benchmarking/benchmarking_tests.R

In sapfluxnet/sapfluxnetr: Working with 'Sapfluxnet' Project Data

library(future)
library(pryr)
library(tidyverse)
library(profvis)
library(microbenchmark)
library(sapfluxnetr)

#####
# folder <- 'tests/testthat/big_test/plant/'
# sites <- list.files(folder, pattern = '.RData')[1:10] %>%
#   stringr::str_remove('.RData')
# metadata <- read_sfn_metadata(folder)
# site_objects <- read_sfn_data(sites, folder)
# metrics_res <- read_sfn_data(sites, folder) %>%
#   daily_metrics()
# interval <- 'general'
# 
# 
# 
# mbm <- microbenchmark(
#   tidyfier_default = metrics_tidyfier(metrics_res, metadata, interval),
#   tidyfier_alt = metrics_tidyfier_alt(metrics_res, metadata, interval),
#   check = function(values) {all_equal(values[[1]], values[[2]])},
#   times = 10
# )
# 
# mbm
# autoplot.microbenchmark(mbm)
# 
# pv_default <- profvis({
#   metrics_tidyfier(metrics_res, sfn_metadata, interval)
# })
# 
# 
# pv_sapf_alt <- profvis({
#   metrics_tidyfier_alt(metrics_res, sfn_metadata, interval)
# })
# 
# pv_daily_metrics <- profvis({
#   daily_metrics(read_sfn_data(sites, folder))
# })
# 
# profvis({
#   site_objects <- read_sfn_data(sites, folder)
#   pause(2)
#   tururu <- function(site_objects) {
#     inherits(site_objects, 'sfn_data_multi')
#     class(site_objects) == 'sfn_data_multi'
#     is(site_objects, 'sfn_data_multi')
#     class(sfn_data) %in% c('sfn_data', 'sfn_data_multi')
#   }
#   
#   tururu(site_objects)
# })
#####

options('future.globals.maxSize' = 4*1014*1024^2)
plan('sequential')
profvis({
  
  init_mem <- mem_used()
  init_mem
  
  folder <- '../sapfluxnet_db/0.0.3/sapwood/'
  sites <- list.files(folder, pattern = '.RData') %>%
    stringr::str_remove('.RData')
  metadata <- read_sfn_metadata(folder, .write_cache = FALSE)
  res <- read_sfn_data(sites, folder) %>%
    daily_metrics(tidy = TRUE, metadata = metadata)
  
  end_mem <- mem_used()
  end_mem
  print(end_mem - init_mem)
  
}) %>%
  htmlwidgets::saveWidget('~/Descargas/pv_complete_seq.html')
browseURL('~/Descargas/pv_complete_seq.html')

options('future.globals.maxSize' = 1014*1024^2)
plan('multicore')

init_mem <- mem_used()
init_mem

tictoc::tic()
folder <- '../sapfluxnet_db/0.0.3/sapwood/'
sites <- list.files(folder, pattern = '.RData') %>%
  stringr::str_remove('.RData')
metadata <- read_sfn_metadata(folder, .write_cache = FALSE)
res <- read_sfn_data(sites, folder) %>%
  daily_metrics(tidy = TRUE, metadata = metadata)
tictoc::toc()

end_mem <- mem_used()
end_mem
print(end_mem - init_mem)
#####
# .write_metadata_cache

.write_metadata_cache_alt <- function(
  folder, .dry = FALSE
) {
  
  site_codes <- list.files(folder, recursive = TRUE, pattern = '.RData') %>%
    stringr::str_remove('.RData')
  
  sites_data <- site_codes %>%
    read_sfn_data(folder = folder)
  
  sfn_metadata <- list(
    site_md = get_site_md(sites_data, collapse = TRUE),
    stand_md = get_stand_md(sites_data, collapse = TRUE),
    species_md = get_species_md(sites_data, collapse = TRUE),
    plant_md = get_plant_md(sites_data, collapse = TRUE),
    env_md = get_env_md(sites_data, collapse = TRUE)
  )
  
  # cache thing
  if (!.dry) {
    save(sfn_metadata, file = file.path(folder, '.metadata_cache.RData'))
  }
  
  return(sfn_metadata)
}

folder <- '../sapfluxnet_db/0.0.3/sapwood'

profvis({
  sapfluxnetr:::.write_metadata_cache(folder, .dry = TRUE)
}) %>%
  htmlwidgets::saveWidget('~/Descargas/pv_write_metadata_cache_def.html')
browseURL('~/Descargas/pv_write_metadata_cache_def.html')

profvis({
  sapfluxnetr:::.write_metadata_cache_alt(folder, .dry = TRUE)
}) %>%
  htmlwidgets::saveWidget('~/Descargas/pv_write_metadata_cache_alt.html')
browseURL('~/Descargas/pv_write_metadata_cache_alt.html')