From fe429e4e58ea5efcfefbbd597ddf6feec5b64d63 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Lo=C3=AFc=20Lehnhoff?= <loic.lehnhoff@gmail.com>
Date: Mon, 5 Jun 2023 16:34:15 +0200
Subject: [PATCH] Update .gitignore and stats_Buzz_Burst-pulse.R : - updated
result prints for BBP models - removed over-complicated burst-pulse
modelisation
---
.gitignore | 4 ++--
Stats/stats_Buzz_Burst-pulse.R | 18 +++++++++---------
2 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/.gitignore b/.gitignore
index 23f6b16..1772753 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,3 @@
*.sav
-*.Rhistory
-*.RData
\ No newline at end of file
+**/.Rhistory
+**/.RData
\ No newline at end of file
diff --git a/Stats/stats_Buzz_Burst-pulse.R b/Stats/stats_Buzz_Burst-pulse.R
index 43d154b..0851b78 100644
--- a/Stats/stats_Buzz_Burst-pulse.R
+++ b/Stats/stats_Buzz_Burst-pulse.R
@@ -133,6 +133,7 @@ ftable(factor(bbp.dta$fishing_net), factor(bbp.dta$behavior), factor(bbp.dta$aco
mod.bbp <- glm.nb(number_of_BBP ~ acoustic + fishing_net + behavior
+ offset(log(number)),
data=bbp.dta)
+summary(mod.bbp)
car::Anova(mod.bbp, type=3)
dwtest(mod.bbp) # H0 -> independent if p>0.05 (autocorrelation if p<0.05)
bptest(mod.bbp) # H0 -> homoscedasticity if p<0.05
@@ -143,11 +144,11 @@ mod.bbp$deviance/mod.bbp$df.residual
### Model for Buzzes
# No normality of residuals for LM
# overdispersion with GLM quasipoisson
-# underdispersion with glm NB
-# Try with ZINB:
+# Try with glm NB
mod.buzz <- glm.nb(Buzz ~ behavior + fishing_net + acoustic
+ offset(log(number)),
data=bbp.dta)
+summary(mod.buzz)
car::Anova(mod.buzz, type=3)
dwtest(mod.buzz) # H0 -> independent if p>0.05 (autocorrelation if p<0.05)
bptest(mod.buzz) # H0 -> homoscedasticity if p<0.05
@@ -157,20 +158,19 @@ mod.buzz$df.null/mod.buzz$df.residual
### Model for Burst-pulses
# No normality of residuals for LM
# overdispersion with quasipoisson
-# underdispersion with NB
-# ZINB is working :
-mod.burst.pulse <- zeroinfl(Burst.pulse ~ fishing_net + acoustic + behavior
- + offset(log(number)), dist="negbin",
+# Try with glm NB
+mod.burst.pulse <- glm.nb(Burst.pulse ~ fishing_net + acoustic + behavior
+ + offset(log(number)),
data=bbp.dta)
+summary(mod.burst.pulse)
car::Anova(mod.burst.pulse, type=3)
dwtest(mod.burst.pulse) # H0 -> independent if p>0.05 (autocorrelation if p<0.05)
bptest(mod.burst.pulse) # H0 -> homoscedasticity if p<0.05
mod.burst.pulse$df.null/mod.burst.pulse$df.residual # -> Overdispersion of != 1
# no overdispersion
-
##################### Boxplots and comparisons #####################
-### Functions to compute stats
+### Functions to compute stats ###----
computeLetters <- function(temp, category) {
test <- multcomp::cld(object = temp$emmeans,
Letters = letters)
@@ -383,4 +383,4 @@ barPlot(computeStats(bbp.dta, behavior, Burst.pulse_per_dolphin, two=acoustic),
new_names = c("BEF","BEF+DUR","DUR", "DUR+AFT", "AFT"),
xname="Activation sequence",
colours=c("#E69F00","#55c041", "#FF3814"), size=5,
- legend_title="Behaviour", legend_labs= c("Foraging", "Travelling", "Socialising"))
+ legend_title="Behaviour", legend_labs=c("Foraging", "Travelling", "Socialising"))
\ No newline at end of file
--
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