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ASNAT_Utilities.R
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###############################################################################
# PURPOSE: ASNAT_Utilities.R - Utility routines used by ASNAT code.
# HISTORY: 2022-10-12 [email protected]
# STATUS: unreviewed tested
###############################################################################
.unused <- require(compiler, quietly = TRUE) && compiler::enableJIT(3)
# Is ASNAT app deployed as a hosted remote server shiny app
# (e.g., on rstudio-connect or shinyapps.io, etc.) or
# as a local app on the user's computer?
ASNAT_is_remote_hosted <- Sys.getenv("R_CONFIG_ACTIVE") == "rsconnect"
###############################################################################
# Load required libraries:
###############################################################################
# URL to download any required R packages from:
repository <- "http://cran.us.r-project.org"
library(methods)
if (ASNAT_is_remote_hosted) {
library(seismicRoll) # For seismicRoll::findOutliers().
} else {
if (!require(seismicRoll)) install.packages("seismicRoll", repos = repository)
}
############################# Tunable Parameters ##############################
# Use C++ versions of functions (defined in ASNAT_Utilities.cpp)
# for 100x speedup?
ASNAT_use_cpp_functions <- TRUE
if (ASNAT_use_cpp_functions) {
if (ASNAT_is_remote_hosted) {
library(Rcpp)
} else {
if (!require(Rcpp)) install.packages("Rcpp", repos = repository)
}
Rcpp::sourceCpp(code = '
#include <Rcpp.h>
// [[Rcpp::export]]
bool RTools_is_installed_and_c_plus_plus_compiler_works() {return true;}')
stopifnot(RTools_is_installed_and_c_plus_plus_compiler_works())
Rcpp::sourceCpp("ASNAT_Utilities.cpp")
}
# Use curl program to get data from webservices?
# If TRUE then the platform/bin/curl program will be used
# if FALSE then httr::GET() will be used.
# Note: if running remote-hosted and the remote server is still mis-configured
# (SSL library mismatch problem) then using httr::GET() will fail and cause
# the app to terminate! Using the curl program will also fail to retrieve data
# but the app will not be terminated and local file loads are still possible.
ASNAT_use_curl_program <- TRUE
if (!ASNAT_use_curl_program) {
if (ASNAT_is_remote_hosted) {
library(httr)
} else {
if (!require(httr)) install.packages("httr", repos = repository)
}
}
# When ASNAT reads data from webservices or files, these missing/problematic
# values will be converted to NA and kept in the resulting data.frame.
# This allows multi-variable/column data to be read in when some columns have
# missing values.
# However, functions such as min(), max(), mean(), var(), quantile(), etc.
# must then include argument na.rm = TRUE to avoid numeric/plot problems.
ASNAT_na_strings =
c("", "''", "NA", "NaN", "nan", "-9999", "-9999.0", "-Inf", "Inf")
# When ASNAT outputs data to a file, any NA values are converted to this:
ASNAT_output_missing_string = "-9999.0"
# Print debug messages to stderr and perform extra checks?
ASNAT_debugging <- FALSE
if (ASNAT_debugging) {
ASNAT_dprint <- function(...) cat(sep = "", file = stderr(), sprintf(...))
ASNAT_check <- function(condition) stopifnot(condition)
ASNAT_debug <- function(a_function, f_args) do.call(a_function, list(f_args))
} else {
ASNAT_dprint <- function(...) NULL
ASNAT_check <- function(...) NULL
ASNAT_debug <- function(...) NULL
}
# Do performance profiling with timing messages printed to stderr?
ASNAT_timing <- FALSE
if (ASNAT_timing) {
ASNAT_start_timer <- function() Sys.time()
ASNAT_elapsed_timer <- function(message, timer) {
cat(sep = "", file = stderr(),
sprintf("%s %0.1f seconds.\n",
message,
as.numeric(difftime(Sys.time(), timer, units = "secs"))))
}
} else {
ASNAT_start_timer <- function(...) {0}
ASNAT_elapsed_timer <- function(...) {}
}
# Provide a warning message callback so failure messages printed to the console
# can be also be displayed in a GUI message area or pop-up:
ASNAT_warning_callback <- NULL
ASNAT_set_warning_callback <- function(callback) {
if (is.function(callback)) {
ASNAT_warning_callback <<- callback
} else {
ASNAT_warning_callback <<- NULL
}
}
ASNAT_warning <- function(failure) {
warning(failure, call. = FALSE, immediate. = TRUE, noBreaks. = FALSE)
if (is.function(ASNAT_warning_callback)) {
ASNAT_warning_callback(failure)
}
}
# Allow fancy labels so pm25(ug/m3) uses subscript 2.5, mu and superscript?
ASNAT_allow_fancy_labels <- TRUE
# Convert string containing ug/m3 to mu and cube and pm25 to subscript:
ASNAT_fancy_label <- function(label) {
stopifnot(nchar(label) > 0L)
result <- label
if (ASNAT_allow_fancy_labels) {
# Convert certain units to fancy versions:
result <- gsub(fixed = TRUE, "ug/m3", "\u03BCg/m\u00B3", result)
# Construct strings for subscripted PM variables:
subs <- c("\u2080", "\u2081", "\u2082", "\u2083", "\u2084", "\u2085")
pm25_subscripted <- as.character(2.5)
lapply(0:5, function(z) {
pm25_subscripted <<-
gsub(pattern = z, replacement = subs[z + 1], x = pm25_subscripted)
})
pm25_subscripted <- paste0("PM", pm25_subscripted)
pm10_subscripted <- as.character(10)
lapply(0:5, function(z) {
pm10_subscripted <<-
gsub(pattern = z, replacement = subs[z + 1], x = pm10_subscripted)
})
pm10_subscripted <- paste0("PM", pm10_subscripted)
pm1_subscripted <- as.character(1)
lapply(0:5, function(z) {
pm1_subscripted <<-
gsub(pattern = z, replacement = subs[z + 1], x = pm1_subscripted)
})
pm1_subscripted <- paste0("PM", pm1_subscripted)
# Replace all occurrences of such variables with fancy versions:
result <- gsub(fixed = TRUE, "pm25", pm25_subscripted, result)
result <- gsub(fixed = TRUE, "pm10", pm10_subscripted, result)
result <- gsub(fixed = TRUE, "pm1", pm1_subscripted, result)
}
return(result)
}
# AQS/AirNow pm25 parameter codes:
# https://aqs.epa.gov/aqsweb/documents/codetables/parameters.html
ASNAT_aqs_pm25_codes <-
c("88101,88500,88501,88502",
"88101,88500,88501",
"88101,88500,88502",
"88101,88501,88502",
"88500,88501,88502",
"88101,88500",
"88101,88501",
"88101,88502",
"88500,88501",
"88500,88502",
"88501,88502",
"88101",
"88500",
"88501",
"88502")
# AQI
# https://aqs.epa.gov/aqsweb/documents/codetables/aqi_breakpoints.html
ASNAT_aqi_names <- c("Good", "Moderate", "Unhealthy for some", "Unhealthy",
"Very Unhealthy", "Hazardous")
# Workaround BUG: Use "#00FF00" for green else "green" appears as "green4".
ASNAT_aqi_colormap <- c("#00FF00", "yellow", "orange", "red", "purple", "maroon")
# pm25(ug/m3), ozone(ppm):
ASNAT_pm25_daily_aqi_breakpoints <- c(9.0, 35.4, 55.4, 125.4, 225.4, 1e6)
ASNAT_pm10_daily_aqi_breakpoints <- c(54.0, 154.0, 254.0, 354.0, 424.0, 1e6)
ASNAT_ozone_8_hour_aqi_breakpoints <- c(0.054, 0.07, 0.085, 0.105, 0.2, 1e3)
ASNAT_ozone_1_hour_aqi_breakpoints <- c(0.124, 0.124, 0.164, 0.204, 0.404, 1e3)
ASNAT_ozone_8_hour_aqi_breakpoints <- ASNAT_ozone_8_hour_aqi_breakpoints * 1000
ASNAT_ozone_1_hour_aqi_breakpoints <- ASNAT_ozone_1_hour_aqi_breakpoints * 1000
# Get AQI statistics target ranges
# targets <- ASNAT_aqi_statistic_target_ranges("pm25_corrected_hourly(ug/m3)")
ASNAT_aqi_statistic_target_ranges <- function(variable_units) {
ASNAT_dprint("ASNAT_aqi_statistic_target_ranges():")
stopifnot(class(variable_units) == "character")
stopifnot(nchar(variable_units) > 0L)
ASNAT_dprint(" %s\n", variable_units)
result <- NULL
# https://www.epa.gov/air-sensor-toolbox/air-sensor-performance-targets-and-testing-protocols
if ((startsWith(variable_units, "pm10") ||
grepl(".pm10", variable_units, fixed = TRUE)) &&
endsWith(variable_units, "(ug/m3)")) {
result <- list(r2 = c(0.7, 1.0),
slope = c(0.65, 1.35),
intercept = c(-10.0, 10.0),
rmse = c(0.0, 14.0),
nrmse = c(0.0, 30.0))
} else if ((startsWith(variable_units, "pm1") ||
grepl(".pm1", variable_units, fixed = TRUE)) &&
endsWith(variable_units, "(ug/m3)")) {
# No standard for pm1 but use same values as for pm2.5:
result <- list(r2 = c(0.7, 1.0),
slope = c(0.65, 1.35),
intercept = c(-5.0, 5.0),
rmse = c(0.0, 7.0),
nrmse = c(0.0, 30.0))
} else if ((startsWith(variable_units, "pm25") ||
grepl(".pm25", variable_units, fixed = TRUE)) &&
endsWith(variable_units, "(ug/m3)")) {
result <- list(r2 = c(0.7, 1.0),
slope = c(0.65, 1.35),
intercept = c(-5.0, 5.0),
rmse = c(0.0, 7.0),
nrmse = c(0.0, 30.0))
} else if ((startsWith(variable_units, "ozone") ||
grepl(".ozone", variable_units, fixed = TRUE)) &&
endsWith(variable_units, "(ppb)")) {
result <- list(r2 = c(0.8, 1.0),
slope = c(0.8, 1.2),
intercept = c(-5.0, 5.0),
rmse = c(0.0, 5.0),
nrmse = c(NA, NA))
} else if ((startsWith(variable_units, "no2") ||
grepl(".no2", variable_units, fixed = TRUE)) &&
endsWith(variable_units, "(ppb)")) {
result <- list(r2 = c(0.7, 1.0),
slope = c(0.65, 1.35),
intercept = c(-5.0, 5.0),
rmse = c(0.0, 15.0),
nrmse = c(NA, NA))
} else if ((startsWith(variable_units, "so2") ||
grepl(".so2", variable_units, fixed = TRUE)) &&
endsWith(variable_units, "(ppb)")) {
result <- list(r2 = c(0.7, 1.0),
slope = c(0.65, 1.35),
intercept = c(-5.0, 5.0),
rmse = c(0.0, 15.0),
nrmse = c(NA, NA))
} else if ((startsWith(variable_units, "co") ||
grepl(".co", variable_units, fixed = TRUE)) &&
endsWith(variable_units, "(ppm)")) {
result <- list(r2 = c(0.8, 1.0),
slope = c(0.8, 1.2),
intercept = c(-0.05, 0.05),
rmse = c(0.0, 0.15),
nrmse = c(NA, NA))
}
ASNAT_debug(str, result)
return(result)
}
# Is variable AQI-compatible?
# is_aqi <- ASNAT_is_aqi_variable("pm25_corrected_hourly(ug/m3)")
ASNAT_is_aqi_variable <- function(variable_units) {
ASNAT_dprint("ASNAT_is_aqi_variable():")
stopifnot(class(variable_units) == "character")
stopifnot(nchar(variable_units) > 0L)
ASNAT_dprint(" %s\n", variable_units)
result <- FALSE
if (startsWith(variable_units, "pm10") ||
grepl(".pm10", variable_units, fixed = TRUE)) {
result <- endsWith(variable_units, "(ug/m3)")
} else if (startsWith(variable_units, "pm1") ||
grepl(".pm1", variable_units, fixed = TRUE)) {
result <- endsWith(variable_units, "(ug/m3)")
} else if (startsWith(variable_units, "pm25") ||
grepl(".pm25", variable_units, fixed = TRUE)) {
result <- endsWith(variable_units, "(ug/m3)")
} else if (startsWith(variable_units, "ozone") ||
grepl(".ozone", variable_units, fixed = TRUE)) {
result <- endsWith(variable_units, "(ppb)")
}
ASNAT_dprint(" result = %d", as.integer(result))
return(result)
}
# Are variables AQI-compatible?
# is_aqi <- ASNAT_is_aqi_compatible("pm25(ug/m3)",
# "pm25_corrected_hourly(ug/m3)")
ASNAT_is_aqi_compatible <- function(variable_units1, variable_units2) {
ASNAT_dprint("ASNAT_is_aqi_compatible():")
stopifnot(class(variable_units1) == "character")
stopifnot(class(variable_units2) == "character")
stopifnot(nchar(variable_units1) > 0L)
stopifnot(nchar(variable_units2) > 0L)
ASNAT_dprint(" %s %s\n", variable_units1, variable_units2)
result <- FALSE
if (startsWith(variable_units1, "pm10") ||
grepl(".pm10", variable_units1, fixed = TRUE)) {
result <-
(startsWith(variable_units2, "pm10") ||
grepl(".pm10", variable_units2, fixed = TRUE)) &&
endsWith(variable_units1, "(ug/m3)") &&
endsWith(variable_units2, "(ug/m3)")
} else if (startsWith(variable_units1, "pm1") ||
grepl(".pm1", variable_units1, fixed = TRUE)) {
result <-
(startsWith(variable_units2, "pm1") ||
grepl(".pm1", variable_units2, fixed = TRUE)) &&
endsWith(variable_units1, "(ug/m3)") &&
endsWith(variable_units2, "(ug/m3)")
} else if (startsWith(variable_units1, "pm25") ||
grepl(".pm25", variable_units1, fixed = TRUE)) {
result <-
(startsWith(variable_units2, "pm25") ||
grepl(".pm25", variable_units1, fixed = TRUE)) &&
endsWith(variable_units1, "(ug/m3)") &&
endsWith(variable_units2, "(ug/m3)")
} else if (startsWith(variable_units1, "ozone") ||
grepl(".ozone", variable_units1, fixed = TRUE)) {
result <-
(startsWith(variable_units2, "ozone") ||
grepl(".ozone", variable_units1, fixed = TRUE)) &&
endsWith(variable_units1, "(ppb)") &&
endsWith(variable_units2, "(ppb)")
}
ASNAT_dprint(" result = %d", as.integer(result))
return(result)
}
# Define function to get AQI indices of values given breakpoints:
ASNAT_aqi_data_indices <- function(values, breakpoints) {
ASNAT_dprint("ASNAT_aqi_data_indices():")
stopifnot(class(values) == "numeric" || class(values) == "integer")
stopifnot(length(values) >= 1L)
stopifnot(length(breakpoints) > 0L)
ASNAT_dprint("values:")
ASNAT_debug(str, values)
ASNAT_dprint("breakpoints:")
ASNAT_debug(str, breakpoints)
count <- length(values)
result <- rep(0L, count)
for (index in seq_along(values)) {
value <- values[[index]]
for (aqi_index in seq_along(breakpoints)) {
aqi_breakpoint <- breakpoints[[aqi_index]]
if (value <= aqi_breakpoint) {
result[[index]] <- aqi_index
break
}
}
}
ASNAT_dprint("ASNAT_aqi_data_indices(): result:")
ASNAT_debug(str, result)
return(result)
}
# Define function to get AQI colors of values given breakpoints:
ASNAT_aqi_data_colors <- function(values, breakpoints, colormap) {
ASNAT_dprint("ASNAT_aqi_data_colors():")
stopifnot(class(values) == "numeric" || class(values) == "integer")
stopifnot(length(values) >= 1L)
stopifnot(length(breakpoints) > 0L)
stopifnot(length(colormap) == length(breakpoints))
ASNAT_dprint("values:")
ASNAT_debug(str, values)
ASNAT_dprint("breakpoints:")
ASNAT_debug(str, breakpoints)
ASNAT_dprint("colormap:")
ASNAT_debug(str, colormap)
count <- length(values)
result <- rep("black", count)
for (index in seq_along(values)) {
value <- values[[index]]
# Skip NA values - assign a default color
if (is.na(value)) {
result[[index]] <- "#858585"
next
}
for (color_index in seq_along(breakpoints)) {
aqi_breakpoint <- breakpoints[[color_index]]
aqi_color <- colormap[[color_index]]
if (value <= aqi_breakpoint) {
result[[index]] <- aqi_color
break
}
}
}
ASNAT_dprint("ASNAT_aqi_data_color(): result:")
ASNAT_debug(str, result)
return(result)
}
# Return array of AQI indices for values or NULL if not applicable to variable:
ASNAT_aqi_indices <- function(variable, is_hourly, values) {
ASNAT_dprint("ASNAT_aqi_value_indices():")
stopifnot(class(variable) == "character")
stopifnot(nchar(variable) > 0L)
stopifnot(is_hourly == TRUE || is_hourly == FALSE)
stopifnot(class(values) == "numeric" || class(values) == "integer")
stopifnot(length(values) >= 1L)
ASNAT_dprint(" variable = %s\n", variable)
result <- NULL
if ((startsWith(variable, "pm10") ||
grepl(".pm10", variable, fixed = TRUE)) &&
endsWith(variable, "(ug/m3)")) {
result <- ASNAT_aqi_data_indices(values, ASNAT_pm10_daily_aqi_breakpoints)
} else if (((startsWith(variable, "pm1") ||
grepl(".pm1", variable, fixed = TRUE)) ||
(startsWith(variable, "pm25") ||
grepl(".pm25", variable, fixed = TRUE))) &&
endsWith(variable, "(ug/m3)")) {
result <- ASNAT_aqi_data_indices(values, ASNAT_pm25_daily_aqi_breakpoints)
} else if ((startsWith(variable, "ozone") ||
grepl(".ozone", variable, fixed = TRUE)) &&
endsWith(variable, "(ppb)")) {
if (is_hourly) {
result <-
ASNAT_aqi_data_indices(values, ASNAT_ozone_1_hour_aqi_breakpoints)
} else {
result <-
ASNAT_aqi_data_indices(values, ASNAT_ozone_8_hour_aqi_breakpoints)
}
}
return(result)
}
# Return array of AQI colors for values or NULL if not applicable to variable:
ASNAT_aqi_colors <- function(variable, is_hourly, values) {
ASNAT_dprint("ASNAT_aqi_value_colors():")
stopifnot(class(variable) == "character")
stopifnot(nchar(variable) > 0L)
stopifnot(is_hourly == TRUE || is_hourly == FALSE)
stopifnot(class(values) == "numeric" || class(values) == "integer")
stopifnot(length(values) >= 1L)
ASNAT_dprint(" variable = %s\n", variable)
result <- NULL
if ((startsWith(variable, "pm10") ||
grepl(".pm10", variable, fixed = TRUE)) &&
endsWith(variable, "(ug/m3)")) {
result <-
ASNAT_aqi_data_colors(values,
ASNAT_pm10_daily_aqi_breakpoints,
ASNAT_aqi_colormap)
} else if (((startsWith(variable, "pm1") ||
grepl(".pm1", variable, fixed = TRUE)) ||
(startsWith(variable, "pm25") ||
grepl(".pm25", variable, fixed = TRUE))) &&
endsWith(variable, "(ug/m3)")) {
result <-
ASNAT_aqi_data_colors(values,
ASNAT_pm25_daily_aqi_breakpoints,
ASNAT_aqi_colormap)
} else if ((startsWith(variable, "ozone") ||
grepl(".ozone", variable, fixed = TRUE)) &&
endsWith(variable, "(ppb)")) {
if (is_hourly) {
result <-
ASNAT_aqi_data_colors(values,
ASNAT_ozone_1_hour_aqi_breakpoints,
ASNAT_aqi_colormap)
} else {
result <-
ASNAT_aqi_data_colors(values,
ASNAT_ozone_8_hour_aqi_breakpoints,
ASNAT_aqi_colormap)
}
}
return(result)
}
# Return array of AQI category neighbor match percentages:
ASNAT_aqi_comparison <- function(aqi_indices_x, aqi_indices_y) {
ASNAT_dprint("ASNAT_aqi_comparison():")
stopifnot(class(aqi_indices_x) == "integer")
stopifnot(class(aqi_indices_y) == "integer")
stopifnot(length(aqi_indices_x) > 0L)
stopifnot(length(aqi_indices_y) == length(aqi_indices_x))
aqi_categories <- length(ASNAT_aqi_names)
result <- rep(0L, aqi_categories * aqi_categories)
index <- 1L
for (aqi_category in 1L:aqi_categories) {
indices_x <- which(aqi_indices_x == aqi_category)
count_x <- length(indices_x)
if (count_x > 0L) {
neighbor_aqi_indices_y <- aqi_indices_y[indices_x]
for (aqi_category2 in 1L:aqi_categories) {
indices_y <- which(neighbor_aqi_indices_y == aqi_category2)
count_y <- length(indices_y)
result[index] <- count_y / count_x * 100.0
index <- index + 1L
}
} else {
index <- index + aqi_categories
}
}
ASNAT_dprint("result:\n")
ASNAT_debug(str, result)
return(result)
}
# Return array of AQI breakpoints for variable or NULL if not applicable:
ASNAT_aqi_variable_breakpoints <- function(variable, is_hourly) {
ASNAT_dprint("ASNAT_aqi_variable_breakpoints():")
stopifnot(class(variable) == "character")
stopifnot(nchar(variable) > 0L)
stopifnot(is_hourly == TRUE || is_hourly == FALSE)
ASNAT_dprint(" variable = %s\n", variable)
result <- NULL
if ((startsWith(variable, "pm10") ||
grepl(".pm10", variable, fixed = TRUE)) &&
endsWith(variable, "(ug/m3)")) {
result <- ASNAT_pm10_daily_aqi_breakpoints
} else if (((startsWith(variable, "pm1") ||
grepl(".pm1", variable, fixed = TRUE)) ||
(startsWith(variable, "pm25") ||
grepl(".pm25", variable, fixed = TRUE))) &&
endsWith(variable, "(ug/m3)")) {
result <- ASNAT_pm25_daily_aqi_breakpoints
} else if ((startsWith(variable, "ozone") ||
grepl(".ozone", variable, fixed = TRUE)) &&
endsWith(variable, "(ppb)")) {
if (is_hourly) {
result <- ASNAT_ozone_1_hour_aqi_breakpoints
} else {
result <- ASNAT_ozone_8_hour_aqi_breakpoints
}
}
return(result)
}
# Return data.frame of neighbor AQI statistics:
ASNAT_neighbor_aqi_statistics <-
function(variable, is_hourly, measures_x, measures_y) {
ASNAT_dprint("ASNAT_neighbor_aqi_statistics():")
stopifnot(class(variable) == "character")
stopifnot(nchar(variable) > 0L)
stopifnot(is_hourly == TRUE || is_hourly == FALSE)
stopifnot(class(measures_x) == "numeric" || class(measures_x) == "integer")
stopifnot(class(measures_y) == "numeric" || class(measures_y) == "integer")
stopifnot(length(measures_x) > 0L)
stopifnot(length(measures_y) == length(measures_x))
ASNAT_dprint(" variable = %s\n", variable)
aqi_categories <- length(ASNAT_aqi_names)
aqi_breakpoints <- ASNAT_aqi_variable_breakpoints(variable, is_hourly)
result <- data.frame(AQI = ASNAT_aqi_names,
breakpoint = aqi_breakpoints,
N = rep(0, aqi_categories),
NMBE = rep(0, aqi_categories),
RMSE = rep(0, aqi_categories),
NRMSE = rep(0, aqi_categories))
aqi_indices_x <- ASNAT_aqi_indices(variable, is_hourly, measures_x)
for (aqi_category in 1L:aqi_categories) {
aqi_indices <- which(aqi_indices_x == aqi_category)
n <- length(aqi_indices)
if (n > 0L) {
aqi_measures_x <- measures_x[aqi_indices]
aqi_measures_y <- measures_y[aqi_indices]
err <- aqi_measures_x - aqi_measures_y
se <- err * err
mse <- mean(se, na.rm = TRUE)
rmse <- sqrt(mse)
mean_x_values <- mean(aqi_measures_x, na.rm = TRUE)
nrmse <- rmse / mean_x_values * 100.0
abs_x_values <- abs(aqi_measures_x)
nmbe <- mean(err / abs_x_values, na.rm = TRUE) * 100.0
aqi_name <- ASNAT_aqi_names[[aqi_category]]
breakpoint <- aqi_breakpoints[[aqi_category]]
result[aqi_category, ] <- c(aqi_name, breakpoint, n, nmbe, rmse, nrmse)
}
}
parts <- unlist(strsplit(variable, "[()]"))
units <- parts[[2L]]
column2 <- sprintf("Upper_Limit(%s)", units)
column5 <- sprintf("RMSE(%s)", units)
colnames(result) <-
c("AQI_Category(-)", column2, "Count(-)", "NMBE(%)", column5, "NRMSE(%)")
# Ensure the non-string columns are integer or numeric:
for (the_column in 2L:6L) {
the_values <- result[[the_column]]
if (the_column == 3L) {
the_values <- as.integer(the_values)
} else {
the_values <- as.numeric(the_values)
}
result[the_column] <- the_values
}
ASNAT_dprint("result:\n")
ASNAT_debug(print, result)
return(result)
}
# Return data.frame of neighbor statistics:
ASNAT_neighbor_statistics <- function(neighbors_data_frame, only_unflagged) {
ASNAT_dprint("ASNAT_neighbor_statistics():")
stopifnot(class(neighbors_data_frame) == "data.frame")
stopifnot(ncol(neighbors_data_frame) >= 6L)
stopifnot(nrow(neighbors_data_frame) > 0L)
stopifnot(only_unflagged == TRUE || only_unflagged == FALSE)
sites_x <- as.integer(neighbors_data_frame[[2L]])
unique_sites_x <- unique(sort.int(sites_x))
count <- length(unique_sites_x)
result <- data.frame(site = rep(0L, count),
R2 = rep(NA, count),
slope = rep(NA, count),
intercept = rep(NA, count),
RMSE = rep(NA, count),
NRMSE = rep(NA, count))
for (index in 1L:count) {
site_x <- unique_sites_x[[index]]
neighbor_indices <- NULL
if (only_unflagged) {
neighbor_indices <-
which(neighbors_data_frame[[2L]] == site_x &
neighbors_data_frame[[6L]] == "0")
} else {
neighbor_indices <- which(neighbors_data_frame[[2L]] == site_x)
}
n <- length(neighbor_indices)
if (n > 0L) {
measures_x <- neighbors_data_frame[neighbor_indices, 3L]
measures_y <- neighbors_data_frame[neighbor_indices, 5L]
correlation <- if (n > 1L) cor(measures_x, measures_y) else 0.0
if (is.na(correlation)) {
correlation <- 0.0
}
r_squared <- correlation * correlation
slope <- cov(measures_x, measures_y) / var(measures_x, na.rm = TRUE)
y_intercept <-
mean(measures_y, na.rm = TRUE) - mean(measures_x, na.rm = TRUE) * slope
err <- measures_x - measures_y
se <- err * err
mse <- mean(se, na.rm = TRUE)
rmse <- sqrt(mse)
mean_measures_x <- mean(measures_x, na.rm = TRUE)
nrmse <- rmse / mean_measures_x * 100.0
result[index, ] <-
c(site_x, r_squared, slope, y_intercept, rmse, nrmse)
}
}
valid_rows <- which(result[[1L]] > 0L)
count <- length(valid_rows)
if (count == 0L) {
result <- NULL
} else {
result <- result[valid_rows, ]
column_names <- colnames(neighbors_data_frame)
variable <- column_names[[3L]]
parts <- unlist(strsplit(variable, "[()]"))
units <- parts[[2L]]
intercept_column <- sprintf("Intercept(%s)", units)
rmse_column <- sprintf("RMSE(%s)", units)
colnames(result) <-
c("Site(-)", "R2(-)", "Slope(-)", intercept_column, rmse_column,
"NRMSE(%)")
}
ASNAT_dprint("result:\n")
ASNAT_debug(print, result)
return(result)
}
###############################################################################
# Get name of platform this program is running on.
ASNAT_platform <- function() {
result <- Sys.info()[["sysname"]]
if (result != "Windows") {
result <- paste0(result, ".", Sys.info()[["machine"]])
}
ASNAT_dprint("ASNAT_platform() returning result = %s\n", result)
return(result)
}
# Use curl program to retrieve data from url to a file and return TRUE if
# successful else FALSE.
ASNAT_http_get_curl <- function(url, timeout_seconds, output_file_name) {
stopifnot(nchar(url) > 0L)
stopifnot(timeout_seconds >= 0L)
stopifnot(nchar(output_file_name) > 0L)
result <- FALSE
single_quote <- "'"
double_quote <- '"'
command <- NULL
args <-
paste0(" -k --silent --retry 0 -L --tcp-nodelay --max-time ",
timeout_seconds,
" --output ", double_quote, output_file_name, double_quote, " ")
current_directory <- getwd()
platform <- ASNAT_platform()
if (startsWith(platform, "Windows")) {
command <-
paste0(current_directory, "/Windows/bin/curl.exe ", args,
double_quote, url, double_quote)
} else if (startsWith(platform, "Darwin") && file.exists("/usr/bin/curl")) {
# New MacOS disallows running curl from other directories!
command <- paste0("/usr/bin/curl ", args, single_quote, url, single_quote)
} else {
command <-
paste0(current_directory, "/", platform, "/bin/curl ", args,
single_quote, url, single_quote)
}
ASNAT_dprint("%s\n", command)
status <- system(command)
ASNAT_dprint("status = %d\n", status)
result <- status == 0L
if (!result) {
cat(sep = "", file = stderr(), "Failed to retrieve data from:\n", url, "\n")
}
ASNAT_dprint("ASNAT_http_get_curl() returning result = %d\n", result)
return(result)
}
# Retrieve data from a url to a file and return TRUE if successful else FALSE.
ASNAT_http_get <- function(url, timeout_seconds, output_file_name) {
stopifnot(nchar(url) > 0L)
stopifnot(timeout_seconds >= 0L)
stopifnot(nchar(output_file_name) > 0L)
result <- FALSE
if (ASNAT_use_curl_program) {
result <- ASNAT_http_get_curl(url, timeout_seconds, output_file_name)
} else {
ASNAT_dprint("httr::GET(%s, timeout = %d)\n", url, timeout_seconds)
response <- httr::GET(url, httr::timeout(timeout_seconds))
status <- httr::status_code(response)
ASNAT_dprint("status = %d\n", status)
if (status == 200L) {
the_content <- httr::content(response, as = "text")
if (!is.null(the_content)) {
output_file <- file(output_file_name, "wb") # wb prevents \r chars.
try(silent = TRUE, writeLines(the_content, output_file))
close(output_file)
result <- file.size(output_file_name) > 0L
}
}
}
if (!result) {
cat(sep = "", file = stderr(), "Failed to retrieve data from:\n", url, "\n")
}
ASNAT_dprint("ASNAT_http_get() returning result = %d\n", result)
return(result)
}
# Declare S4 class method and ensure isGeneric():
# https://adv-r.hadley.nz/s4.html
ASNAT_declare_method <- function(class_name, method_name, method_body) {
stopifnot(!is.null(class_name))
stopifnot(!is.null(method_name))
stopifnot(nchar(class_name) > 0L)
stopifnot(nchar(method_name) > 0L)
stopifnot(!is.null(method_body))
if (!methods::isGeneric(method_name)) {
suppressWarnings(methods::setGeneric(method_name, function(object, ...)
standardGeneric(method_name)))
}
methods::setMethod(method_name, class_name, method_body)
stopifnot(isGeneric(method_name))
}
# HACK work-around Windows EPA laptop configuration that hijacks ~:
ASNAT_home_path <- function() {
result <- path.expand("~")
if (nchar(result) > 3L &&
substr(result, 2L, 2L) == ":" &&
length(grep(fixed = TRUE, "OneDrive", result)) > 0L) {
parts_list <- strsplit(result, "OneDrive", fixed = TRUE)
first_part <- unlist(parts_list[[1L]])
result <- first_part[[1L]]
}
return(result)
}
# Add $PWD/$PLATFORM/bin to $PATH so phantomjs and pandoc executables are found
# and also ensure the executables are executable.
ASNAT_augment_path <- function() {
current_path <- Sys.getenv("PATH")
current_directory <- getwd()
platform <- ASNAT_platform()
new_path <- NULL
if (platform == "Windows") {
new_path <- paste0(current_path, ";", current_directory, "\\Windows\\bin")
} else {
new_path <-
paste0(current_path, ":", current_directory, "/", platform, "/bin")
# Also ensure the executables are executable:
chmod_command <- paste0("chmod -R +x ", platform)
system(chmod_command)
}
Sys.setenv(PATH = new_path)
}
# Return unique numbered file name:
# result <- ASNAT_unique_file_name("/tmp/data/map_movie.mp4")
# result is next unique file name such as
# /tmp/data/map_movie.mp4
# /tmp/data/map_movie_2.mp4
# /tmp/data/map_movie_3.mp4
# ...
ASNAT_unique_file_name <- function(file_name) {
stopifnot(nchar(file_name) > 0L)
result <- file_name
if (file.exists(result)) {
first <- file_name
extension <- ""
parts <- unlist(strsplit(file_name, ".", fixed = TRUE))
parts_length <- length(parts)
if (parts_length > 1L) {
extension <- paste0(".", parts[[parts_length]])
last <- nchar(file_name) - nchar(extension)
first <- substr(file_name, 1L, last)
}
i <- 2L