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Merge pull request #942 from wadpac/issue938_dictionaryPart5
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@@ -11,3 +11,4 @@ RELEASE_CYCLE.md | |
| ^docs$ | ||
| ^pkgdown$ | ||
| ^vignettes/chapter*.Rmd | ||
| ^data-raw$ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,278 @@ | ||
| g.report.part5_dictionary = function(metadatadir, sep_reports = ",") { | ||
| # internal function to get class ------------------------------------------ | ||
| getclass = function(x) { | ||
| if (length(x) == 0) return(NULL) | ||
| class = NULL | ||
| if (grepl("2", x)) x = unlist(strsplit(x, "2")) | ||
| for (i in 1:length(x)) { | ||
| if (x[i] == "IN") class[i] = "inactivity" | ||
| if (x[i] == "LIG" | x[i] == "LIPA") class[i] = "light physical activity" | ||
| if (x[i] == "MOD") class[i] = "moderate physical activity" | ||
| if (x[i] == "VIG") class[i] = "vigorous physical activity" | ||
| if (x[i] == "MVPA") class[i] = "moderate-to-vigorous physical activity" | ||
| if (x[i] == "PA") class[i] = "physical activity" | ||
| if (x[i] == "sleep") class[i] = "sleep" | ||
| if (x[i] == "wake") class[i] = "awake" | ||
| if (x[i] == "nonwear") class[i] = "non-wear time" | ||
| if (x[i] == "mostactive60min") class = "the most active 60 minutes of the day are accumulated" | ||
| if (x[i] == "mostactive30min") class = "the most active 30 minutes of the day are accumulated" | ||
| } | ||
| if (length(class) == 2) class = paste(class[1], "to", class[2]) | ||
| return(class) | ||
| } | ||
| # ------------------------------------------------------------------------- | ||
| # main script ------------------------------------------------------------- | ||
| # ------------------------------------------------------------------------- | ||
| # identify individual reports | ||
| reports = dir(file.path(metadatadir, "results"), full.names = TRUE, | ||
| pattern = "^part5.*\\.csv$") | ||
| # Select one daysummary, personsummary, and Segment report as variables are the same across configurations | ||
| ds = grep("^part5_daysummary", basename(reports))[1] | ||
| ps = grep("^part5_personsummary", basename(reports))[1] | ||
| reports = reports[c(ds, ps)] | ||
| # read col names of each report and derive definitions | ||
| for (ri in 1:length(reports)) { | ||
| # read report | ||
| R = data.table::fread(reports[ri], verbose = FALSE, nrows = 2) | ||
| cnames = colnames(R) | ||
| # initialise dictionary | ||
| dictionary = data.frame(Variable = cnames, | ||
| Definition = NA) | ||
| # get definitions | ||
| for (coli in 1:length(cnames)) { | ||
| # definitions will be a combination of what, window, when (only for LUX segments), class, unit | ||
| what = window = class = unit = NULL | ||
| # get variable names from baseDictionary | ||
| nam = gsub("_pla|_wei|_WD|_WE", "", cnames[coli]) | ||
| if (grepl("Nvalid", cnames[coli])) nam = cnames[coli] | ||
| if (nam %in% names(baseDictionary)) { | ||
| what = baseDictionary[[nam]] | ||
| } | ||
| # if the variable is not in baseDictionary, extract definition: | ||
| if (is.null(what)) { | ||
| # split up variable name | ||
| elements = unlist(strsplit(cnames[coli], "[.]|_")) | ||
| # WHAT ------------------------------------------------------------- | ||
| if ("dur" %in% elements | "nonwear" %in% elements) { | ||
| what = "Time accumulated" | ||
| } else if ("ACC" %in% elements) { | ||
| what = "Mean acceleration" | ||
| } else if ("Nbouts" %in% elements) { | ||
| what = "Number of bouts" | ||
| } else if ("Nblocks" %in% elements) { | ||
| what = "Number of blocks (defined as consecutive series of epochs with the same behavioural class)" | ||
| } else if ("quantile" %in% elements) { | ||
| what = "Acceleration above which (percentile)" | ||
| } else if ("LUX" %in% elements) { | ||
| if ("min" %in% elements | "above1000" %in% elements) { | ||
| # time in lux ranges | ||
| what = "Time accumulated with LUX" | ||
| if ("above1000" %in% elements) { | ||
| numbers = 1000 | ||
| } else { | ||
| numbers = suppressWarnings(as.numeric(elements)) | ||
| numbers = numbers[!is.na(numbers)] | ||
| } | ||
| if (any(numbers == Inf) | length(numbers) == 1) { | ||
| thresholds = paste("above", numbers[1]) | ||
| } else if (length(numbers) == 2) { | ||
| thresholds = paste("between", numbers[1], "and", numbers[2]) | ||
| } else { | ||
| thresholds = "" | ||
| } | ||
| what = paste(what, thresholds, "luxes") | ||
| unit = "(minutes)" | ||
| } else if ("mean" %in% elements) { | ||
| what = "Mean LUX value" | ||
| if ("mvpa" %in% elements) what = paste(what, "in moderate-to-vigorous physical activity time") | ||
| unit = "(luxes)" | ||
| } else if ("max" %in% elements) { | ||
| what = "Maximum LUX value" | ||
| unit = "(luxes)" | ||
| } else if ("timeawake" %in% elements) { | ||
| what = "Time classified as awake" | ||
| unit = "(minutes)" | ||
| } else if ("imputed" %in% elements) { | ||
| what = "Time in which the LUX has been imputed" | ||
| unit = "(minutes)" | ||
| } else if ("ignored" %in% elements) { | ||
| what = "Time in which the LUX has been ignored" | ||
| unit = "(minutes)" | ||
| } | ||
| # lux segments | ||
| if (any(grepl("hr", elements))) { | ||
| t1 = elements[grep("hr", elements)]; t1 = gsub("hr", ":00", t1) | ||
| t0 = elements[grep("hr", elements) - 1] | ||
| if (nchar(t0) == 1) t0 = paste0(t0, ":00") | ||
| what = paste(what, "in the segment from", t0, "to", t1) | ||
| } | ||
| } | ||
| # fragmentation metrics | ||
| if ("FRAG" %in% elements) { | ||
| what_bu = tolower(what) | ||
| what = "Fragmentation analysis:" | ||
| if ("TP" %in% elements) { | ||
| what = paste(what, "transition probability (%)") | ||
| } else if ("Nfrag" %in% elements) { | ||
| what = paste(what, "number of fragments") | ||
| } else if ("NFragPM" %in% elements) { | ||
| what = paste(what, "number of fragments per minute") | ||
| } else if ("mean" %in% elements) { | ||
| what = paste(what, "mean duration in the") | ||
| } else if ("Gini" %in% elements) { | ||
| what = paste(what, "Gini inequality index as calculated in the ineq R package") | ||
| } else if ("CoV" %in% elements) { | ||
| what = paste(what, "Coefficient of variance as proposed in https://shorturl.at/nsDU9") | ||
| } else if ("alpha" %in% elements) { | ||
| what = paste(what, "Alpha power law exponent metric as proposed in https://shorturl.at/gwzB8") | ||
| } else if ("x0" %in% elements) { | ||
| what = paste(what, "x0.5 power law exponent metric as proposed in https://shorturl.at/gwzB8") | ||
| } else if ("W0" %in% elements) { | ||
| what = paste(what, "W0.5 power law exponent metric as proposed in https://shorturl.at/gwzB8") | ||
| } else if ("SD" %in% elements) { | ||
| what = paste(what, "standard deviation in the") | ||
| } | ||
| what = paste(what, what_bu) | ||
| } | ||
| # WINDOW ----------------------------------------------------------- | ||
| if ("day" %in% elements & "spt" %in% elements) { | ||
| window = "during the waking time and sleep period time (i.e., full window)" | ||
| } else if ("day" %in% elements) { | ||
| window = "during the waking time" | ||
| } else if ("spt" %in% elements) { | ||
| window = "during the sleep period time" | ||
| } | ||
| # CLASS ------------------------------------------------------------ | ||
| classes = c("IN", "LIG", "LIPA", "MOD", "VIG", "MVPA", "PA", | ||
| "sleep", "nonwear", "mostactive60min", "mostactive30min", | ||
| "IN2PA", "PA2IN", "IN2LIPA", "IN2MVPA", "sleep2wake", "wake2sleep") | ||
| x = elements[which(elements %in% classes)] | ||
| class = getclass(x) | ||
| # sleep efficiency (overwrite prev classification as sleep) | ||
| if ("sleep" %in% elements & "efficiency" %in% elements) { | ||
| class = "Sleep efficiency" | ||
| unit = "(%)" | ||
| } | ||
| # wakefulness after sleep onset (overwrite prev classification of intensity) | ||
| if ("wake" %in% elements) class = paste("awake", class) | ||
| # bouts | ||
| if ("bts" %in% elements & !("Nbouts" %in% elements)) { | ||
| numbers = suppressWarnings(as.numeric(elements)) | ||
| boutdur = numbers[!is.na(numbers)] | ||
| class = paste("bouts of", paste(boutdur, collapse = "-"), "min", class) | ||
| } | ||
| # unbouted time | ||
| if ("unbt" %in% elements & !("Nbouts" %in% elements)) { | ||
| intensity = elements[which(elements %in% c("IN", "LIG", "MOD", "VIG"))] | ||
| if (intensity %in% c("MOD", "VIG")) intensity = "MVPA" | ||
| look4 = paste("dur_day", intensity, "bts", sep = "_") | ||
| boutVars = grep(look4, cnames, value = TRUE) | ||
| boutdurs = c() | ||
| for (i in 1:length(boutVars)) { | ||
| x = unlist(strsplit(boutVars[i], split = "_")) | ||
| numbers = suppressWarnings(as.numeric(x)) | ||
| boutdurs = c(boutdurs, numbers[!is.na(numbers)]) | ||
| } | ||
| minboutdur = min(boutdurs) | ||
| class = paste("unbouted", class, paste0("(",0,"-",minboutdur, " min)")) | ||
| } | ||
| # intensity gradient | ||
| if ("ig" %in% elements) { | ||
| if ("gradient" %in% elements) class = "Intensity gradient" | ||
| if ("rsquared" %in% elements) class = paste("R-squared from the log-log time to intensity regression to calculate the intensity gradient") | ||
| if ("intercept" %in% elements) class = paste("Intercept from the log-log time to intensity regression to calculate the intensity gradient") | ||
| } | ||
| # connector (in) | ||
| if (!is.null(class)) { | ||
| if (class != "Sleep efficiency" | ||
| & substr(class, 1, 8) != "the most" | ||
| & !("ig" %in% elements)) class = paste("in", class) | ||
| } | ||
| # UNITS ------------------------------------------------------------------- | ||
| if ("min" %in% elements) { | ||
| unit = "(minutes)" | ||
| } else if ("mg" %in% elements) { | ||
| unit = "(mili-gravity units)" | ||
| } else if ("perc" %in% elements) { | ||
| unit = "(%)" | ||
| } | ||
| # ------------------------------------------------------------------ | ||
| # Rest of column names... | ||
| if (is.null(what)) { | ||
| if ("sleeponset" %in% elements | "wakeup" %in% elements) { | ||
| if ("sleeponset" %in% elements) what = "Sleep onset time" | ||
| if ("wakeup" %in% elements) what = "Sleep onset time" | ||
| if ("ts" %in% elements) { | ||
| unit = "(hh:mm:ss)" | ||
| } else { | ||
| unit = "(hours from previous midnight)" | ||
| } | ||
| } else if ((substr(elements[1], 1, 1) == "L" | substr(elements[1], 1, 1) == "M") | ||
| & elements[1] != "LUX") { | ||
| # LX and MX metrics | ||
| # what | ||
| if (grepl("TIME", elements[1])) { | ||
| what = "Starting time" | ||
| unit = "(timestamp)" | ||
| if ("num" %in% elements) { | ||
| unit = "(timestamp)" | ||
| } | ||
| } else if (grepl("VALUE", elements[1])) { | ||
| what = "Mean acceleration" | ||
| unit = "(mili-gravity units)" | ||
| } else if ("peakLUX" %in% elements) { | ||
| if ("mean" %in% elements) { | ||
| what = "Mean peak Lux" | ||
| } else if ("max" %in% elements) { | ||
| what = "Max peak Lux" | ||
| } | ||
| } | ||
| # class | ||
| X = as.numeric(gsub("\\D", "", elements))[1] | ||
| if (substr(elements[1], 1, 1) == "L") { | ||
| class = paste("during the", X, "consecutive hours with the lowest acceleration") | ||
| } else if (substr(elements[1], 1, 1) == "M") { | ||
| class = paste("during the", X, "consecutive hours with the highest acceleration") | ||
| } | ||
| } else if ("daytype" %in% elements) { | ||
| what = "WD = weekday; WE = weekend day" | ||
| } else { | ||
| what = "" | ||
| } | ||
| } | ||
| } | ||
| # build up definition | ||
| def = paste(what, class, window, unit) | ||
| # only for personsummary - aggregation method | ||
| if (grepl("personsummary", reports[ri])) { | ||
| agg = NULL | ||
| if (!grepl("Nvalid", cnames[coli])) { | ||
| if ("pla" %in% elements) agg = "- plain average" | ||
| if ("wei" %in% elements) agg = "- weighted average" | ||
| if ("WD" %in% elements) agg = "- weekdays average" | ||
| if ("WE" %in% elements) agg = "- weekend days average" | ||
| } else { | ||
| # adapt definition of valid days to part 5 reports | ||
| def = gsub("part 2, 4, and 5", "part 5", def) | ||
| } | ||
| def = paste(def, agg) | ||
| } | ||
| def = gsub("\\s+", " ", def) # this removes extra spaces | ||
| def = gsub("^ ", "", def) # this removes leading spaces | ||
|
|
||
| # if window and class have not been identified, then return blank definition | ||
| if (is.null(what) & is.null(class)) def = NA | ||
|
|
||
| # store definition | ||
| dictionary[coli, "Definition"] = def | ||
| } | ||
| # write csv reports with data dictionaries | ||
| directory = file.path(metadatadir, "results", "variableDictionary/") | ||
| if (!dir.exists(directory)) dir.create(directory) | ||
| fn = gsub("part5_", "part5_dictionary_", basename(reports[ri])) | ||
| fn = unlist(strsplit(fn, "_MM|_WW|_OO"))[1] | ||
| fn = paste0(fn, ".csv") | ||
| data.table::fwrite(dictionary, file = file.path(directory, fn), | ||
| row.names = FALSE, na = "", sep = sep_reports) | ||
| } | ||
| } |
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