From 2b4678fa4f57527662a186ef0ede91036396c698 Mon Sep 17 00:00:00 2001
From: Adriano Fantini <adr.fantini@gmail.com>
Date: Sun, 24 Feb 2019 16:26:08 +0100
Subject: [PATCH] Fix for only 0s in output; NA values are now treated as Bs
 (values that do not affect event status)

---
 ncspellR.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/ncspellR.R b/ncspellR.R
index 38f952a..f870592 100755
--- a/ncspellR.R
+++ b/ncspellR.R
@@ -259,7 +259,12 @@ spi_spell = function(v, yrs, eventstart = -1, eventend = 0) {
     stopifnot( length(v) == length(yrs) )
     # Define what the labels mean, for clarity
     A = 1; B = 2; C = 3
-    # Categorize input values: lower than eventstart (A), higher than eventend (C) and in-between (B)
+    # Categorize input values:
+    # (A) lower than eventstart, start an event
+    # (B) higher than eventend, stop an event if 2 consecutives are found
+    # (B) in-between, event status not affected
+    # We treat any NA as Bs
+    v[is.na(v)] <- (eventstart + eventend) / 2
     values = as.numeric(cut(v, c(-Inf, eventstart, eventend, Inf), labels = c(A, B, C)))
     # Split values and years into separate groups, divided by a C
     idx <- 1 + cumsum( values == C )