 1), ylim = c(0, 1), expand = FALSE) +
  annotate("text", x = 0.1, y = 0.2, label = "Score de difficulté (brut)", color = "white", fontface = "bold", hjust = 0, size = 6) +
  theme_void() +
  theme(
    panel.background = element_rect(fill = "#00CEF1", color = "white", size = 10)
  )

amount_raw <-
  ggplot(data = data.frame(x = 0.1, y = 0.6, label = params$cppac_amount_raw), aes(x, y, label = paste0(label, " / 15"))) +
  geom_text(size = 17, color = "white", fontface = "bold", hjust = 0) +
  coord_cartesian(xlim = c(0, 1), ylim = c(0, 1), expand = FALSE) +
  annotate("text", x = 0.1, y = 0.2, label = "Score de quantité (brut)", color = "white", fontface = "bold", hjust = 0, size = 6) +
  theme_void() +
  theme(
    panel.background = element_rect(fill = "#39cccc", color = "white", size = 10)
  )

total_raw <-
  ggplot(data = data.frame(x = 0.1, y = 0.6, label = params$cppac_total_raw), aes(x, y, label = paste0(label, " / 55"))) +
  geom_text(size = 17, color = "white", fontface = "bold", hjust = 0) +
  coord_cartesian(xlim = c(0, 1), ylim = c(0, 1), expand = FALSE) +
  annotate("text", x = 0.1, y = 0.2, label = "Score total (brut)", color = "white", fontface = "bold", hjust = 0, size = 6) +
  theme_void() +
  theme(
    panel.background = element_rect(fill = "#605ca8", color = "white", size = 10)
  )

if (params$rendered_by_shiny)
  shiny::setProgress(0.5)  # set progress to 50%

diff_rasch <-
  ggplot(data = data.frame(x = 0.1, y = 0.6, label = params$cppac_diff_rasch), aes(x, y, label = paste0(label, " / 100"))) +
  geom_text(size = 17, color = "white", fontface = "bold", hjust = 0) +
  coord_cartesian(xlim = c(0, 1), ylim = c(0, 1), expand = FALSE) +
  annotate("text", x = 0.1, y = 0.2, label = "Score de difficulté (Rasch)", color = "white", fontface = "bold", hjust = 0, size = 6) +
  theme_void() +
  theme(
    panel.background = element_rect(fill = "#00CEF1", color = "white", size = 10)
  )

amount_rasch <-
  ggplot(data = data.frame(x = 0.1, y = 0.6, label = params$cppac_amount_rasch), aes(x, y, label = paste0(label, " / 100"))) +
  geom_text(size = 17, color = "white", fontface = "bold", hjust = 0) +
  coord_cartesian(xlim = c(0, 1), ylim = c(0, 1), expand = FALSE) +
  annotate("text", x = 0.1, y = 0.2, label = "Score de quantité (Rasch)", color = "white", fontface = "bold", hjust = 0, size = 6) +
  theme_void() +
  theme(
    panel.background = element_rect(fill = "#39cccc", color = "white", size = 10)
  )

total_rasch <-
  ggplot(data = data.frame(x = 0.1, y = 0.6, label = params$cppac_total_rasch), aes(x, y, label = paste0(label, " / 100"))) +
  geom_text(size = 17, color = "white", fontface = "bold", hjust = 0) +
  coord_cartesian(xlim = c(0, 1), ylim = c(0, 1), expand = FALSE) +
  annotate("text", x = 0.1, y = 0.2, label = "Score total (Rasch)", color = "white", fontface = "bold", hjust = 0, size = 6) +
  theme_void() +
  theme(
    panel.background = element_rect(fill = "#605ca8", color = "white", size = 10)
  )

(diff_raw | amount_raw | total_raw) / (diff_rasch | amount_rasch | total_rasch)

if (params$rendered_by_shiny)
  shiny::setProgress(1)  # set progress to 100%

\pagebreak

Détails

flextable::set_flextable_defaults(fonts_ignore = TRUE)
flextable::flextable(params$cppac_table) %>%
   flextable::theme_zebra() %>%
   flextable::align(align = "left", part = "all" ) %>%
   flextable::width(width = 1.9) %>%
   flextable::width(j = "Item", width = 2.3) %>%
   flextable::align(j = "Score de difficulté", align = "center", part = "body") %>%
   flextable::align(j = "Score de quantité", align = "center", part = "body") %>%
   flextable::align(j = "Score de difficulté", align = "center", part = "header") %>%
   flextable::align(j = "Score de quantité", align = "center", part = "header")

activAnalyzer documentation built on Sept. 24, 2024, 1:07 a.m.