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anampcanampc
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added time diving test
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‎Benthos.Rmd‎

Lines changed: 152 additions & 57 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ editor_options:
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```{r setup, include = FALSE}
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knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE,
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options(knitr.kable.NA = '',
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rows.print=48))
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rows.print=12, digits = 3))
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```
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# Libraries and settings
@@ -92,13 +92,14 @@ theme(legend.position="top",
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# Transformacion de los datos
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General.data$T_Coral<- asin(sqrt(General.data$Coral/100))
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95-
Coral_Cover_model <- lm(T_Coral ~1 + Zona + Sitio%in%Zona +
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Metodo + Buzo + Buzo*Metodo +
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Zona*Metodo + Zona*Buzo +
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Zona*Metodo*Buzo +
99-
Sitio%in%Zona*Metodo +
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Sitio%in%Zona*Buzo +
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Sitio%in%Zona*Metodo*Buzo,
95+
Coral_Cover_model <- lm(T_Coral ~1 + Metodo + Buzo +
96+
Zona + Sitio%in%Zona +
97+
Metodo*Buzo +
98+
Metodo*Zona + Buzo*Zona +
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Metodo*Buzo*Zona +
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Metodo*Sitio%in%Zona +
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Buzo*Sitio%in%Zona +
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Metodo*Buzo*Sitio%in%Zona,
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data = General.data)
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# summary(Coral_Cover_model)
@@ -121,11 +122,14 @@ Coral_Cover<- ggplot(General.data) + facet_grid(~Transecto)+
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MyTheme+ scale_shape_manual(values=c(21,22,25))+
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stat_summary(aes(x=Metodo, y=Coral, fill=Metodo, group=Metodo),
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fun.data = "mean_cl_boot", geom = "bar",
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position=position_dodge(width=0.8), alpha=0.8)+
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position=position_dodge(width=0.8), alpha=0.7)+
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stat_summary(aes(x=Metodo, y=Coral, group=Metodo, color=Metodo),
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fun.data = "mean_cl_boot", geom = "errorbar",
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position=position_dodge(width=0.8))+
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geom_jitter( aes (x=Metodo, y=Coral, shape=Buzo, fill=Metodo, group=Metodo))+
129+
geom_point(aes (x=Metodo, y=Coral, shape=Buzo,
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fill=Metodo), position = position_dodge(0.8))+
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#geom_jitter( aes (x=Metodo, y=Coral, shape=Buzo,
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# fill=Metodo, group=Metodo))+
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scale_y_continuous(limits = c(0,99),
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expand = c(0.03, 0.03),
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breaks = seq(0, 99, 20),
@@ -144,13 +148,14 @@ Coral_Cover<-Coral_Cover +
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```{r}
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General.data$T_Alga<- asin(sqrt((General.data$Alga/100)))
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147-
Alga_Cover_model<-lm(T_Alga~ 1 + Zona + Sitio%in%Zona +
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Metodo + Buzo + Buzo*Metodo +
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Zona*Metodo + Zona*Buzo +
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Zona*Metodo*Buzo +
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Sitio%in%Zona*Metodo +
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Sitio%in%Zona*Buzo +
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Sitio%in%Zona*Metodo*Buzo,
151+
Alga_Cover_model<-lm(T_Alga~ 1 + Metodo + Buzo +
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Zona + Sitio%in%Zona +
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Metodo*Buzo +
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Metodo*Zona + Buzo*Zona +
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Metodo*Buzo*Zona +
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Metodo*Sitio%in%Zona +
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Buzo*Sitio%in%Zona +
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Metodo*Buzo*Sitio%in%Zona,
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data = General.data)
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#summary(Alga_Cover_model)
@@ -174,12 +179,15 @@ Algae_Cover<- ggplot(General.data) + facet_grid(~Transecto)+
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MyTheme+ scale_shape_manual(values=c(21,22,25))+
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stat_summary(aes(x=Metodo, y=Alga, fill=Metodo),
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fun.data = "mean_cl_boot", geom = "bar",
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position=position_dodge(width=0.8), alpha=0.8)+
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position=position_dodge(width=0.8), alpha=0.7)+
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stat_summary(aes(x=Metodo, y=Alga, colour=Metodo),
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fun.data = "mean_cl_boot", geom = "errorbar",
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position=position_dodge(width=0.8))+
182-
geom_jitter( aes (x=Metodo, y=Alga, shape=Buzo, fill=Metodo, group=Buzo))+
187+
geom_point(aes (x=Metodo, y=Alga, shape=Buzo,
188+
fill=Metodo), position = position_dodge(0.5))+
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#geom_jitter( aes (x=Metodo, y=Alga, shape=Buzo,
190+
# fill=Metodo, group=Metodo))+
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scale_y_continuous(limits = c(0, 90),
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expand = c(0.03, 0.3),
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breaks = seq(0, 100, 20),
@@ -199,13 +207,14 @@ Algae_Cover<- Algae_Cover +
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```{r}
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General.data$T_Sustrato<- acos(General.data$Sustrato /100)
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202-
Sus_Cover_model<-lm(T_Sustrato ~ 1 + Zona + Sitio%in%Zona +
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Metodo + Buzo + Buzo*Metodo +
204-
Zona*Metodo + Zona*Buzo +
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Zona*Metodo*Buzo +
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Sitio%in%Zona*Metodo +
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Sitio%in%Zona*Buzo +
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Sitio%in%Zona*Metodo*Buzo,
210+
Sus_Cover_model<-lm(T_Sustrato ~ 1 + Metodo + Buzo +
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Zona + Sitio%in%Zona +
212+
Metodo*Buzo +
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Metodo*Zona + Buzo*Zona +
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Metodo*Buzo*Zona +
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Metodo*Sitio%in%Zona +
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Buzo*Sitio%in%Zona +
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Metodo*Buzo*Sitio%in%Zona,
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data = General.data)
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211220
#summary(Sus_Cover_model)
@@ -228,7 +237,7 @@ Substrate_Cover<- ggplot(General.data) + facet_grid(~Transecto)+
228237
MyTheme+ scale_shape_manual(values=c(21,22,25))+
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stat_summary(aes(x=Metodo, y=Sustrato, fill=Metodo),
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fun.data = "mean_cl_boot", geom = "bar",
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position=position_dodge(width=0.8), alpha=0.8)+
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position=position_dodge(width=0.8), alpha=0.7)+
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233242
stat_summary(aes(x=Metodo, y=Sustrato, colour=Metodo),
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fun.data = "mean_cl_boot", geom = "errorbar",
@@ -251,13 +260,14 @@ hist(Riqueza.data$Riqueza..S.)
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252261
```{r}
253262
254-
Richness_model<-lm(Riqueza..S. ~ 1 + Zona + Sitio%in%Zona +
255-
Metodo + Buzo + Buzo*Metodo +
256-
Zona*Metodo + Zona*Buzo +
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Zona*Metodo*Buzo +
258-
Sitio%in%Zona*Metodo +
259-
Sitio%in%Zona*Buzo +
260-
Sitio%in%Zona*Metodo*Buzo,
263+
Richness_model<-lm(Riqueza..S. ~ 1 + Metodo + Buzo +
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Zona + Sitio%in%Zona +
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Metodo*Buzo +
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Metodo*Zona + Buzo*Zona +
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Metodo*Buzo*Zona +
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Metodo*Sitio%in%Zona +
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Buzo*Sitio%in%Zona +
270+
Metodo*Buzo*Sitio%in%Zona,
261271
data = Riqueza.data)
262272
263273
# summary(Richness_model)
@@ -277,13 +287,14 @@ Richness_model<-lm(Riqueza..S. ~ 1 + Zona + Sitio%in%Zona +
277287
## Modelo Poisson
278288

279289
```{r}
280-
Richness_model_2<-glm(Riqueza..S. ~ 1 + Zona + Sitio%in%Zona +
281-
Metodo + Buzo + Buzo*Metodo +
282-
Zona*Metodo + Zona*Buzo +
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Zona*Metodo*Buzo +
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Sitio%in%Zona*Metodo +
285-
Sitio%in%Zona*Buzo +
286-
Sitio%in%Zona*Metodo*Buzo,
290+
Richness_model_2<-glm(Riqueza..S. ~ 1 + Metodo + Buzo +
291+
Zona + Sitio%in%Zona +
292+
Metodo*Buzo +
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Metodo*Zona + Buzo*Zona +
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Metodo*Buzo*Zona +
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Metodo*Sitio%in%Zona +
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Buzo*Sitio%in%Zona +
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Metodo*Buzo*Sitio%in%Zona,
287298
data = Riqueza.data,
288299
family = poisson(link = "log"))
289300
@@ -311,12 +322,14 @@ Coral_Richness<- ggplot(Riqueza.data) + facet_grid(~Transecto)+
311322
stat_summary(aes(x=Metodo, y=Riqueza..S.,
312323
fill=Metodo, group=Metodo),
313324
fun.data = "mean_cl_boot", geom = "bar",
314-
position=position_dodge(width=0.8), alpha=0.8)+
325+
position=position_dodge(width=0.8), alpha=0.7)+
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stat_summary(aes(x=Metodo, y=Riqueza..S., group=Metodo, color=Metodo),
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fun.data = "mean_cl_boot", geom = "errorbar",
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position=position_dodge(width=0.8))+
318-
geom_jitter( aes (x=Metodo, y=Riqueza..S., shape=Buzo,
319-
fill=Metodo, group=Metodo))+
329+
geom_point(aes (x=Metodo, y=Riqueza..S., shape=Buzo,
330+
fill=Metodo), position = position_dodge(0.8))+
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#geom_jitter( aes (x=Metodo, y=Riqueza..S., shape=Buzo,
332+
# fill=Metodo, group=Metodo))+
320333
scale_y_continuous(limits = c(0,6),
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expand = c(0.01, 0.01),
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breaks = seq(0, 6, 1),
@@ -333,29 +346,93 @@ Coral_Richness<-Coral_Richness +
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334347
# 5. Time
335348

336-
## Model
349+
## Model diving time
350+
351+
```{r}
352+
Time_model_underwater<-lm(Minutos_campo ~ 1 + Metodo + Buzo + Buzo*Metodo +
353+
Zona + Sitio%in%Zona +
354+
Zona*Metodo + Zona*Buzo +
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Zona*Metodo*Buzo +
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Sitio%in%Zona*Metodo +
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Sitio%in%Zona*Buzo +
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Sitio%in%Zona*Metodo*Buzo,
359+
data = Time.data)
360+
361+
# summary(Time_model_underwater)
362+
anova(Time_model_underwater)
363+
par(mfrow=c(1,2))
364+
plot(Time_model_underwater)
365+
par(mfrow=c(1,1))
366+
367+
Comp9<-emmeans(Time_model_underwater, ~Metodo)
368+
Comp9
369+
pairs(Comp9, adj="tukey")
370+
371+
Comp10<-emmeans(Time_model_underwater, ~Metodo|Zona)
372+
pairs(Comp10, adj="tukey")
373+
374+
Comp11<-emmeans(Time_model_underwater, ~Buzo|Metodo)
375+
pairs(Comp11, adj="tukey")
376+
377+
```
378+
379+
## Model proccessing time
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338381
```{r}
339-
Time_model<-lm(Riqueza..S. ~ 1 + Zona + Sitio%in%Zona +
340-
Metodo + Buzo + Buzo*Metodo +
382+
Time_model_lab<-lm(Minutos_lab ~ 1 + Metodo + Buzo + Buzo*Metodo +
383+
Zona + Sitio%in%Zona +
341384
Zona*Metodo + Zona*Buzo +
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Zona*Metodo*Buzo +
343386
Sitio%in%Zona*Metodo +
344387
Sitio%in%Zona*Buzo +
345388
Sitio%in%Zona*Metodo*Buzo,
346-
data = Riqueza.data)
389+
data = Time.data)
390+
391+
# summary(Time_model_lab)
392+
anova(Time_model_lab)
393+
par(mfrow=c(1,2))
394+
plot(Time_model_lab)
395+
par(mfrow=c(1,1))
396+
397+
Comp12<-emmeans(Time_model_lab, ~Metodo)
398+
Comp12
399+
pairs(Comp12, adj="tukey")
400+
401+
Comp13<-emmeans(Time_model_lab, ~Metodo|Zona)
402+
pairs(Comp13, adj="tukey")
403+
404+
Comp14<-emmeans(Time_model_lab, ~Buzo|Metodo)
405+
pairs(Comp14, adj="tukey")
406+
407+
```
408+
409+
## Model total time
410+
411+
```{r}
412+
Time_model<-lm(Tiempo.Total.1 ~ 1 + Metodo + Buzo + Buzo*Metodo +
413+
Zona + Sitio%in%Zona +
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Zona*Metodo + Zona*Buzo +
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Zona*Metodo*Buzo +
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Sitio%in%Zona*Metodo +
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Sitio%in%Zona*Buzo +
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Sitio%in%Zona*Metodo*Buzo,
419+
data = Time.data)
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# summary(Time_model)
349422
anova(Time_model)
350423
par(mfrow=c(1,2))
351424
plot(Time_model)
352425
par(mfrow=c(1,1))
353426
354-
Comp9<-emmeans(Time_model, ~Metodo|Zona)
355-
pairs(Comp9, adj="tukey")
427+
Comp15<-emmeans(Time_model, ~Metodo)
428+
Comp15
429+
pairs(Comp15, adj="tukey")
356430
357-
Comp10<-emmeans(Time_model, ~Buzo|Metodo)
358-
pairs(Comp10, adj="tukey")
431+
Comp16<-emmeans(Time_model, ~Metodo|Zona)
432+
pairs(Comp16, adj="tukey")
433+
434+
Comp17<-emmeans(Time_model, ~Buzo|Metodo)
435+
pairs(Comp17, adj="tukey")
359436
360437
```
361438

@@ -371,17 +448,18 @@ Method_time<- ggplot(Time.data) +
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fun.data = "mean_cl_boot", geom = "bar",
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position=position_dodge(width=0.8), alpha=0.5)+
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374-
stat_summary(aes(x=Metodo, y=Minutos.toma.de.datos,
451+
stat_summary(aes(x=Metodo, y=Minutos_campo,
375452
fill=Metodo, group=Metodo),
376453
fun.data = "mean_cl_boot", geom = "bar",
377-
position=position_dodge(width=0.8), alpha=0.5)+
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position=position_dodge(width=0.8), alpha=0.7)+
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stat_summary(aes(x=Metodo, y=Tiempo.Total.1,
379456
group=Metodo, color=Metodo),
380457
fun.data = "mean_cl_boot", geom = "errorbar",
381458
position=position_dodge(width=0.8))+
382-
geom_jitter( aes (x=Metodo, y=Tiempo.Total.1,
383-
shape=Buzo,
384-
fill=Metodo, group=Metodo), alpha=1)+
459+
geom_point(aes (x=Metodo, y=Tiempo.Total.1, shape=Buzo,
460+
fill=Metodo), position = position_dodge(0.8))+
461+
#geom_jitter( aes (x=Metodo, y=Riqueza..S., shape=Buzo,
462+
# fill=Metodo, group=Metodo))+
385463
386464
scale_y_continuous(limits = c(0,60),
387465
expand = c(0.01, 0.01),
@@ -404,6 +482,23 @@ Figure
404482
#ggsave(file="Chapter_figure.svg", plot=Figure, dpi = 300, width=6.5, height=9)
405483
```
406484

485+
# Model summary
486+
```{r}
487+
488+
library(modelsummary) # model results in table
489+
490+
Summary_models<-list("Corales (%)" = Coral_Cover_model,
491+
"Algas (%)" = Alga_Cover_model,
492+
"Riqueza (S)" = Richness_model_2,
493+
"Tiempo" = Time_model)
494+
495+
modelsummary(Summary_models, stars = TRUE,
496+
#statistic = c('std.error', 'p.value', 'conf.int'),
497+
title = 'Seasonal and spatial models'#,
498+
#coef_map=factor_order
499+
)
500+
```
501+
407502
# Packages used
408503

409504
```{r}

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