From 5bdfe2f54b02a42e2c5c38694f89b299cd197663 Mon Sep 17 00:00:00 2001
From: Jonathan Van Elslander <jonnyvan1@gmail.com>
Date: Thu, 17 Apr 2025 15:04:11 -0700
Subject: [PATCH 1/9] add a title parameter for `scfmDiagnostics` plots

---
 DESCRIPTION            |   2 +-
 NEWS.md                |   1 +
 R/comparePredictions.R | 111 ++++++++++++++++++++++++-----------------
 R/plot_wrappers.R      |   7 ++-
 4 files changed, 72 insertions(+), 49 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index adb85ad..872f0c9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,7 +9,7 @@ URL: https://scfmutils.predictiveecology.org,
     https://github.com/PredictiveEcology/scfmutils,
     https://predictiveecology.github.io/scfmutils/
 Date: 2025-03-12
-Version: 2.0.9.9003
+Version: 2.0.9.9004
 Authors@R: c(
     person("Steve", "Cumming", email = "Steve.Cumming@sbf.ulaval.ca",
            role = c("aut")),
diff --git a/NEWS.md b/NEWS.md
index 3ceb22b..2ba8d1b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,7 @@
 - streamline `prepInputsFireRegimePolys()` for BEC;
 - `prepInputsFireRegimePolys()` gets a new argument `subsetType` to retrieve entire polygons
   bordering `studyArea` or only the spatial intersection (default, preserving previous behaviour) 
+- add a title parameter for `scfmDiagnostics` plots 
 
 # scfmutils 2.0.8
 
diff --git a/R/comparePredictions.R b/R/comparePredictions.R
index 624cbb1..01ad6a3 100644
--- a/R/comparePredictions.R
+++ b/R/comparePredictions.R
@@ -21,17 +21,19 @@ utils::globalVariables(c(
 #' @examples
 #' \dontrun{
 #' ## assumes user has run scfm to produce the simList `mySimOut`
-#' dt <- comparePredictions_summaryDT(fireRegimePoints = mySimOut$fireRegimePoints,
-#'                                    burnSummary = mySimOut$burnSummary,
-#'                                    fireRegimePolys = mySimOut$fireRegimePolys,
-#'                                    times = times(mySimOut))
+#' dt <- comparePredictions_summaryDT(
+#'   fireRegimePoints = mySimOut$fireRegimePoints,
+#'   burnSummary = mySimOut$burnSummary,
+#'   fireRegimePolys = mySimOut$fireRegimePolys,
+#'   times = times(mySimOut)
+#' )
 #'
 #' gg_mfs <- comparePredictions_meanFireSize(dt)
 #' gg_fri <- comparePredictions_fireReturnInterval(dt)
 #' gg_ign <- comparePredictions_annualIgnitions(dt)
 #' gg_frp <- plot_fireRegimePolys(mySimOut$fireRegimePolys)
 #'
-#' gridExtra::grid.arrange(fps,  gg_mfs,  gg_fri,  gg_ign, nrow = 2, ncol = 2)
+#' gridExtra::grid.arrange(fps, gg_mfs, gg_fri, gg_ign, nrow = 2, ncol = 2)
 #' }
 #'
 #' @author Ian Eddy
@@ -43,9 +45,11 @@ utils::globalVariables(c(
 #' @rdname comparePredictions
 comparePredictions_summaryDT <- function(fireRegimePoints = NULL, burnSummary = NULL,
                                          fireRegimePolys = NULL, times = NULL) {
-  if (any(is.null(fireRegimePolys$pSpread), is.null(fireRegimePolys$xBar),
-          is.null(fireRegimePolys$burnyArea), is.null(fireRegimePoints),
-          is.null(burnSummary), is.null(times))) {
+  if (any(
+    is.null(fireRegimePolys$pSpread), is.null(fireRegimePolys$xBar),
+    is.null(fireRegimePolys$burnyArea), is.null(fireRegimePoints),
+    is.null(burnSummary), is.null(times)
+  )) {
     stop("fireRegimePolys is missing columns or insufficient args provided")
   }
 
@@ -62,14 +66,16 @@ comparePredictions_summaryDT <- function(fireRegimePoints = NULL, burnSummary =
     ## median fire size is not used by scfm but is worth recording
     ## regimes where mean is much greater than median will be hard to recreate
     escaped <- fireRegimePoints[fireRegimePoints$SIZE_HA > fireRegimePoly$cellSize, ]
-    medianFireSize <- median(escaped$SIZE_HA) #should be no need for na.rm
+    medianFireSize <- median(escaped$SIZE_HA) # should be no need for na.rm
 
     pSpread <- fireRegimePoly$pSpread
     pIg <- fireRegimePoly$ignitionRate
 
     if (!"grp" %in% names(burnSummary)) {
-      stop("burnSummary data.table does not have a 'grp' column.\n",
-           "Are you running a recent version of scfmSpread (>= 2.0.0)?")
+      stop(
+        "burnSummary data.table does not have a 'grp' column.\n",
+        "Are you running a recent version of scfmSpread (>= 2.0.0)?"
+      )
     }
 
     ## burnSummary data.table from scfmSpread is coded as follows:
@@ -81,12 +87,12 @@ comparePredictions_summaryDT <- function(fireRegimePoints = NULL, burnSummary =
     targetIgnitions <- pIg * fireRegimePoly$burnyArea
     achievedIgnitions <- nrow(burnSum[grp %in% 1, ]) / simLength ## incl grp 2 double counts igns
 
-    #escapes
+    # escapes
     targetEscapes <- fireRegimePoly$pEscape * targetIgnitions
     achievedEscapes <- nrow(burnSum[grp %in% 1 & N > 1]) / simLength
 
     ## mean fire size: mean size of all fires ignited and escaped in SAR, regardless of where spread
-    burnSum1 <- burnSum[grp %in% c(1, 2), lapply(.SD, sum), by = c("igLoc", "year"), .SDcols = "areaBurned"]  # nolint
+    burnSum1 <- burnSum[grp %in% c(1, 2), lapply(.SD, sum), by = c("igLoc", "year"), .SDcols = "areaBurned"] # nolint
     burnSum1 <- burnSum1[areaBurned %>>% fireRegimePoly$cellSize, ]
     meanFireSize <- ifelse(nrow(burnSum1) == 0, 0, mean(burnSum1$areaBurned))
 
@@ -96,23 +102,25 @@ comparePredictions_summaryDT <- function(fireRegimePoints = NULL, burnSummary =
     MAAB <- sum(burnSum2$areaBurned) / simLength
 
     achievedFRI <- simLength / (sum(0, burnSum2$areaBurned) / fireRegimePoly$burnyArea)
-    targetFRI  <- 1 / fireRegimePoly$empiricalBurnRate
-
-    pred <- data.frame("PolyID" = x,
-                       "histMeanSize" = fireRegimePoly$xBar, ## predicted (empirical) mean fire size
-                       "histMedianSize" = medianFireSize,
-                       "modMeanSize" = meanFireSize,
-                       "achievedFRI" = achievedFRI,
-                       "targetFRI" = targetFRI,
-                       "burnableArea_ha" = fireRegimePoly$burnyArea,
-                       "targetIgnitions" = targetIgnitions,
-                       "achievedIgnitions" = achievedIgnitions,
-                       "targetEscapes" = targetEscapes,
-                       "achievedEscapes" = achievedEscapes,
-                       "pEscape" = fireRegimePoly$pEscape, ## escape prob (no. fires > cellSize / no. fires)
-                       "p0" = fireRegimePoly$p0,  ## p0 and pEscape may indicate something incorrect
-                       "pSpread" = pSpread, ## spread probability estimated from the SCAM model
-                       "pIgnition" = pIg) ## ignition probability of a single pixel
+    targetFRI <- 1 / fireRegimePoly$empiricalBurnRate
+
+    pred <- data.frame(
+      "PolyID" = x,
+      "histMeanSize" = fireRegimePoly$xBar, ## predicted (empirical) mean fire size
+      "histMedianSize" = medianFireSize,
+      "modMeanSize" = meanFireSize,
+      "achievedFRI" = achievedFRI,
+      "targetFRI" = targetFRI,
+      "burnableArea_ha" = fireRegimePoly$burnyArea,
+      "targetIgnitions" = targetIgnitions,
+      "achievedIgnitions" = achievedIgnitions,
+      "targetEscapes" = targetEscapes,
+      "achievedEscapes" = achievedEscapes,
+      "pEscape" = fireRegimePoly$pEscape, ## escape prob (no. fires > cellSize / no. fires)
+      "p0" = fireRegimePoly$p0, ## p0 and pEscape may indicate something incorrect
+      "pSpread" = pSpread, ## spread probability estimated from the SCAM model
+      "pIgnition" = pIg
+    ) ## ignition probability of a single pixel
     return(pred)
   })
   return(rbindlist(out))
@@ -120,11 +128,13 @@ comparePredictions_summaryDT <- function(fireRegimePoints = NULL, burnSummary =
 
 #' @param dt scfm summary `data.table` produced by `comparePredictions_summaryDT()`
 #'
+#' @param title character, the plot title
+#'
 #' @export
 #' @importFrom ggplot2 aes geom_abline geom_point geom_text ggplot labs
 #' @importFrom ggplot2 scale_x_continuous scale_y_continuous theme_bw xlab ylab
 #' @rdname comparePredictions
-comparePredictions_meanFireSize <- function(dt) {
+comparePredictions_meanFireSize <- function(dt, title) {
   if (any(is.null(dt))) {
     stop("all arguments must be provided and cannot be NULL.")
   }
@@ -136,12 +146,13 @@ comparePredictions_meanFireSize <- function(dt) {
     scale_y_continuous(limits = c(0, NA)) +
     scale_x_continuous(limits = c(0, NA)) +
     geom_text(aes(label = PolyID), vjust = "inward", hjust = "inward") +
-    geom_abline(slope = 1)
+    geom_abline(slope = 1) +
+    ggtitle(title)
 }
 
 #' @export
 #' @rdname comparePredictions
-comparePredictions_fireReturnInterval <- function(dt, times) {
+comparePredictions_fireReturnInterval <- function(dt, times, title) {
   if (any(is.null(dt), is.null(times))) {
     stop("all arguments must be provided and cannot be NULL.")
   }
@@ -155,25 +166,28 @@ comparePredictions_fireReturnInterval <- function(dt, times) {
   }
 
   ## TODO: remove targetFRI filter below. plot those points differently to indicate poor estimates
-  ggplot(dt[!is.infinite(achievedFRI) & targetFRI < c(times$end - times$start) * 4],
-         aes(x = targetFRI, y = achievedFRI)) +
+  ggplot(
+    dt[!is.infinite(achievedFRI) & targetFRI < c(times$end - times$start) * 4],
+    aes(x = targetFRI, y = achievedFRI)
+  ) +
     geom_point() +
     labs(y = "simulation FRI (years)", x = "estimated FRI (years)") +
     theme_bw() +
     geom_abline(slope = 1) +
     scale_y_continuous(limits = c(0, NA)) +
     scale_x_continuous(limits = c(0, NA)) +
-    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
+    ggtitle(title)
 }
 
 #' @export
 #' @rdname comparePredictions
-comparePredictions_annualIgnitions <- function(dt) {
+comparePredictions_annualIgnitions <- function(dt, title) {
   if (any(is.null(dt))) {
     stop("all arguments must be provided and cannot be NULL.")
   }
 
-  dt <- copy(dt) #avoid adding per ha cols (or add them?)
+  dt <- copy(dt) # avoid adding per ha cols (or add them?)
   dt[, targetIgnitions_Mha := targetIgnitions / burnableArea_ha * 1e6]
   dt[, achievedIgnitions_Mha := achievedIgnitions / burnableArea_ha * 1e6]
 
@@ -185,17 +199,18 @@ comparePredictions_annualIgnitions <- function(dt) {
     geom_abline(slope = 1) +
     scale_y_continuous(limits = c(0, NA)) +
     scale_x_continuous(limits = c(0, NA)) +
-    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
+    ggtitle(title)
 }
 
 #' @export
 #' @rdname comparePredictions
-comparePredictions_annualEscapes <- function(dt) {
+comparePredictions_annualEscapes <- function(dt, title) {
   if (any(is.null(dt))) {
     stop("all arguments must be provided and cannot be NULL.")
   }
 
-  dt <- copy(dt) #avoid adding per ha cols (or add them?)
+  dt <- copy(dt) # avoid adding per ha cols (or add them?)
   dt[, targetEscapes_Mha := targetEscapes / burnableArea_ha * 1e6]
   dt[, achievedEscapes_Mha := achievedEscapes / burnableArea_ha * 1e6]
 
@@ -207,19 +222,22 @@ comparePredictions_annualEscapes <- function(dt) {
     geom_abline(slope = 1) +
     scale_y_continuous(limits = c(0, NA)) +
     scale_x_continuous(limits = c(0, NA)) +
-    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
+    ggtitle(title)
 }
 
 #' @param size minimum fire size (ha)
 #'
+#' @param title character, the plot title
+#'
 #' @export
 #' @importFrom data.table as.data.table setnames
 #' @importFrom fpCompare %>>%
 #' @importFrom ggplot2 facet_wrap geom_histogram
 #' @rdname comparePredictions
-comparePredictions_fireDistribution <- function(fireRegimePoints = NULL, burnSummary = NULL, size) {
+comparePredictions_fireDistribution <- function(fireRegimePoints = NULL, burnSummary = NULL, size, title) {
   histDistribution <- fireRegimePoints[fireRegimePoints$SIZE_HA %>>% size, ]
-  if (nrow(histDistribution) < 1){
+  if (nrow(histDistribution) < 1) {
     warning("no historical fires > escape size - showing all fires instead")
     histDistribution <- fireRegimePoints
   }
@@ -235,11 +253,12 @@ comparePredictions_fireDistribution <- function(fireRegimePoints = NULL, burnSum
   simDistribution[, source := "simulated"]
 
   allFires <- rbind(simDistribution, histDistribution, fill = TRUE)
-  allFires[ , PolyID := as.factor(PolyID)]
+  allFires[, PolyID := as.factor(PolyID)]
 
   ggplot(allFires, aes(x = log(areaBurned), fill = PolyID)) +
     geom_histogram() +
     xlab("log of escaped fire size (ha)") +
     theme_bw() +
-    facet_wrap(~source, scales = "free_y", nrow = 2)
+    facet_wrap(~source, scales = "free_y", nrow = 2) +
+    ggtitle(title)
 }
diff --git a/R/plot_wrappers.R b/R/plot_wrappers.R
index 6372b2f..19b2e96 100644
--- a/R/plot_wrappers.R
+++ b/R/plot_wrappers.R
@@ -4,13 +4,15 @@ utils::globalVariables(c(
 
 #' Plot fire regime polygons
 #'
-#' @template fireRegimePolys
+#' @template fireRegimePolys#'
+#'
+#' @param title character, the plot title
 #'
 #' @returns a `ggplot` object
 #'
 #' @export
 #' @importFrom ggplot2 aes geom_sf ggplot scale_fill_discrete theme_minimal
-plot_fireRegimePolys <- function(fireRegimePolys) {
+plot_fireRegimePolys <- function(fireRegimePolys, title) {
   if (!is.factor(fireRegimePolys$PolyID)) {
     fireRegimePolys$PolyID <- as.factor(fireRegimePolys$PolyID)
   }
@@ -18,6 +20,7 @@ plot_fireRegimePolys <- function(fireRegimePolys) {
   ggplot(fireRegimePolys) +
     geom_sf(aes(fill = PolyID)) +
     scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
+    ggtitle(title) +
     theme_bw()
 }
 

From cf0227273beb8d5180830becdbc6f5b6a889c611 Mon Sep 17 00:00:00 2001
From: Jonathan Van Elslander <jonnyvan1@gmail.com>
Date: Thu, 17 Apr 2025 15:26:27 -0700
Subject: [PATCH 2/9] ran document and rcmdcheck

---
 R/plot_wrappers.R           |  2 +-
 man/comparePredictions.Rd   | 25 +++++++++++++++----------
 man/plot_fireRegimePolys.Rd |  4 +++-
 3 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/R/plot_wrappers.R b/R/plot_wrappers.R
index 19b2e96..902e540 100644
--- a/R/plot_wrappers.R
+++ b/R/plot_wrappers.R
@@ -4,7 +4,7 @@ utils::globalVariables(c(
 
 #' Plot fire regime polygons
 #'
-#' @template fireRegimePolys#'
+#' @template fireRegimePolys
 #'
 #' @param title character, the plot title
 #'
diff --git a/man/comparePredictions.Rd b/man/comparePredictions.Rd
index 784f8fc..39a38a6 100644
--- a/man/comparePredictions.Rd
+++ b/man/comparePredictions.Rd
@@ -16,18 +16,19 @@ comparePredictions_summaryDT(
   times = NULL
 )
 
-comparePredictions_meanFireSize(dt)
+comparePredictions_meanFireSize(dt, title)
 
-comparePredictions_fireReturnInterval(dt, times)
+comparePredictions_fireReturnInterval(dt, times, title)
 
-comparePredictions_annualIgnitions(dt)
+comparePredictions_annualIgnitions(dt, title)
 
-comparePredictions_annualEscapes(dt)
+comparePredictions_annualEscapes(dt, title)
 
 comparePredictions_fireDistribution(
   fireRegimePoints = NULL,
   burnSummary = NULL,
-  size
+  size,
+  title
 )
 }
 \arguments{
@@ -41,6 +42,8 @@ comparePredictions_fireDistribution(
 
 \item{dt}{scfm summary \code{data.table} produced by \code{comparePredictions_summaryDT()}}
 
+\item{title}{character, the plot title}
+
 \item{size}{minimum fire size (ha)}
 }
 \value{
@@ -53,17 +56,19 @@ Create \code{data.table} to compare scfm predictions with historical observation
 \examples{
 \dontrun{
 ## assumes user has run scfm to produce the simList `mySimOut`
-dt <- comparePredictions_summaryDT(fireRegimePoints = mySimOut$fireRegimePoints,
-                                   burnSummary = mySimOut$burnSummary,
-                                   fireRegimePolys = mySimOut$fireRegimePolys,
-                                   times = times(mySimOut))
+dt <- comparePredictions_summaryDT(
+  fireRegimePoints = mySimOut$fireRegimePoints,
+  burnSummary = mySimOut$burnSummary,
+  fireRegimePolys = mySimOut$fireRegimePolys,
+  times = times(mySimOut)
+)
 
 gg_mfs <- comparePredictions_meanFireSize(dt)
 gg_fri <- comparePredictions_fireReturnInterval(dt)
 gg_ign <- comparePredictions_annualIgnitions(dt)
 gg_frp <- plot_fireRegimePolys(mySimOut$fireRegimePolys)
 
-gridExtra::grid.arrange(fps,  gg_mfs,  gg_fri,  gg_ign, nrow = 2, ncol = 2)
+gridExtra::grid.arrange(fps, gg_mfs, gg_fri, gg_ign, nrow = 2, ncol = 2)
 }
 
 }
diff --git a/man/plot_fireRegimePolys.Rd b/man/plot_fireRegimePolys.Rd
index 1e53826..cee5fe8 100644
--- a/man/plot_fireRegimePolys.Rd
+++ b/man/plot_fireRegimePolys.Rd
@@ -4,10 +4,12 @@
 \alias{plot_fireRegimePolys}
 \title{Plot fire regime polygons}
 \usage{
-plot_fireRegimePolys(fireRegimePolys)
+plot_fireRegimePolys(fireRegimePolys, title)
 }
 \arguments{
 \item{fireRegimePolys}{\code{sf} polygon or multipolygon object defining the fire regime polygons}
+
+\item{title}{character, the plot title}
 }
 \value{
 a \code{ggplot} object

From a68e768ffad4bfd2e74c867ff664e87721f4f5bb Mon Sep 17 00:00:00 2001
From: Jonathan Van Elslander <jonnyvan1@gmail.com>
Date: Tue, 29 Apr 2025 11:40:17 -0700
Subject: [PATCH 3/9] added ifElse to allow plots to run if runName not
 provided

---
 R/comparePredictions.R | 150 +++++++++++++++++++++++++++--------------
 R/plot_wrappers.R      |  19 ++++--
 2 files changed, 114 insertions(+), 55 deletions(-)

diff --git a/R/comparePredictions.R b/R/comparePredictions.R
index 01ad6a3..2c753ef 100644
--- a/R/comparePredictions.R
+++ b/R/comparePredictions.R
@@ -139,22 +139,33 @@ comparePredictions_meanFireSize <- function(dt, title) {
     stop("all arguments must be provided and cannot be NULL.")
   }
 
-  ggplot(dt, aes(x = histMeanSize, y = modMeanSize)) +
-    geom_point(aes(histMeanSize, modMeanSize)) +
-    labs(x = "historical mean fire size (ha)", y = "modeled mean fire size (ha)") +
-    theme_bw() +
-    scale_y_continuous(limits = c(0, NA)) +
-    scale_x_continuous(limits = c(0, NA)) +
-    geom_text(aes(label = PolyID), vjust = "inward", hjust = "inward") +
-    geom_abline(slope = 1) +
-    ggtitle(title)
+  if (is.null(title)) {
+    ggplot(dt, aes(x = histMeanSize, y = modMeanSize)) +
+      geom_point(aes(histMeanSize, modMeanSize)) +
+      labs(x = "historical mean fire size (ha)", y = "modeled mean fire size (ha)") +
+      theme_bw() +
+      scale_y_continuous(limits = c(0, NA)) +
+      scale_x_continuous(limits = c(0, NA)) +
+      geom_text(aes(label = PolyID), vjust = "inward", hjust = "inward") +
+      geom_abline(slope = 1)
+  } else {
+    ggplot(dt, aes(x = histMeanSize, y = modMeanSize)) +
+      geom_point(aes(histMeanSize, modMeanSize)) +
+      labs(x = "historical mean fire size (ha)", y = "modeled mean fire size (ha)") +
+      theme_bw() +
+      scale_y_continuous(limits = c(0, NA)) +
+      scale_x_continuous(limits = c(0, NA)) +
+      geom_text(aes(label = PolyID), vjust = "inward", hjust = "inward") +
+      geom_abline(slope = 1) +
+      ggtitle(title)
+  }
 }
 
 #' @export
 #' @rdname comparePredictions
 comparePredictions_fireReturnInterval <- function(dt, times, title) {
   if (any(is.null(dt), is.null(times))) {
-    stop("all arguments must be provided and cannot be NULL.")
+    stop("dt and times must be provided and cannot be NULL.")
   }
 
   ## remove the infinite FRI caused by no simulated fires
@@ -164,20 +175,33 @@ comparePredictions_fireReturnInterval <- function(dt, times, title) {
     ## TODO: confirm wording of this, with comment above
     warning("achievedFRI may be off where targetFRI is less than 4x the simulated time.")
   }
-
   ## TODO: remove targetFRI filter below. plot those points differently to indicate poor estimates
-  ggplot(
-    dt[!is.infinite(achievedFRI) & targetFRI < c(times$end - times$start) * 4],
-    aes(x = targetFRI, y = achievedFRI)
-  ) +
-    geom_point() +
-    labs(y = "simulation FRI (years)", x = "estimated FRI (years)") +
-    theme_bw() +
-    geom_abline(slope = 1) +
-    scale_y_continuous(limits = c(0, NA)) +
-    scale_x_continuous(limits = c(0, NA)) +
-    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
-    ggtitle(title)
+  if (is.null(title)) {
+    ggplot(
+      dt[!is.infinite(achievedFRI) & targetFRI < c(times$end - times$start) * 4],
+      aes(x = targetFRI, y = achievedFRI)
+    ) +
+      geom_point() +
+      labs(y = "simulation FRI (years)", x = "estimated FRI (years)") +
+      theme_bw() +
+      geom_abline(slope = 1) +
+      scale_y_continuous(limits = c(0, NA)) +
+      scale_x_continuous(limits = c(0, NA)) +
+      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+  } else {
+    ggplot(
+      dt[!is.infinite(achievedFRI) & targetFRI < c(times$end - times$start) * 4],
+      aes(x = targetFRI, y = achievedFRI)
+    ) +
+      geom_point() +
+      labs(y = "simulation FRI (years)", x = "estimated FRI (years)") +
+      theme_bw() +
+      geom_abline(slope = 1) +
+      scale_y_continuous(limits = c(0, NA)) +
+      scale_x_continuous(limits = c(0, NA)) +
+      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
+      ggtitle(title)
+  }
 }
 
 #' @export
@@ -191,16 +215,26 @@ comparePredictions_annualIgnitions <- function(dt, title) {
   dt[, targetIgnitions_Mha := targetIgnitions / burnableArea_ha * 1e6]
   dt[, achievedIgnitions_Mha := achievedIgnitions / burnableArea_ha * 1e6]
 
-
-  ggplot(dt, aes(x = targetIgnitions_Mha, y = achievedIgnitions_Mha)) +
-    geom_point() +
-    labs(y = "simulation annual ignitions (per Mha)", x = "estimated annual ignitions (per Mha)") +
-    theme_bw() +
-    geom_abline(slope = 1) +
-    scale_y_continuous(limits = c(0, NA)) +
-    scale_x_continuous(limits = c(0, NA)) +
-    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
-    ggtitle(title)
+  if (is.null(title)) {
+    ggplot(dt, aes(x = targetIgnitions_Mha, y = achievedIgnitions_Mha)) +
+      geom_point() +
+      labs(y = "simulation annual ignitions (per Mha)", x = "estimated annual ignitions (per Mha)") +
+      theme_bw() +
+      geom_abline(slope = 1) +
+      scale_y_continuous(limits = c(0, NA)) +
+      scale_x_continuous(limits = c(0, NA)) +
+      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+  } else {
+    ggplot(dt, aes(x = targetIgnitions_Mha, y = achievedIgnitions_Mha)) +
+      geom_point() +
+      labs(y = "simulation annual ignitions (per Mha)", x = "estimated annual ignitions (per Mha)") +
+      theme_bw() +
+      geom_abline(slope = 1) +
+      scale_y_continuous(limits = c(0, NA)) +
+      scale_x_continuous(limits = c(0, NA)) +
+      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
+      ggtitle(title)
+  }
 }
 
 #' @export
@@ -214,16 +248,26 @@ comparePredictions_annualEscapes <- function(dt, title) {
   dt[, targetEscapes_Mha := targetEscapes / burnableArea_ha * 1e6]
   dt[, achievedEscapes_Mha := achievedEscapes / burnableArea_ha * 1e6]
 
-
-  ggplot(dt, aes(x = targetEscapes_Mha, y = achievedEscapes_Mha)) +
-    geom_point() +
-    labs(y = "simulation annual escapes (per Mha)", x = "estimated annual escapes (per Mha)") +
-    theme_bw() +
-    geom_abline(slope = 1) +
-    scale_y_continuous(limits = c(0, NA)) +
-    scale_x_continuous(limits = c(0, NA)) +
-    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
-    ggtitle(title)
+  if (is.null(title)) {
+    ggplot(dt, aes(x = targetEscapes_Mha, y = achievedEscapes_Mha)) +
+      geom_point() +
+      labs(y = "simulation annual escapes (per Mha)", x = "estimated annual escapes (per Mha)") +
+      theme_bw() +
+      geom_abline(slope = 1) +
+      scale_y_continuous(limits = c(0, NA)) +
+      scale_x_continuous(limits = c(0, NA)) +
+      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+  } else {
+    ggplot(dt, aes(x = targetEscapes_Mha, y = achievedEscapes_Mha)) +
+      geom_point() +
+      labs(y = "simulation annual escapes (per Mha)", x = "estimated annual escapes (per Mha)") +
+      theme_bw() +
+      geom_abline(slope = 1) +
+      scale_y_continuous(limits = c(0, NA)) +
+      scale_x_continuous(limits = c(0, NA)) +
+      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
+      ggtitle(title)
+  }
 }
 
 #' @param size minimum fire size (ha)
@@ -255,10 +299,18 @@ comparePredictions_fireDistribution <- function(fireRegimePoints = NULL, burnSum
   allFires <- rbind(simDistribution, histDistribution, fill = TRUE)
   allFires[, PolyID := as.factor(PolyID)]
 
-  ggplot(allFires, aes(x = log(areaBurned), fill = PolyID)) +
-    geom_histogram() +
-    xlab("log of escaped fire size (ha)") +
-    theme_bw() +
-    facet_wrap(~source, scales = "free_y", nrow = 2) +
-    ggtitle(title)
+  if (is.null(title)) {
+    ggplot(allFires, aes(x = log(areaBurned), fill = PolyID)) +
+      geom_histogram() +
+      xlab("log of escaped fire size (ha)") +
+      theme_bw() +
+      facet_wrap(~source, scales = "free_y", nrow = 2)
+  } else {
+    ggplot(allFires, aes(x = log(areaBurned), fill = PolyID)) +
+      geom_histogram() +
+      xlab("log of escaped fire size (ha)") +
+      theme_bw() +
+      facet_wrap(~source, scales = "free_y", nrow = 2) +
+      ggtitle(title)
+  }
 }
diff --git a/R/plot_wrappers.R b/R/plot_wrappers.R
index 902e540..2e6c5d8 100644
--- a/R/plot_wrappers.R
+++ b/R/plot_wrappers.R
@@ -16,12 +16,19 @@ plot_fireRegimePolys <- function(fireRegimePolys, title) {
   if (!is.factor(fireRegimePolys$PolyID)) {
     fireRegimePolys$PolyID <- as.factor(fireRegimePolys$PolyID)
   }
-
-  ggplot(fireRegimePolys) +
-    geom_sf(aes(fill = PolyID)) +
-    scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
-    ggtitle(title) +
-    theme_bw()
+  if (is.null(title)) {
+    ggplot(fireRegimePolys) +
+      geom_sf(aes(fill = PolyID)) +
+      scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
+      theme_bw()
+  }
+  else {
+    ggplot(fireRegimePolys) +
+      geom_sf(aes(fill = PolyID)) +
+      scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
+      ggtitle(title) +
+      theme_bw()
+  }
 }
 
 #' Plot fire regime raster

From 73ecf75034bb80d1c20bab747fb4bb9d2c52c97d Mon Sep 17 00:00:00 2001
From: Jonathan Van Elslander <jonnyvan1@gmail.com>
Date: Tue, 29 Apr 2025 14:40:01 -0700
Subject: [PATCH 4/9] changed diagnostic plot titles default to NULL

---
 R/comparePredictions.R | 10 +++++-----
 R/plot_wrappers.R      |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/comparePredictions.R b/R/comparePredictions.R
index 2c753ef..fed71e7 100644
--- a/R/comparePredictions.R
+++ b/R/comparePredictions.R
@@ -134,7 +134,7 @@ comparePredictions_summaryDT <- function(fireRegimePoints = NULL, burnSummary =
 #' @importFrom ggplot2 aes geom_abline geom_point geom_text ggplot labs
 #' @importFrom ggplot2 scale_x_continuous scale_y_continuous theme_bw xlab ylab
 #' @rdname comparePredictions
-comparePredictions_meanFireSize <- function(dt, title) {
+comparePredictions_meanFireSize <- function(dt, title = NULL) {
   if (any(is.null(dt))) {
     stop("all arguments must be provided and cannot be NULL.")
   }
@@ -163,7 +163,7 @@ comparePredictions_meanFireSize <- function(dt, title) {
 
 #' @export
 #' @rdname comparePredictions
-comparePredictions_fireReturnInterval <- function(dt, times, title) {
+comparePredictions_fireReturnInterval <- function(dt, times, title = NULL) {
   if (any(is.null(dt), is.null(times))) {
     stop("dt and times must be provided and cannot be NULL.")
   }
@@ -206,7 +206,7 @@ comparePredictions_fireReturnInterval <- function(dt, times, title) {
 
 #' @export
 #' @rdname comparePredictions
-comparePredictions_annualIgnitions <- function(dt, title) {
+comparePredictions_annualIgnitions <- function(dt, title = NULL) {
   if (any(is.null(dt))) {
     stop("all arguments must be provided and cannot be NULL.")
   }
@@ -239,7 +239,7 @@ comparePredictions_annualIgnitions <- function(dt, title) {
 
 #' @export
 #' @rdname comparePredictions
-comparePredictions_annualEscapes <- function(dt, title) {
+comparePredictions_annualEscapes <- function(dt, title = NULL) {
   if (any(is.null(dt))) {
     stop("all arguments must be provided and cannot be NULL.")
   }
@@ -279,7 +279,7 @@ comparePredictions_annualEscapes <- function(dt, title) {
 #' @importFrom fpCompare %>>%
 #' @importFrom ggplot2 facet_wrap geom_histogram
 #' @rdname comparePredictions
-comparePredictions_fireDistribution <- function(fireRegimePoints = NULL, burnSummary = NULL, size, title) {
+comparePredictions_fireDistribution <- function(fireRegimePoints = NULL, burnSummary = NULL, size, title = NULL) {
   histDistribution <- fireRegimePoints[fireRegimePoints$SIZE_HA %>>% size, ]
   if (nrow(histDistribution) < 1) {
     warning("no historical fires > escape size - showing all fires instead")
diff --git a/R/plot_wrappers.R b/R/plot_wrappers.R
index 2e6c5d8..d34e42e 100644
--- a/R/plot_wrappers.R
+++ b/R/plot_wrappers.R
@@ -12,7 +12,7 @@ utils::globalVariables(c(
 #'
 #' @export
 #' @importFrom ggplot2 aes geom_sf ggplot scale_fill_discrete theme_minimal
-plot_fireRegimePolys <- function(fireRegimePolys, title) {
+plot_fireRegimePolys <- function(fireRegimePolys, title = NULL) {
   if (!is.factor(fireRegimePolys$PolyID)) {
     fireRegimePolys$PolyID <- as.factor(fireRegimePolys$PolyID)
   }

From 3f1c08dd3df7e1e280891484f6966e41b87ec334 Mon Sep 17 00:00:00 2001
From: Jonathan Van Elslander <jonnyvan1@gmail.com>
Date: Fri, 30 May 2025 14:52:45 -0700
Subject: [PATCH 5/9] Updates coding for plot titles for concision

---
 R/comparePredictions.R | 146 ++++++++++++++---------------------------
 1 file changed, 50 insertions(+), 96 deletions(-)

diff --git a/R/comparePredictions.R b/R/comparePredictions.R
index fed71e7..6b8e985 100644
--- a/R/comparePredictions.R
+++ b/R/comparePredictions.R
@@ -138,26 +138,16 @@ comparePredictions_meanFireSize <- function(dt, title = NULL) {
   if (any(is.null(dt))) {
     stop("all arguments must be provided and cannot be NULL.")
   }
-
-  if (is.null(title)) {
-    ggplot(dt, aes(x = histMeanSize, y = modMeanSize)) +
-      geom_point(aes(histMeanSize, modMeanSize)) +
-      labs(x = "historical mean fire size (ha)", y = "modeled mean fire size (ha)") +
-      theme_bw() +
-      scale_y_continuous(limits = c(0, NA)) +
-      scale_x_continuous(limits = c(0, NA)) +
-      geom_text(aes(label = PolyID), vjust = "inward", hjust = "inward") +
-      geom_abline(slope = 1)
-  } else {
-    ggplot(dt, aes(x = histMeanSize, y = modMeanSize)) +
-      geom_point(aes(histMeanSize, modMeanSize)) +
-      labs(x = "historical mean fire size (ha)", y = "modeled mean fire size (ha)") +
-      theme_bw() +
-      scale_y_continuous(limits = c(0, NA)) +
-      scale_x_continuous(limits = c(0, NA)) +
-      geom_text(aes(label = PolyID), vjust = "inward", hjust = "inward") +
-      geom_abline(slope = 1) +
-      ggtitle(title)
+  gg_mfs <- ggplot(dt, aes(x = histMeanSize, y = modMeanSize)) +
+    geom_point(aes(histMeanSize, modMeanSize)) +
+    labs(x = "historical mean fire size (ha)", y = "modeled mean fire size (ha)") +
+    theme_bw() +
+    scale_y_continuous(limits = c(0, NA)) +
+    scale_x_continuous(limits = c(0, NA)) +
+    geom_text(aes(label = PolyID), vjust = "inward", hjust = "inward") +
+    geom_abline(slope = 1)
+  if (!is.null(title)) {
+    gg_mfs + ggtitle(title)
   }
 }
 
@@ -176,31 +166,19 @@ comparePredictions_fireReturnInterval <- function(dt, times, title = NULL) {
     warning("achievedFRI may be off where targetFRI is less than 4x the simulated time.")
   }
   ## TODO: remove targetFRI filter below. plot those points differently to indicate poor estimates
-  if (is.null(title)) {
-    ggplot(
-      dt[!is.infinite(achievedFRI) & targetFRI < c(times$end - times$start) * 4],
-      aes(x = targetFRI, y = achievedFRI)
-    ) +
-      geom_point() +
-      labs(y = "simulation FRI (years)", x = "estimated FRI (years)") +
-      theme_bw() +
-      geom_abline(slope = 1) +
-      scale_y_continuous(limits = c(0, NA)) +
-      scale_x_continuous(limits = c(0, NA)) +
-      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
-  } else {
-    ggplot(
-      dt[!is.infinite(achievedFRI) & targetFRI < c(times$end - times$start) * 4],
-      aes(x = targetFRI, y = achievedFRI)
-    ) +
-      geom_point() +
-      labs(y = "simulation FRI (years)", x = "estimated FRI (years)") +
-      theme_bw() +
-      geom_abline(slope = 1) +
-      scale_y_continuous(limits = c(0, NA)) +
-      scale_x_continuous(limits = c(0, NA)) +
-      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
-      ggtitle(title)
+  gg_fri <- ggplot(
+    dt[!is.infinite(achievedFRI) & targetFRI < c(times$end - times$start) * 4],
+    aes(x = targetFRI, y = achievedFRI)
+  ) +
+    geom_point() +
+    labs(y = "simulation FRI (years)", x = "estimated FRI (years)") +
+    theme_bw() +
+    geom_abline(slope = 1) +
+    scale_y_continuous(limits = c(0, NA)) +
+    scale_x_continuous(limits = c(0, NA)) +
+    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+  if (!is.null(title)) {
+    gg_fri + ggtitle(title)
   }
 }
 
@@ -215,25 +193,16 @@ comparePredictions_annualIgnitions <- function(dt, title = NULL) {
   dt[, targetIgnitions_Mha := targetIgnitions / burnableArea_ha * 1e6]
   dt[, achievedIgnitions_Mha := achievedIgnitions / burnableArea_ha * 1e6]
 
-  if (is.null(title)) {
-    ggplot(dt, aes(x = targetIgnitions_Mha, y = achievedIgnitions_Mha)) +
-      geom_point() +
-      labs(y = "simulation annual ignitions (per Mha)", x = "estimated annual ignitions (per Mha)") +
-      theme_bw() +
-      geom_abline(slope = 1) +
-      scale_y_continuous(limits = c(0, NA)) +
-      scale_x_continuous(limits = c(0, NA)) +
-      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
-  } else {
-    ggplot(dt, aes(x = targetIgnitions_Mha, y = achievedIgnitions_Mha)) +
-      geom_point() +
-      labs(y = "simulation annual ignitions (per Mha)", x = "estimated annual ignitions (per Mha)") +
-      theme_bw() +
-      geom_abline(slope = 1) +
-      scale_y_continuous(limits = c(0, NA)) +
-      scale_x_continuous(limits = c(0, NA)) +
-      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
-      ggtitle(title)
+  gg_ai <- ggplot(dt, aes(x = targetIgnitions_Mha, y = achievedIgnitions_Mha)) +
+    geom_point() +
+    labs(y = "simulation annual ignitions (per Mha)", x = "estimated annual ignitions (per Mha)") +
+    theme_bw() +
+    geom_abline(slope = 1) +
+    scale_y_continuous(limits = c(0, NA)) +
+    scale_x_continuous(limits = c(0, NA)) +
+    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+  if (!is.null(title)) {
+    gg_ai + ggtitle(title)
   }
 }
 
@@ -248,25 +217,16 @@ comparePredictions_annualEscapes <- function(dt, title = NULL) {
   dt[, targetEscapes_Mha := targetEscapes / burnableArea_ha * 1e6]
   dt[, achievedEscapes_Mha := achievedEscapes / burnableArea_ha * 1e6]
 
-  if (is.null(title)) {
-    ggplot(dt, aes(x = targetEscapes_Mha, y = achievedEscapes_Mha)) +
-      geom_point() +
-      labs(y = "simulation annual escapes (per Mha)", x = "estimated annual escapes (per Mha)") +
-      theme_bw() +
-      geom_abline(slope = 1) +
-      scale_y_continuous(limits = c(0, NA)) +
-      scale_x_continuous(limits = c(0, NA)) +
-      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
-  } else {
-    ggplot(dt, aes(x = targetEscapes_Mha, y = achievedEscapes_Mha)) +
-      geom_point() +
-      labs(y = "simulation annual escapes (per Mha)", x = "estimated annual escapes (per Mha)") +
-      theme_bw() +
-      geom_abline(slope = 1) +
-      scale_y_continuous(limits = c(0, NA)) +
-      scale_x_continuous(limits = c(0, NA)) +
-      geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward")) +
-      ggtitle(title)
+  gg_ae <- ggplot(dt, aes(x = targetEscapes_Mha, y = achievedEscapes_Mha)) +
+    geom_point() +
+    labs(y = "simulation annual escapes (per Mha)", x = "estimated annual escapes (per Mha)") +
+    theme_bw() +
+    geom_abline(slope = 1) +
+    scale_y_continuous(limits = c(0, NA)) +
+    scale_x_continuous(limits = c(0, NA)) +
+    geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
+  if (!is.null(title)) {
+    gg_ae + ggtitle(title)
   }
 }
 
@@ -299,18 +259,12 @@ comparePredictions_fireDistribution <- function(fireRegimePoints = NULL, burnSum
   allFires <- rbind(simDistribution, histDistribution, fill = TRUE)
   allFires[, PolyID := as.factor(PolyID)]
 
-  if (is.null(title)) {
-    ggplot(allFires, aes(x = log(areaBurned), fill = PolyID)) +
-      geom_histogram() +
-      xlab("log of escaped fire size (ha)") +
-      theme_bw() +
-      facet_wrap(~source, scales = "free_y", nrow = 2)
-  } else {
-    ggplot(allFires, aes(x = log(areaBurned), fill = PolyID)) +
-      geom_histogram() +
-      xlab("log of escaped fire size (ha)") +
-      theme_bw() +
-      facet_wrap(~source, scales = "free_y", nrow = 2) +
-      ggtitle(title)
+  gg_fd <- ggplot(allFires, aes(x = log(areaBurned), fill = PolyID)) +
+    geom_histogram() +
+    xlab("log of escaped fire size (ha)") +
+    theme_bw() +
+    facet_wrap(~source, scales = "free_y", nrow = 2)
+  if (!is.null(title)) {
+    gg_fd + ggtitle(title)
   }
 }

From 70f6c513af9a497dcbe8c02ca7282b1b2620d183 Mon Sep 17 00:00:00 2001
From: vanelslander-ecology <jonnyvan1@gmail.com>
Date: Tue, 10 Jun 2025 15:41:09 -0700
Subject: [PATCH 6/9] updating coding for plot titles for concision pt2

---
 R/plot_wrappers.R | 44 ++++++++++++++++++++++++++------------------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/R/plot_wrappers.R b/R/plot_wrappers.R
index d34e42e..dd0c7de 100644
--- a/R/plot_wrappers.R
+++ b/R/plot_wrappers.R
@@ -16,18 +16,13 @@ plot_fireRegimePolys <- function(fireRegimePolys, title = NULL) {
   if (!is.factor(fireRegimePolys$PolyID)) {
     fireRegimePolys$PolyID <- as.factor(fireRegimePolys$PolyID)
   }
-  if (is.null(title)) {
-    ggplot(fireRegimePolys) +
+  gg_frp <- ggplot(fireRegimePolys) +
       geom_sf(aes(fill = PolyID)) +
       scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
       theme_bw()
-  }
-  else {
-    ggplot(fireRegimePolys) +
-      geom_sf(aes(fill = PolyID)) +
-      scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
-      ggtitle(title) +
-      theme_bw()
+  
+  if (!is.null(title)) {
+    gg_frp + ggtitle(title)
   }
 }
 
@@ -43,12 +38,15 @@ plot_fireRegimePolys <- function(fireRegimePolys, title = NULL) {
 #' @importFrom ggplot2 ggplot ggtitle scale_fill_brewer theme_bw
 #' @importFrom tidyterra geom_spatraster
 plot_fireRegimeRas <- function(x, title) {
-  ggplot() +
+  gg_frr <- ggplot() +
     geom_spatraster(data = terra::as.factor(x)) +
     scale_fill_brewer(palette = "Paired", type = "qual", na.value = "transparent") +
-    ggtitle(title) +
     theme_bw()
-}
+  
+  if (!is.null(title)) {
+    gg_frr + ggtitle(title)
+  }
+  }
 
 #' Plot age map
 #'
@@ -66,11 +64,14 @@ plot_fireRegimeRas <- function(x, title) {
 plot_ageMap <- function(x, title, maxAge) {
   x[x > maxAge] <- maxAge
 
-  ggplot() +
+  gg_am <- ggplot() +
     geom_spatraster(data = x) +
     scale_fill_distiller(palette = "Greens", direction = 1, na.value = "transparent") +
-    ggtitle(title) +
     theme_bw()
+  
+  if (!is.null(title)) {
+    gg_am + ggtitle(title)
+  }
 }
 
 #' Plot burn maps
@@ -86,11 +87,15 @@ plot_ageMap <- function(x, title, maxAge) {
 #' @importFrom tidyterra geom_spatraster
 #' @importFrom viridis scale_fill_viridis
 plot_burnMap <- function(x, title) {
-  ggplot() +
+  gg_bm <- ggplot() +
     geom_spatraster(data = x) +
     scale_fill_viridis(na.value = "transparent") +
-    ggtitle(title) +
     theme_bw()
+  
+  if (!is.null(title)) {
+    gg_bm + ggtitle(title)
+  }
+  
 }
 
 #' Plot flammable map
@@ -105,9 +110,12 @@ plot_burnMap <- function(x, title) {
 #' @importFrom ggplot2 ggplot ggtitle scale_fill_distiller theme_bw
 #' @importFrom tidyterra geom_spatraster
 plot_flammableMap <- function(x, title) {
-  ggplot() +
+  gg_fm <- ggplot() +
     geom_spatraster(data = x) +
     scale_fill_distiller(palette = "RdBu", na.value = "transparent") +
-    ggtitle(title) +
     theme_bw()
+  
+  if (!is.null(title)) {
+    gg_fm + ggtitle(title)
+  }
 }

From c34851003c97f0d0c560559a876c2a77851aabbc Mon Sep 17 00:00:00 2001
From: vanelslander-ecology <jonnyvan1@gmail.com>
Date: Tue, 10 Jun 2025 15:45:38 -0700
Subject: [PATCH 7/9] update coding for plot title for concision pt 2

---
 R/plot_wrappers.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/plot_wrappers.R b/R/plot_wrappers.R
index dd0c7de..7144caf 100644
--- a/R/plot_wrappers.R
+++ b/R/plot_wrappers.R
@@ -17,9 +17,9 @@ plot_fireRegimePolys <- function(fireRegimePolys, title = NULL) {
     fireRegimePolys$PolyID <- as.factor(fireRegimePolys$PolyID)
   }
   gg_frp <- ggplot(fireRegimePolys) +
-      geom_sf(aes(fill = PolyID)) +
-      scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
-      theme_bw()
+    geom_sf(aes(fill = PolyID)) +
+    scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
+    theme_bw()
   
   if (!is.null(title)) {
     gg_frp + ggtitle(title)
@@ -46,7 +46,7 @@ plot_fireRegimeRas <- function(x, title) {
   if (!is.null(title)) {
     gg_frr + ggtitle(title)
   }
-  }
+}
 
 #' Plot age map
 #'
@@ -63,7 +63,7 @@ plot_fireRegimeRas <- function(x, title) {
 #' @importFrom tidyterra geom_spatraster
 plot_ageMap <- function(x, title, maxAge) {
   x[x > maxAge] <- maxAge
-
+  
   gg_am <- ggplot() +
     geom_spatraster(data = x) +
     scale_fill_distiller(palette = "Greens", direction = 1, na.value = "transparent") +
@@ -118,4 +118,4 @@ plot_flammableMap <- function(x, title) {
   if (!is.null(title)) {
     gg_fm + ggtitle(title)
   }
-}
+}
\ No newline at end of file

From e8d9824c99112ac88430cfa22d91632315fa1ba9 Mon Sep 17 00:00:00 2001
From: vanelslander-ecology <jonnyvan1@gmail.com>
Date: Wed, 11 Jun 2025 10:43:59 -0700
Subject: [PATCH 8/9] Updated diagnostic plot functions so allow for runName =
 NULL

---
 R/comparePredictions.R      | 15 ++++++++++-----
 R/plot_wrappers.R           | 16 ++++++++++------
 man/comparePredictions.Rd   | 10 +++++-----
 man/plot_fireRegimePolys.Rd |  2 +-
 4 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/R/comparePredictions.R b/R/comparePredictions.R
index db5d568..e3b81c9 100644
--- a/R/comparePredictions.R
+++ b/R/comparePredictions.R
@@ -147,8 +147,9 @@ comparePredictions_meanFireSize <- function(dt, title = NULL) {
     geom_text(aes(label = PolyID), vjust = "inward", hjust = "inward") +
     geom_abline(slope = 1)
   if (!is.null(title)) {
-    gg_mfs + ggtitle(title)
+    gg_mfs <- gg_mfs + ggtitle(title)
   }
+  return(gg_mfs)
 }
 
 #' @export
@@ -178,8 +179,9 @@ comparePredictions_fireReturnInterval <- function(dt, times, title = NULL) {
     scale_x_continuous(limits = c(0, NA)) +
     geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
   if (!is.null(title)) {
-    gg_fri + ggtitle(title)
+    gg_fri <- gg_fri + ggtitle(title)
   }
+  return(gg_fri)
 }
 
 #' @export
@@ -202,8 +204,9 @@ comparePredictions_annualIgnitions <- function(dt, title = NULL) {
     scale_x_continuous(limits = c(0, NA)) +
     geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
   if (!is.null(title)) {
-    gg_ai + ggtitle(title)
+    gg_ai <- gg_ai + ggtitle(title)
   }
+  return(gg_ai)
 }
 
 #' @export
@@ -226,8 +229,9 @@ comparePredictions_annualEscapes <- function(dt, title = NULL) {
     scale_x_continuous(limits = c(0, NA)) +
     geom_text(aes(label = PolyID, vjust = "inward", hjust = "inward"))
   if (!is.null(title)) {
-    gg_ae + ggtitle(title)
+    gg_ae <- gg_ae + ggtitle(title)
   }
+  return(gg_ae)
 }
 
 #' @param size minimum fire size (ha)
@@ -265,6 +269,7 @@ comparePredictions_fireDistribution <- function(fireRegimePoints = NULL, burnSum
     theme_bw() +
     facet_wrap(~source, scales = "free_y", nrow = 2)
   if (!is.null(title)) {
-    gg_fd + ggtitle(title)
+    gg_fd <- gg_fd + ggtitle(title)
   }
+  return(gg_fd)
 }
diff --git a/R/plot_wrappers.R b/R/plot_wrappers.R
index 7144caf..2fecb78 100644
--- a/R/plot_wrappers.R
+++ b/R/plot_wrappers.R
@@ -22,8 +22,9 @@ plot_fireRegimePolys <- function(fireRegimePolys, title = NULL) {
     theme_bw()
   
   if (!is.null(title)) {
-    gg_frp + ggtitle(title)
+    gg_frp <- gg_frp + ggtitle(title)
   }
+  return(gg_frp)
 }
 
 #' Plot fire regime raster
@@ -44,8 +45,9 @@ plot_fireRegimeRas <- function(x, title) {
     theme_bw()
   
   if (!is.null(title)) {
-    gg_frr + ggtitle(title)
+    gg_frr <- gg_frr + ggtitle(title)
   }
+  return(gg_frr)
 }
 
 #' Plot age map
@@ -70,8 +72,9 @@ plot_ageMap <- function(x, title, maxAge) {
     theme_bw()
   
   if (!is.null(title)) {
-    gg_am + ggtitle(title)
+    gg_am <- gg_am + ggtitle(title)
   }
+  return(gg_am)
 }
 
 #' Plot burn maps
@@ -93,9 +96,9 @@ plot_burnMap <- function(x, title) {
     theme_bw()
   
   if (!is.null(title)) {
-    gg_bm + ggtitle(title)
+    gg_bm <- gg_bm + ggtitle(title)
   }
-  
+  return(gg_bm) 
 }
 
 #' Plot flammable map
@@ -116,6 +119,7 @@ plot_flammableMap <- function(x, title) {
     theme_bw()
   
   if (!is.null(title)) {
-    gg_fm + ggtitle(title)
+    gg_fm <- gg_fm + ggtitle(title)
   }
+  return(gg_fm)
 }
\ No newline at end of file
diff --git a/man/comparePredictions.Rd b/man/comparePredictions.Rd
index 39a38a6..4dae0d1 100644
--- a/man/comparePredictions.Rd
+++ b/man/comparePredictions.Rd
@@ -16,19 +16,19 @@ comparePredictions_summaryDT(
   times = NULL
 )
 
-comparePredictions_meanFireSize(dt, title)
+comparePredictions_meanFireSize(dt, title = NULL)
 
-comparePredictions_fireReturnInterval(dt, times, title)
+comparePredictions_fireReturnInterval(dt, times, title = NULL)
 
-comparePredictions_annualIgnitions(dt, title)
+comparePredictions_annualIgnitions(dt, title = NULL)
 
-comparePredictions_annualEscapes(dt, title)
+comparePredictions_annualEscapes(dt, title = NULL)
 
 comparePredictions_fireDistribution(
   fireRegimePoints = NULL,
   burnSummary = NULL,
   size,
-  title
+  title = NULL
 )
 }
 \arguments{
diff --git a/man/plot_fireRegimePolys.Rd b/man/plot_fireRegimePolys.Rd
index cee5fe8..5392428 100644
--- a/man/plot_fireRegimePolys.Rd
+++ b/man/plot_fireRegimePolys.Rd
@@ -4,7 +4,7 @@
 \alias{plot_fireRegimePolys}
 \title{Plot fire regime polygons}
 \usage{
-plot_fireRegimePolys(fireRegimePolys, title)
+plot_fireRegimePolys(fireRegimePolys, title = NULL)
 }
 \arguments{
 \item{fireRegimePolys}{\code{sf} polygon or multipolygon object defining the fire regime polygons}

From 567c0c1fe79d903d9670861ea6c985c7f76ef4ef Mon Sep 17 00:00:00 2001
From: Jonathan Van Elslander <jonnyvan1@gmail.com>
Date: Fri, 4 Jul 2025 12:58:07 -0700
Subject: [PATCH 9/9] added runName subtitle to burnmaps

---
 R/plot_wrappers.R   | 21 +++++++++++----------
 man/plot_burnMap.Rd |  4 +++-
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/R/plot_wrappers.R b/R/plot_wrappers.R
index 2fecb78..a6b77d0 100644
--- a/R/plot_wrappers.R
+++ b/R/plot_wrappers.R
@@ -20,7 +20,7 @@ plot_fireRegimePolys <- function(fireRegimePolys, title = NULL) {
     geom_sf(aes(fill = PolyID)) +
     scale_fill_discrete() + ## TODO: use same palette as plot_fireRegimeRas ??
     theme_bw()
-  
+
   if (!is.null(title)) {
     gg_frp <- gg_frp + ggtitle(title)
   }
@@ -43,7 +43,7 @@ plot_fireRegimeRas <- function(x, title) {
     geom_spatraster(data = terra::as.factor(x)) +
     scale_fill_brewer(palette = "Paired", type = "qual", na.value = "transparent") +
     theme_bw()
-  
+
   if (!is.null(title)) {
     gg_frr <- gg_frr + ggtitle(title)
   }
@@ -65,12 +65,12 @@ plot_fireRegimeRas <- function(x, title) {
 #' @importFrom tidyterra geom_spatraster
 plot_ageMap <- function(x, title, maxAge) {
   x[x > maxAge] <- maxAge
-  
+
   gg_am <- ggplot() +
     geom_spatraster(data = x) +
     scale_fill_distiller(palette = "Greens", direction = 1, na.value = "transparent") +
     theme_bw()
-  
+
   if (!is.null(title)) {
     gg_am <- gg_am + ggtitle(title)
   }
@@ -83,22 +83,23 @@ plot_ageMap <- function(x, title, maxAge) {
 #'
 #' @param title character, the plot title
 #'
+#' @param subtitle character, the plot subtitle
+#'
 #' @returns `ggplot` object
 #'
 #' @export
 #' @importFrom ggplot2 ggplot ggtitle theme_bw
 #' @importFrom tidyterra geom_spatraster
 #' @importFrom viridis scale_fill_viridis
-plot_burnMap <- function(x, title) {
+plot_burnMap <- function(x, title = NULL, subtitle = NULL) {
   gg_bm <- ggplot() +
     geom_spatraster(data = x) +
     scale_fill_viridis(na.value = "transparent") +
     theme_bw()
-  
-  if (!is.null(title)) {
-    gg_bm <- gg_bm + ggtitle(title)
-  }
-  return(gg_bm) 
+
+    gg_bm <- gg_bm + ggtitle(title) + labs(subtitle = subtitle)
+
+  return(gg_bm)
 }
 
 #' Plot flammable map
diff --git a/man/plot_burnMap.Rd b/man/plot_burnMap.Rd
index d07f7a8..2fd1744 100644
--- a/man/plot_burnMap.Rd
+++ b/man/plot_burnMap.Rd
@@ -4,12 +4,14 @@
 \alias{plot_burnMap}
 \title{Plot burn maps}
 \usage{
-plot_burnMap(x, title)
+plot_burnMap(x, title = NULL, subtitle = NULL)
 }
 \arguments{
 \item{x}{\code{SpatRaster} object corresponding to a current or cumulative burn map.}
 
 \item{title}{character, the plot title}
+
+\item{subtitle}{character, the plot subtitle}
 }
 \value{
 \code{ggplot} object