Skip to content

Commit

Permalink
Add files via upload
Browse files Browse the repository at this point in the history
  • Loading branch information
@rholser
rholser committed Apr 25, 2023
1 parent 9c4632d commit 71668ea
Show file tree
Hide file tree
Showing 4 changed files with 991 additions and 0 deletions.
25 changes: 25 additions & 0 deletions DiseaseAtSea_6018Stats.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
load('2017001_6018_RRHmod_TV3.mat');

std(DiveStat.PDI/60,'omitnan')
std(DiveStat.PDI(DiveStat.SolarEl>=0)/60,'omitnan')
std(DiveStat.PDI(DiveStat.SolarEl<0)/60,'omitnan')

std(DiveStat.Dduration/60,'omitnan')
std(DiveStat.Dduration(DiveStat.SolarEl>=0)/60,'omitnan')
std(DiveStat.Dduration(DiveStat.SolarEl<0)/60,'omitnan')

std(DiveStat.Botttime/60,'omitnan')
std(DiveStat.Botttime(DiveStat.SolarEl>=0)/60,'omitnan')
std(DiveStat.Botttime(DiveStat.SolarEl<0)/60,'omitnan')

std(DiveStat.AscRate,'omitnan')
std(DiveStat.AscRate(DiveStat.SolarEl>=0),'omitnan')
std(DiveStat.AscRate(DiveStat.SolarEl<0),'omitnan')

std(DiveStat.DescRate,'omitnan')
std(DiveStat.DescRate(DiveStat.SolarEl>=0),'omitnan')
std(DiveStat.DescRate(DiveStat.SolarEl<0),'omitnan')

std(DiveStat.Maxdepth,'omitnan')
std(DiveStat.Maxdepth(DiveStat.SolarEl>=0),'omitnan')
std(DiveStat.Maxdepth(DiveStat.SolarEl<0),'omitnan')
292 changes: 292 additions & 0 deletions DiseaseAtSea_DiveANOVA_V1.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,292 @@
%Rachel Holser ([email protected])
%Last Updated: 19-Sep-2022

%Compile data for ANOVAs to compare dive metrics of seal 6018 to other individuals

%Uses TV3.mat file for 6018 due to missing chunk of foieGras track
%(affects day/night seaparation)

%Excludes first n dives (100) from analysis due to transit off the shelf

%% Compile All Dives
clear
cd('d:\Dropbox\MATLAB\Sick Seal 6018\TV4_alpha ANNU\')
files = dir('*.mat');

pb=[];
pb_track=[];
n=100; %number of dives to remove from start of record
pb_count=0;
pbt_count=0;

for j=1:size(files,1)
%Compile tracking data, sorted into post-molt and post-breeing
A=load(files(j).name);
if A.MetaData.Group.Season==1
if ~isempty(A.DiveStat)==1
pb_count=pb_count+1;
%DiveStats
DayOfTrip=ceil(A.DiveStat.JulDate)-floor(A.MetaData.DepartDate);
DayOfYear=floor(A.DiveStat.JulDate)-datenum(num2str(A.DiveStat.Year),...
'yyyy')+1;
temp=[DayOfTrip DayOfYear A.DiveStat.JulDate...
A.DiveStat.Year...
A.DiveStat.Hour...
A.DiveStat.Maxdepth...
A.DiveStat.Dduration...
A.DiveStat.Botttime...
A.DiveStat.DWigglesBott...
A.DiveStat.SolarEl...
A.DiveStat.Efficiency...
A.DiveStat.DescRate...
A.DiveStat.DescTime...
A.DiveStat.AscRate...
A.DiveStat.AscTime...
A.DiveStat.TotVertDistBot...
A.DiveStat.BottRange...
A.DiveStat.PDI];
temp(:,19)=A.TOPPID;
m=size(temp,1);
%remove first n dives
pb=[pb;temp(n:m-n,:)];
clear DayOfTrip DayOfYear temp TOPPID
end
if ~isempty(A.Track_Best)==1
pbt_count=pbt_count+1;
%Track
DayOfTrip=ceil(A.Track_Best.JulDate)-floor(A.MetaData.DepartDate);
DayOfYear=floor(A.Track_Best.JulDate)-datenum(datestr...
(A.Track_Best.JulDate,'yyyy'),'yyyy')+1;
temp=[DayOfTrip DayOfYear table2array(A.Track_Best(:,1:3)) table2array(A.Track_Best(:,6:8))];
temp(:,9)=A.TOPPID;
pb_track=[pb_track;temp];
clear DayOfTrip DayOfYear temp
end
end
clear A
end

%Convert to table and create rounded depth and duration
pb=array2table(pb,'VariableNames',{'DayOfTrip','DayOfYear','JulDate','Year',...
'Hour','Maxdepth','Duration','BottTime','DWigglesBott','SolarEl',...
'Efficiency','DescRate','DescTime','AscRate','AscTime','TVD','BottRange','PDI','TOPPID'});
pb.MaxdepthR=roundn(pb.Maxdepth,1);
pb.DurationM=pb.Duration/60;
pb.BottTimeM=pb.BottTime/60;
pb.PDIM=pb.PDI/60;

%Remove data outliers (very short or extremely deep dives)
pb(pb.Duration<120,:)=[];
pb(pb.Maxdepth>1900,:)=[];
pb(pb.PDI>43200,:)=[];
pb(pb.TOPPID==2015002,:)=[];

%Convert to table and create date vector
pb_track=array2table(pb_track,'VariableNames',{'DayOfTrip','DayOfYear','JulDate','Lat',...
'Long','Long360','TransitRate','Dist','TOPPID'});
[pb_track.Year,pb_track.Month,pb_track.Day,pb_track.Hour,pb_track.Min,...
pb_track.Sec]=datevec(pb_track.JulDate);

%% Separate 2017 and pre-2021 and Day/Night
PB2017=pb(pb.Year==2017,:);
AllPB=pb(pb.Year<2021,:);

AllPB_Day=AllPB(AllPB.SolarEl>=0,:);
AllPB_Night=AllPB(AllPB.SolarEl<0,:);

PB2017_Day=PB2017(PB2017.SolarEl>=0,:);
PB2017_Night=PB2017(PB2017.SolarEl<0,:);

clear pm_count pb_count model model2 j m n count

%% Run ANOVA for Durations

[~,~,stats]=anova1(AllPB.DurationM,AllPB.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Day.DurationM,AllPB_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Night.DurationM,AllPB_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s


[~,~,stats]=anova1(PB2017.DurationM,PB2017.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Day.DurationM,PB2017_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Night.DurationM,PB2017_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

%% Run ANOVA for MaxDepth
[~,~,stats]=anova1(AllPB.MaxdepthR,AllPB.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Day.MaxdepthR,AllPB_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Night.MaxdepthR,AllPB_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017.MaxdepthR,PB2017.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Day.MaxdepthR,PB2017_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Night.MaxdepthR,PB2017_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

%% Run ANOVA for Bottom Time
[~,~,stats]=anova1(AllPB.BottTimeM,AllPB.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Day.BottTimeM,AllPB_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Night.BottTimeM,AllPB_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017.BottTimeM,PB2017.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Day.BottTimeM,PB2017_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Night.BottTimeM,PB2017_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

%% Run ANOVA for AscRate

[~,~,stats]=anova1(AllPB.AscRate,AllPB.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Day.AscRate,AllPB_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Night.AscRate,AllPB_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017.AscRate(PB2017.TOPPID<2017009),PB2017.TOPPID(PB2017.TOPPID<2017009));
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Day.AscRate,PB2017_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Night.AscRate,PB2017_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

%% Run ANOVA for DescRate

[~,~,stats]=anova1(AllPB.DescRate,AllPB.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Day.DescRate,AllPB_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Night.DescRate,AllPB_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017.DescRate(PB2017.TOPPID<2017009),PB2017.TOPPID(PB2017.TOPPID<2017009));
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Day.DescRate,PB2017_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Night.DescRate,PB2017_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

%% Run ANOVA for PDI

[~,~,stats]=anova1(AllPB.PDIM,AllPB.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Day.PDIM,AllPB_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(AllPB_Night.PDIM,AllPB_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017.PDIM,PB2017.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Day.PDIM,PB2017_Day.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

[~,~,stats]=anova1(PB2017_Night.PDIM,PB2017_Night.TOPPID);
multcompare(stats);
mean(stats.means)
stats.s

Loading

0 comments on commit 71668ea

Please sign in to comment.