data-raw/reduced_youth_models_create2.R

In paulhibbing/Sojourn: Apply Sojourn Methods for Processing ActiGraph Accelerometer Data

## Load everything

rm(list = ls())
load("R/sysdata.rda")

## Track the original number of objects, and the total size

num_objects <- length(ls())
total_size <- sum(
  sapply(
    setdiff(ls(), "num_objects"),
    function(x) object.size(get(x, envir = globalenv()))
  )
)

## Isolate the offending objects that need to be shrunk down

objects <- sapply(
  ls(),
  function(x) object.size(get(x, envir = globalenv()))
)
objects <- names(
  objects[order(objects, decreasing = TRUE)][1:4]
)
objects <- setNames(
  lapply(objects, get, envir = globalenv()),
  objects
)

rm(
  list = setdiff(
    ls(), c("objects", "num_objects", "total_size")
  )
)

## Reduce the object sizes (reduction tracking in the comments)

# size <- data.frame(
#   object = names(objects),
#   pre = sapply(objects, object.size),
#   stringsAsFactors = FALSE,
#   row.names = NULL
# )

objects <- lapply(
  objects,
  function(x) {
    x$residuals <- NULL
    return(x)
  }
)

# size$post <- sapply(objects, object.size)
# size$pct_reduction <- with(
#   size,
#   paste(
#     round(((pre - post) / pre) * 100, 1),
#     "%", sep = ""
#   )
# )

list2env(objects, globalenv())
rm(objects)

## Save in data-raw

save(
  youth_hipCounts,
  youth_hipRaw,
  youth_wristCounts,
  youth_wristRaw,
  num_objects,
  total_size,
  file = "data-raw/reduced_youth_models2.RData"
)

## Load existing sysdata to overwrite with old objects

objects <- setdiff(ls(), c("num_objects", "total_size"))
load("R/sysdata.rda")
rm(list = objects)
load("data-raw/reduced_youth_models2.RData")
suppressMessages(rm(objects))

## Check against the original number/size of objects in sysdata

# ORIGINAL:
# > num_objects
# [1] 43
# > total_size
# [1] 5577728

rm(num_objects, total_size)

num_objects <- length(ls())
total_size <- sum(
  sapply(
    setdiff(ls(), "num_objects"),
    function(x) object.size(get(x, envir = globalenv()))
  )
)

# NEW:
# > num_objects
# [1] 43
# > total_size
# [1] 3975144

# > diff(c(3975144, 5577728))
# [1] 1602584

rm(num_objects, total_size)

# SANITY CHECK:
# > length(ls())
# [1] 43

## Save new sysdata file

objects <- ls()
file.remove("R/sysdata.rda")
command <- paste(
  "usethis::use_data(",
  paste(objects, collapse = ", "),
  ", ",
  "internal = TRUE, overwrite = TRUE)",
  sep = ""
)
eval(parse(text = command))

# Test apply_youth_sojourn() with smaller models

rm(list = ls())
devtools::load_all()
load("data/example_data.rda")
new_results <- apply_youth_sojourn(
  AG = example_data, vm = "Vector.Magnitude", Site = "Hip"
)

save(
  new_results,
  file = "data-raw/example_results_new2.RData"
)

# Compare with predictions from the original method (using the enormous objects)

##NOTE: These results generated in a very particular way. See
##"data-raw/example_results_old_create.R" for clarification.

load("data-raw/example_results_old.RData")

all.equal(new_results[ ,names(old_results)], old_results)
identical(new_results[ ,names(old_results)], old_results)

# GOOD TO GO