From e18622ca299f6537e64cead487750247d7039f30 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rog=C3=A9rio?= <rogerio.felino@outlook.com>
Date: Sat, 9 Dec 2023 15:34:16 -0300
Subject: [PATCH] Initial commit

---
 .Rbuildignore |   2 +
 .gitignore    |   8 +++
 DESCRIPTION   |  12 +++++
 Fangorn.Rproj |  20 ++++++++
 NAMESPACE     |   1 +
 R/palantir.R  | 133 ++++++++++++++++++++++++++++++++++++++++++++++++++
 R/rohirrim.R  |  58 ++++++++++++++++++++++
 man/hello.Rd  |  12 +++++
 8 files changed, 246 insertions(+)
 create mode 100644 .Rbuildignore
 create mode 100644 .gitignore
 create mode 100644 DESCRIPTION
 create mode 100644 Fangorn.Rproj
 create mode 100644 NAMESPACE
 create mode 100644 R/palantir.R
 create mode 100644 R/rohirrim.R
 create mode 100644 man/hello.Rd

diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..91114bf
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..accfb7b
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,8 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.Rdata
+.httr-oauth
+.DS_Store
+.quarto
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..d253093
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,12 @@
+Package: Fangorn
+Type: Package
+Title: Automate SDMtune tasks
+Version: 1.0.0
+Authors@R: 
+    person("Rogério", "Nunes", , "rogerio.felino@outlook.com", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-6706-0791"))
+Description: Automates some SDMtune and enmSdmX tasks, and calculates OPR, UPR, PPI and PAI.
+License: GPL (>= 3)
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
diff --git a/Fangorn.Rproj b/Fangorn.Rproj
new file mode 100644
index 0000000..497f8bf
--- /dev/null
+++ b/Fangorn.Rproj
@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..d75f824
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1 @@
+exportPattern("^[[:alpha:]]+")
diff --git a/R/palantir.R b/R/palantir.R
new file mode 100644
index 0000000..5a672fd
--- /dev/null
+++ b/R/palantir.R
@@ -0,0 +1,133 @@
+#' palantir Function
+#'
+#' This function calculates AUC, TSS, prediction, thresholds, and CBI.
+#'
+#' @param model SDMtune model object.
+#' @param model_name character. The name of the model.
+#' @param test numeric. The percentage of data withhold for testing.
+#' @param variables Spatrast stack.
+#' @param p data.frame. Presence data with Longitude/Latitude.
+#' @param bg data.frame. Background data with Longitude/Latitude.
+#' @param output_dir The output directory for writing the raster prediction.
+#'
+#' @return A data frame with AUC, TSS, Threshold, Omission and CBI values.
+#'
+#' @examples
+#' palantir(model, "my_model", test, variables, p, bg)
+palantir <- function(model, model_name, test, variables, p, bg, output_dir = ".") {
+  # Check required packages
+  if (!requireNamespace("dismo", quietly = TRUE)) {
+    stop("Required package 'dismo' not installed.")
+  }
+  if (!requireNamespace("enmSdmX", quietly = TRUE)) {
+    stop("Required package 'enmSdmX' not installed.")
+  }
+  if (!requireNamespace("SDMtune", quietly = TRUE)) {
+    stop("Required package 'SDMtune' not installed.")
+  }
+  if (!requireNamespace("terra", quietly = TRUE)) {
+    stop("Required package 'terra' not installed.")
+  }
+
+  # Check required objects
+  if (any(sapply(list(model, test, variables, p, bg), is.null))) {
+    stop("One or more required objects (model, test, variables, p, bg) are NULL.")
+  }
+
+  # Validate jaguar and bg data frames
+  stopifnot(
+    is.data.frame(p),
+    is.data.frame(bg),
+    setequal(names(p), c("Longitude", "Latitude")),
+    setequal(names(bg), c("Longitude", "Latitude"))
+  )
+
+  # AUC and TSS calculation
+  auc_value <- SDMtune::auc(model, test = test)
+  tss_value <- SDMtune::tss(model, test = test)
+
+  cat("\nAUC and TSS values:\n")
+  cat("AUC : ", auc_value, "\n")
+  cat("TSS : ", tss_value, "\n")
+
+  # Prediction
+  p_model <- predict(model, data = variables, type = "cloglog")
+  assign(paste0("p_", model_name), p_model, envir = .GlobalEnv)  # Assign prediction object with model name
+
+  # Define a pool of phrases
+  phrases <- c(
+    "Exporting Fangorn's ecological portrait...",
+    "Mapping species distribution in Middle-earth...",
+    "Unveiling Fangorn's biodiversity...",
+    "Orc Territory Snapshot...",
+    "Quendi Domain Unveiled..."
+  )
+
+  # Randomly select a phrase from the pool
+  selected_phrase <- sample(phrases, 1)
+
+  # Print the selected phrase with green color for non-orc phrases
+  if (grepl("Orc", selected_phrase, ignore.case = TRUE)) {
+    cat(crayon::red$bold("\n", selected_phrase, "\n"))
+  } else {
+    cat(crayon::green$bold("\n", selected_phrase, "\n"))
+  }
+
+  # Export prediction raster
+  raster_file <- file.path(output_dir, paste0("p_", model_name, ".tif"))
+  terra::writeRaster(p_model, filename = raster_file, overwrite = TRUE)
+
+  # Combine cross-validation and calculate thresholds
+  model_cv <- SDMtune::combineCV(model)
+  thresholds_result <- SDMtune::thresholds(model_cv, type = "cloglog", test = test)
+
+  # Find the row corresponding to "Maximum test sensitivity plus specificity"
+  max_sensitivity_row <- thresholds_result[thresholds_result$Threshold == "Maximum test sensitivity plus specificity", ]
+
+  # Extract Cloglog value and Test omission rate
+  cloglog_value <- max_sensitivity_row$`Cloglog value`
+  test_omission_rate <- max_sensitivity_row$`Test omission rate`
+
+  # Print the extracted information
+  cat("\nThresholds Information (Maximum test sensitivity plus specificity):\n")
+  cat("Cloglog Value: ", cloglog_value, "\n")
+  cat("Test Omission Rate: ", test_omission_rate, "\n")
+
+  # Assign thresholds object with model name
+  assign(paste0("ths_", model_name), thresholds_result, envir = .GlobalEnv)
+
+  # Head for CBI calculation
+  cat(blue$bold("\nCalculating Boyce Index...\n"))
+
+  # CBI calculation
+  species_presence <- terra::vect(jaguar, geom = c("Longitude", "Latitude"), crs = "WGS84")
+  background_points <- terra::vect(bg, geom = c("Longitude", "Latitude"), crs = "WGS84")
+
+  # Extract values of prediction raster
+  pres <- extract(p_model, species_presence)[, 1]
+  contrast <- extract(p_model, background_points)[, 1]
+
+  # Converts to numeric
+  pres <- as.numeric(pres)
+  contrast <- as.numeric(contrast)
+
+  # Calculate Boyce Index using evalContBoyce function
+  cbiMax <- enmSdmX::evalContBoyce(pres, contrast, na.rm = TRUE)
+  assign(paste0("cbi_", model_name), cbiMax, envir = .GlobalEnv)  # Assign cbi object with model name
+
+  # Print only the CBI value
+  cat("Boyce Index (CBI):", cbiMax, "\n")
+
+  # Organize results in a data frame
+  results_table <- data.frame(
+    AUC = auc_value,
+    TSS = tss_value,
+    Threshold = cloglog_value,
+    Omission = test_omission_rate,
+    CBI = cbiMax
+  )
+
+  return(results_table)
+}
+# Example usage:
+palantir(model, "model_name", test, variables, jaguar, bg)
diff --git a/R/rohirrim.R b/R/rohirrim.R
new file mode 100644
index 0000000..e6f6a97
--- /dev/null
+++ b/R/rohirrim.R
@@ -0,0 +1,58 @@
+#' Calculate Over-Prediction Rate (OPR), Under-Prediction Rate (UPR),
+#' Potential Presence Increment (PPI), and Potential Absence Increment (PAI).
+#'
+#' This function takes an input object with components 'tp', 'fp', 'fn', and 'tn'
+#' representing the counts of true positives, false positives, false negatives,
+#' and true negatives, respectively. It calculates OPR, UPR, PPI, and PAI based
+#' on the input counts and returns the results in a data frame.
+#'
+#' @param obj An object containing counts of true positives (tp), false positives (fp),
+#'   false negatives (fn), and true negatives (tn).
+#'
+#' @return A data frame with columns for OPR, UPR, PPI, and PAI.
+#'
+#' @examples
+#' obj <- list(tp = 10, fp = 5, fn = 3, tn = 20)
+#' result <- rohirrim(obj)
+#' print(result)
+#'
+#' @seealso
+#' \code{\link{print}} for printing the result data frame.
+#'
+#' @keywords rohirrim metrics performance
+#' @export
+rohirrim <- function(obj) {
+  # Input validation
+  if (!all(c("tp", "fp", "fn", "tn") %in% names(obj))) {
+    stop("Input object must contain 'tp', 'fp', 'fn', and 'tn' components.")
+  }
+
+  # Extract values
+  tp <- obj$tp
+  fp <- obj$fp
+  fn <- obj$fn
+  tn <- obj$tn
+
+  # Avoid division by zero
+  if (tp + fp == 0) {
+    stop("The sum of 'tp' and 'fp' is zero. Cannot calculate OPR and PPI.")
+  }
+  if (fn + tn == 0) {
+    stop("The sum of 'fn' and 'tn' is zero. Cannot calculate UPR and PAI.")
+  }
+
+  # Calculate metrics
+  OPR <- fp / (tp + fp)
+  UPR <- fn / (fn + tn)
+  PPI <- (tp + fp) / (tp + fn) - 1
+  PAI <- (fn + tn) / (fp + tn) - 1
+
+  # Create data frame
+  result_df <- data.frame(OPR = OPR,
+                          UPR = UPR,
+                          PPI = PPI,
+                          PAI = PAI)
+
+  return(result_df)
+}
+
diff --git a/man/hello.Rd b/man/hello.Rd
new file mode 100644
index 0000000..0fa7c4b
--- /dev/null
+++ b/man/hello.Rd
@@ -0,0 +1,12 @@
+\name{hello}
+\alias{hello}
+\title{Hello, World!}
+\usage{
+hello()
+}
+\description{
+Prints 'Hello, world!'.
+}
+\examples{
+hello()
+}