From 5d403dfc0678d64083238ebcdcfe55265e6e8bee Mon Sep 17 00:00:00 2001
From: macvicab <bmacvicar@uwaterloo.ca>
Date: Thu, 30 Jun 2022 15:46:50 -0700
Subject: [PATCH 1/3] Update PITtrack2.m

Error noted when Sdist values are provided in the input files but Ndist values are not.
code added from lines 75 to 78 to check for Ndist field and create one with NaN values if no number is available
---
 PITtrack2.m | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/PITtrack2.m b/PITtrack2.m
index f36de95..6b07b88 100644
--- a/PITtrack2.m
+++ b/PITtrack2.m
@@ -72,8 +72,11 @@ function PITtrack2(site,C)
         placedData(nf).Sdist = Sdist;
         placedData(nf).Ndist = Ndist;
     end
+elseif ~isfield(placedData,'Ndist')
+    for nf = 1:nftot
+        placedData(nf).Ndist = NaN;
+    end
 end
-
 % use taglist to cut labData to only the requested particles
 if ~isempty(taglist)
     % shorten the labdata to only the requested tags
@@ -237,4 +240,4 @@ function PITtrack2(site,C)
     eval([datee,' = data(:,',num2str(n),');']);
     evalstr = [evalstr,',',datee];
 end
-eval(['T = table(',evalstr,');']);
\ No newline at end of file
+eval(['T = table(',evalstr,');']);

From fbd4ae2ccedb9dfb50ea7c0538167c325165cf50 Mon Sep 17 00:00:00 2001
From: macvicab <bmacvicar@uwaterloo.ca>
Date: Thu, 21 Jul 2022 07:15:42 -0700
Subject: [PATCH 2/3] Update PITtrack_default.m

changed to reflect directory structure of depository.  Note that as a user you should alter this file to match your data.
---
 PITtrack_default.m | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/PITtrack_default.m b/PITtrack_default.m
index 69e2c3d..91e0af0 100644
--- a/PITtrack_default.m
+++ b/PITtrack_default.m
@@ -9,16 +9,10 @@
 % site 2 = Ganny = 0; % Wilket Creek (Papangelakis et al 2019)
 
 if site == 1
-    % for Bradley
-    def_data.D50 = 55; % mm
-    def_data.szcat = 2.^[5:1:6];
-    def_data.fdir = 'F:\Research\Publications\In Preparation\2020 Elli Nature Geoscience\Bradley 2017 data\tagged\';
-    def_data.fchar = 'Tag Characteristics Halfmoon.csv';
-elseif site == 2
     def_data.D50 = 37; % mm
     def_data.szcat = 2.^[5:1:8];
-    def_data.fdir = 'F:\Research\Publications\In Preparation\2020 Elli Nature Geoscience\Elli Thesis Data\Ganny\';
+    def_data.fdir = 'Ganatsekaigon\';
     def_data.fchar = 'Tag Characteristics 2.csv';
     def_data.thalname = 'GCrk_Thalweg_rev.csv';
     def_data.taglist = 'DS_Ganny_tagnum.csv';
-end
\ No newline at end of file
+end

From 766da9f27f3121d0ad1535df80e84fe50f7b7ca3 Mon Sep 17 00:00:00 2001
From: macvicab <bmacvicar@uwaterloo.ca>
Date: Thu, 21 Jul 2022 07:18:15 -0700
Subject: [PATCH 3/3] Update PITtrack_default.m

added some comments to the parameters to help user understand what is required here
---
 PITtrack_default.m | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/PITtrack_default.m b/PITtrack_default.m
index 91e0af0..42faf30 100644
--- a/PITtrack_default.m
+++ b/PITtrack_default.m
@@ -10,9 +10,9 @@
 
 if site == 1
     def_data.D50 = 37; % mm
-    def_data.szcat = 2.^[5:1:8];
-    def_data.fdir = 'Ganatsekaigon\';
-    def_data.fchar = 'Tag Characteristics 2.csv';
-    def_data.thalname = 'GCrk_Thalweg_rev.csv';
-    def_data.taglist = 'DS_Ganny_tagnum.csv';
+    def_data.szcat = 2.^[5:1:8]; % size categories in -phi values (log base 2 classification system)
+    def_data.fdir = 'Ganatsekaigon\'; % directory path
+    def_data.fchar = 'Tag Characteristics 2.csv'; % name of file that contains tracer characteristics such as sizes
+    def_data.thalname = 'GCrk_Thalweg_rev.csv'; % name of file that has the thalweg data
+    def_data.taglist = 'DS_Ganny_tagnum.csv'; % list of tag numbers to include in analysis (may be a subset of all tags in river)
 end