## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----warning = FALSE, message = FALSE, eval = FALSE--------------------------- # devtools::install_github("barnzilla/capl", upgrade = "never", build_vignettes = TRUE, force = TRUE) # library(capl) ## ----warning = FALSE, message = FALSE, echo = FALSE--------------------------- library(capl) ## ----warning = FALSE, message = FALSE, eval = FALSE--------------------------- # browseVignettes("capl") ## ----warning = FALSE, error = FALSE, eval = FALSE----------------------------- # data <- import_capl_data( # file_path = "c:/path/to/raw-data.xlsx", # sheet_name = "Sheet1" # ) ## ----warning = FALSE, message = FALSE, eval = FALSE--------------------------- # ?get_missing_capl_variables ## ----warning = FALSE, message = FALSE----------------------------------------- data("capl_demo_data") ## ----warning = FALSE, message = FALSE----------------------------------------- str(capl_demo_data) ## ----warning = FALSE, message = FALSE----------------------------------------- colnames(capl_demo_data) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data2 <- get_capl_demo_data(n = 10000) ## ----warning = FALSE, message = FALSE----------------------------------------- str(capl_demo_data2) ## ----warning = FALSE, message = FALSE, eval = FALSE--------------------------- # export_capl_data(capl_demo_data2, "c:/path/to/store/capl_demo_data2.xlsx") ## ----------------------------------------------------------------------------- # Create fake data raw_data <- data.frame( age_years = sample(8:12, 100, replace = TRUE), genders = sample(c("girl", "boy"), 100, replace = TRUE, prob = c(0.51, 0.49)), step_counts1 = sample(1000:30000, 100, replace = TRUE), step_counts2 = sample(1000:30000, 100, replace = TRUE), step_counts3 = sample(1000:30000, 100, replace = TRUE), step_counts4 = sample(1000:30000, 100, replace = TRUE), step_counts5 = sample(1000:30000, 100, replace = TRUE), step_counts6 = sample(1000:30000, 100, replace = TRUE), step_counts7 = sample(1000:30000, 100, replace = TRUE) ) # Examine the structure of this data str(raw_data) # Rename the variables raw_data <- rename_variable( x = raw_data, search = c( "age_years", "genders", "step_counts1", "step_counts2", "step_counts3", "step_counts4", "step_counts5", "step_counts6", "step_counts7" ), replace = c( "age", "gender", "steps1", "steps2", "steps3", "steps4", "steps5", "steps6", "steps7" ) ) # Examine the structure of this data str(raw_data) ## ----eval = FALSE------------------------------------------------------------- # ?validate_age # ?validate_character # ?validate_domain_score # ?validate_gender # ?validate_integer # ?validate_number # ?validate_scale # ?validate_steps ## ----------------------------------------------------------------------------- validated_age <- validate_age(c(7, 8, 9, 10, 11, 12, 13, "", NA, "12", 8.5)) ## ----------------------------------------------------------------------------- validated_age ## ----------------------------------------------------------------------------- validated_gender <- validate_gender(c("Girl", "GIRL", "g", "G", "Female", "f", "F", "", NA, 1)) validated_gender ## ----------------------------------------------------------------------------- validated_gender <- validate_gender(c("Boy", "BOY", "b", "B", "Male", "m", "M", "", NA, 0)) validated_gender ## ----warning = FALSE, message = FALSE----------------------------------------- capl_results <- get_capl(raw_data = capl_demo_data, sort = "asis") ## ----------------------------------------------------------------------------- str(capl_results, list.len = nrow(capl_results)) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pacer_laps_20m <- get_pacer_20m_laps( lap_distance = capl_demo_data$pacer_lap_distance, laps_run = capl_demo_data$pacer_laps ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pacer_laps_20m ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pacer_score <- get_pacer_score(capl_demo_data$pacer_laps_20m) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pacer_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pacer_interpretation <- get_capl_interpretation( age = capl_demo_data$age, gender = capl_demo_data$gender, score = capl_demo_data$pacer_score, protocol = "pacer" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pacer_interpretation ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$plank_score <- get_plank_score(capl_demo_data$plank_time) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$plank_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$plank_interpretation <- get_capl_interpretation( age = capl_demo_data$age, gender = capl_demo_data$gender, score = capl_demo_data$plank_time, protocol = "plank" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$plank_interpretation ## ----warning = FALSE, message = FALSE----------------------------------------- # Trial 1 capl_demo_data$camsa_time_score1 <- get_camsa_time_score(capl_demo_data$camsa_time1) # Trial 2 capl_demo_data$camsa_time_score2 <- get_camsa_time_score(capl_demo_data$camsa_time2) ## ----warning = FALSE, message = FALSE----------------------------------------- # Time scores for trial 1 capl_demo_data$camsa_time_score1 ## ----warning = FALSE, message = FALSE----------------------------------------- # Time scores for trial 2 capl_demo_data$camsa_time_score2 ## ----warning = FALSE, message = FALSE----------------------------------------- # Trial 1 capl_demo_data$camsa_skill_time_score1 <- get_camsa_skill_time_score( camsa_skill_score = capl_demo_data$camsa_skill_score1, camsa_time_score = capl_demo_data$camsa_time_score1 ) # Trial 2 capl_demo_data$camsa_skill_time_score2 <- get_camsa_skill_time_score( camsa_skill_score = capl_demo_data$camsa_skill_score2, camsa_time_score = capl_demo_data$camsa_time_score2 ) ## ----warning = FALSE, message = FALSE----------------------------------------- # Time scores for trial 1 capl_demo_data$camsa_skill_time_score1 ## ----warning = FALSE, message = FALSE----------------------------------------- # Time scores for trial 2 capl_demo_data$camsa_skill_time_score2 ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$camsa_score <- get_camsa_score( camsa_skill_time_score1 = capl_demo_data$camsa_skill_time_score1, camsa_skill_time_score2 = capl_demo_data$camsa_skill_time_score2 ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$camsa_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$camsa_interpretation <- get_capl_interpretation( age = capl_demo_data$age, gender = capl_demo_data$gender, score = capl_demo_data$camsa_score, protocol = "camsa" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$camsa_interpretation ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pc_score <- get_pc_score( pacer_score = capl_demo_data$pacer_score, plank_score = capl_demo_data$plank_score, camsa_score = capl_demo_data$camsa_score ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pc_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pc_interpretation <- get_capl_interpretation( age = capl_demo_data$age, gender = capl_demo_data$gender, score = capl_demo_data$pc_score, protocol = "pc" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pc_interpretation ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pc_status <- get_capl_domain_status( x = capl_demo_data, domain = "pc" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pc_status ## ----warning = FALSE, message = FALSE----------------------------------------- step_df <- get_step_average(capl_demo_data) ## ----warning = FALSE, message = FALSE----------------------------------------- str(step_df) ## ----warning = FALSE, message = FALSE----------------------------------------- # Add the step average to the dataset capl_demo_data$step_average <- step_df$step_average ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$step_average ## ----warning = FALSE, message = FALSE----------------------------------------- wear_time1 <- get_pedometer_wear_time( time_on = capl_demo_data$time_on1, time_off = capl_demo_data$time_off1, non_wear_time = capl_demo_data$non_wear_time1 ) ## ----warning = FALSE, message = FALSE----------------------------------------- wear_time1 ## ----warning = FALSE, message = FALSE----------------------------------------- valid_steps1 <- validate_steps( steps = capl_demo_data$steps1, wear_time = wear_time1 ) ## ----warning = FALSE, message = FALSE----------------------------------------- valid_steps1 ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$step_score <- get_step_score(capl_demo_data$step_average) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$step_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$self_report_pa_score <- get_self_report_pa_score(capl_demo_data$self_report_pa) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$self_report_pa_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$db_score <- get_db_score( step_score = capl_demo_data$step_score, self_report_pa_score = capl_demo_data$self_report_pa_score ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$db_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$db_interpretation <- get_capl_interpretation( age = capl_demo_data$age, gender = capl_demo_data$gender, score = capl_demo_data$db_score, protocol = "db" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$db_interpretation ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$db_status <- get_capl_domain_status( x = capl_demo_data, domain = "db" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$db_status ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$predilection_score <- get_predilection_score( csappa1 = capl_demo_data$csappa1, csappa3 = capl_demo_data$csappa3, csappa5 = capl_demo_data$csappa5 ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$predilection_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$adequacy_score <- get_adequacy_score( csappa2 = capl_demo_data$csappa2, csappa4 = capl_demo_data$csappa4, csappa6 = capl_demo_data$csappa6 ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$adequacy_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$intrinsic_motivation_score <- get_intrinsic_motivation_score( why_active1 = capl_demo_data$why_active1, why_active2 = capl_demo_data$why_active2, why_active3 = capl_demo_data$why_active3 ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$intrinsic_motivation_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pa_competence_score <- get_pa_competence_score( feelings_about_pa1 = capl_demo_data$feelings_about_pa1, feelings_about_pa2 = capl_demo_data$feelings_about_pa2, feelings_about_pa3 = capl_demo_data$feelings_about_pa3 ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pa_competence_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$mc_score <- get_mc_score( predilection_score = capl_demo_data$predilection_score, adequacy_score = capl_demo_data$adequacy_score, intrinsic_motivation_score = capl_demo_data$intrinsic_motivation_score, pa_competence_score = capl_demo_data$pa_competence_score ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$mc_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$mc_interpretation <- get_capl_interpretation( age = capl_demo_data$age, gender = capl_demo_data$gender, score = capl_demo_data$mc_score, protocol = "mc" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$mc_interpretation ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$mc_status <- get_capl_domain_status( x = capl_demo_data, domain = "mc" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$mc_status ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pa_guideline_score <- get_binary_score( capl_demo_data$pa_guideline, c(3, "60 minutes or 1 hour") ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$pa_guideline_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$crf_means_score <- get_binary_score( capl_demo_data$crf_means, c(2, "How well the heart can pump blood and the lungs can provide oxygen") ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$crf_means_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$ms_means_score <- get_binary_score( capl_demo_data$ms_means, c(1, "How well the muscles can push, pull or stretch") ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$ms_means_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$sports_skill_score <- get_binary_score( capl_demo_data$sports_skill, c(4, "Watch a video, take a lesson or have a coach teach you how to kick and catch") ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$sports_skill_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$fill_in_the_blanks_score <- get_fill_in_the_blanks_score( pa_is = capl_demo_data$pa_is, pa_is_also = capl_demo_data$pa_is_also, improve = capl_demo_data$improve, increase = capl_demo_data$increase, when_cooling_down = capl_demo_data$when_cooling_down, heart_rate = capl_demo_data$heart_rate ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$fill_in_the_blanks_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$ku_score <- get_ku_score( pa_guideline_score = capl_demo_data$pa_guideline_score, crf_means_score = capl_demo_data$crf_means_score, ms_means_score = capl_demo_data$ms_means_score, sports_skill_score = capl_demo_data$sports_skill_score, fill_in_the_blanks_score = capl_demo_data$fill_in_the_blanks_score ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$ku_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$ku_interpretation <- get_capl_interpretation( age = capl_demo_data$age, gender = capl_demo_data$gender, score = capl_demo_data$ku_score, protocol = "ku" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$ku_interpretation ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$ku_status <- get_capl_domain_status( x = capl_demo_data, domain = "ku" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$ku_status ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$capl_score <- get_capl_score( pc_score = capl_demo_data$pc_score, db_score = capl_demo_data$db_score, mc_score = capl_demo_data$mc_score, ku_score = capl_demo_data$ku_score ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$capl_score ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$capl_interpretation <- get_capl_interpretation( age = capl_demo_data$age, gender = capl_demo_data$gender, score = capl_demo_data$capl_score, protocol = "capl" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$capl_interpretation ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$capl_status <- get_capl_domain_status( x = capl_demo_data, domain = "capl" ) ## ----warning = FALSE, message = FALSE----------------------------------------- capl_demo_data$capl_status ## ----warning = FALSE, message = FALSE, fig.width = 7.25, fig.height = 7.25---- get_capl_bar_plot( score = capl_results$pc_score, interpretation = capl_results$pc_interpretation, x_label = "Interpretation", y_label = "Physical competence domain score (/30)" ) ## ----warning = FALSE, message = FALSE, fig.width = 7.25, fig.height = 7.25---- get_capl_bar_plot( score = capl_results$db_score, interpretation = capl_results$db_interpretation, x_label = "Interpretation", y_label = "Daily behaviour domain score (/30)", colors = c("#daf7a6", "#ffc300", "#ff5733", "#c70039") ) ## ----warning = FALSE, message = FALSE, eval = FALSE--------------------------- # export_capl_data( # x = capl_results, # file_path = "c:/path/to/store/capl-results.xlsx" # ) # # export_capl_data( # x = capl_results, # type = "spss", # file_path = "c:/path/to/store/capl-results.sav" # )