#' Evaluate entire MAVEn dataset
#'
#' @param datadir data directory
#' @param outdir name of output directory. Defaults to "output"
#' @param maven_datafile name of data file to be evaluated. Must be ".csv".
#' @param maven_experiment name of experiment
#' @param interval specified interval for activity calculations. Must be in secoonds and defaults to 60.
#' @param activity_baseline Activity measurement baseline. Used to exclude values from dataset.
#' @param activity_threshold Activity threshold used for calculating activity status (e.g. inactive vs. active)
#' @param figures figures to be produced. Select from "overview", "diag", or "trend". Supply all three in list if you want all to be created.
#'
#' @export
#'
evaluate_maven <- function(datadir = "", outdir = NULL,
maven_datafile = "maven_output.csv",
interval = 60,
activity_baseline = 0.01,
activity_threshold = 1,
figures = c("trend","diag","overview")){
maven_experiment_name <- strsplit(split = ".csv", maven_datafile)[[1]]
outdir <- paste0("./output/analysis_",format(Sys.time(), "%Y%m%d-%H%M"),
"_", maven_experiment_name)
fpath <- file.path(outdir)
if(!dir.exists(fpath)){
dir.create(fpath)
}
# Load data
maven_raw <- read_maven(datadir = datadir,
maven_datafile = maven_datafile, baseline = T)
maven <- read_maven(datadir = datadir,
maven_datafile = maven_datafile, baseline = F)
# assign a cycle
maven.cycle <- assign_cyclenumber(maven)
# animal metabolism
animal_metabolism <- extract_metabolism(maven.cycle)
metabolism_summary_cycle <- summarize_metabolism(animal_metabolism,
type = "by_cycle")
#animal activity
animal_activity <- extract_activity(maven.cycle, metabolism_summary_cycle,
interval = interval,
activity_baseline = activity_baseline)
activity_summary_cycle <- summarize_activity(animal_activity,
type = "by_cycle",
activity_threshold =
activity_threshold)
if ("overview" %in% figures) {
plot_maven_overview(maven_raw, maven_experiment = maven_experiment_name,
outdir = outdir)
}
if ("trend" %in% figures){
metabolism_trend(animal_metabolism, maven_experiment = maven_experiment_name,
outdir = outdir)
activity_trend(animal_activity, maven_experiment = maven_experiment_name,
activity_baseline = activity_baseline,
outdir = outdir)
}
if ("diag" %in% figures){
metabolism_diag(maven_raw, metabolism_summary_cycle,
maven_experiment = maven_experiment_name,
outdir = outdir)
activity_diag(maven_raw, metabolism_summary_cycle,
activity_summary_cycle,
maven_experiment = maven_experiment_name,
interval = interval,
outdir = outdir)
}
# final data table
out <- maven_datatable(outdir = outdir,
metabolism_summary_cycle, activity_summary_cycle,
maven_experiment = maven_experiment_name)
return(out)
}
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