Ircinia_Community_manuscript_supplemental.Rmd

---
title: "Electronic Supplemental Material" 
# subtitle: "For *Sponges presence increases diversity and abundance of fish and invertebrates in subtropical seagrass beds*"
output:
  bookdown::pdf_document2:
      toc: false
header-includes:
    \usepackage{caption}
    \renewcommand{\arraystretch}{1.2}
editor_options:
  markdown:
    wrap: sentence
---

```{r setup, include=FALSE}
options(tinytex.verbose = TRUE)
knitr::opts_chunk$set(
  echo = FALSE,
  message = FALSE,
  warning = FALSE,
  collapse = TRUE,
  comment = "#>"
)

source("scripts_comm/08_import_results.R")
if(!require(kableExtra))install.packages("kableExtra");library(kableExtra)
```

```{r, include=FALSE}
options(tinytex.verbose = TRUE)
```

Article title: 

*Sponges presence increases diversity and abundance of fish and invertebrates in subtropical seagrass beds*

Journal name: Estuaries and Coasts

Author names: Finella M. Campanino^1^, Philina A. English^2^, Craig A. Layman^3^, Stephanie K. Archer^1^*
 
Affiliations: 

1. Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA

2. School of Renewable Natural Resources, Louisiana State University Agricultural Center,	Baton Rouge, LA, USA

3. Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada

4. Center for Energy, Environment, and Sustainability, Department of Biology, Wake Forest University, Winston-Salem, North Carolina, USA
  
*corresponding author: sarcher@lumcon.edu

Submission Date: July 7, 2022
Revision 1 Submission Date: January X, 2023

\clearpage

```{r extreats, echo=FALSE, fig.align='left', out.width="100%", message=FALSE, warning=FALSE}
knitr::include_graphics("figures/plotphotos.png")
```

Figure S1. Photos of the live sponge (panel A) and structure control (panel B) treatments. Panel A, the photo of the live *Ircinia felix* was taken immediately after the sponge was placed in the plot. The photo of the sponge replica in panel B was taken at the end of this study, 12 months into the experiment. Mounds are likely those of burrowing sea cucumbers, *Holothuria arenicola*.

```{r expdes, echo=FALSE, fig.align='left', out.width="100%", message=FALSE, warning=FALSE}
knitr::include_graphics("figures/Experimental_design_2.pdf")
```

Figure S2. Illustrates the experimental design and sampling scheme. Data was collected prior to treatment establishment, and 1 and 12 months after treatments were established. Fish abundance and taxa richness were counted for whole plots. Other taxonomic groups and seagrass measurements were made in the locations indicated. 

\clearpage


\captionsetup[table]{labelformat=empty}

```{r fishtab}
knitr::kable(fish.models[,c(-1:-2,-7,-10)],
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
    col.names = c("","k","AICc","Delta AICc",
                  "Akaike Weight","LL"),
    caption="Table S1. All models evaluating competing hypotheses of the drivers of fish abundance and taxa richness.")%>%
  kableExtra::kable_styling(latex_options = "scale_down",font_size=11)%>%
  kableExtra::pack_rows("Abundance",1,14)%>%
  kableExtra::pack_rows("Taxa Richness",15,28)
```

<!-- \clearpage -->

\captionsetup[table]{labelformat=empty}

```{r fishabund}
trt.model.terms<-c("Intercept (Live sponge)",
                 "Control",
                 "Structure",
                 "+1 month",
                 "+12 months",
                 "Control : +1 month",
                 "Structure : +1 month",
                 "Control : +12 months",
                 "Structure : +12 months")
fa<-data.frame(fa.treat.sum$coefficients$cond)
row.names(fa)<-trt.model.terms

knitr::kable(round(fa,2),
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
             col.names = c("Estimate","SE","Z","p value"),
    caption="Table S2. Effect sizes, error estimates (SE), z and p values for fixed effects in the best fit model of fish abundance.")%>%
  column_spec(1:4,width_max = "1.5cm")%>%
  kableExtra::kable_styling(font_size=7, full_width = F)


```

\clearpage
\captionsetup[table]{labelformat=empty}

```{r fistich}
fspr<-data.frame(fspr.treat.sum$coefficients$cond)
row.names(fspr)<-trt.model.terms
knitr::kable(round(fspr,2),
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
             col.names = c("Estimate","SE","Z","p value"),
    caption="Table S3. Effect sizes, error estimates (SE), z and p values for fixed effects in the best fit model of fish taxa richness.")%>%
  column_spec(1:4, width_max = "1.5cm")%>%
  kableExtra::kable_styling( font_size=7, full_width = F)
```


\captionsetup[table]{labelformat=empty}


```{r inverttab}
knitr::kable(invert.models[,c(-1:-2,-7,-10)],
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
    col.names = c("","k","AICc","Delta AICc",
                  "Akaike Weight","LL"),
    caption="Table S4. All models evaluating competing hypotheses of the drivers of invertebrate abundance and taxa richness.")%>%
  kable_styling(latex_options = "scale_down",font_size=11)%>%
  pack_rows("Abundance",1,14)%>%
  pack_rows("Taxa Richness",15,28)
```

\clearpage
\captionsetup[table]{labelformat=empty}

```{r invabundlsp}
ia<-data.frame(ia.treat.sum$coefficients$cond)
row.names(ia)<-trt.model.terms
knitr::kable(round(ia,2),
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
    col.names = c("Estimate","SE","Z","p value"),
    caption="Table S5. Effect sizes, error estimates (SE), z and p values for fixed effects in the treatment-only model for invertebrate abundance.")%>%
  column_spec(1:4, width_max = "1.5cm")%>%
  kableExtra::kable_styling( font_size=7, full_width = F)
```


\captionsetup[table]{labelformat=empty}


```{r invabundprod}
ia2<-data.frame(ia.treat.prod.sum$coefficients$cond)
row.names(ia2)<-c("Intercept (Live sponge)",
                 "Control",
                 "Structure",
                 "+1 month",
                 "+12 months",
                 "Seagrass productivity",
                 "Control : +1 month",
                 "Structure : +1 month",
                 "Control : +12 months",
                 "Structure : +12 months")
knitr::kable(round(ia2,2),
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
    col.names = c("Estimate","SE","Z","p value"),
    caption="Table S6. Effect sizes, error estimates (SE), z and p values for fixed effects in the treatment + seagrass productivity model for invertebrate abundance.")%>%
  column_spec(1:4, width_max = "1.5cm")%>%
  kableExtra::kable_styling( font_size=7, full_width = F)
```


\captionsetup[table]{labelformat=empty}


```{r invabundstruct}
ia3<-data.frame(ia.treat.struct.sum$coefficients$cond)
row.names(ia3)<-c("Intercept (Live sponge)",
                 "Control",
                 "Structure",
                 "+1 month",
                 "+12 months",
                 "Seagrass structure",
                 "Control : +1 month",
                 "Structure : +1 month",
                 "Control : +12 months",
                 "Structure : +12 months")
knitr::kable(round(ia3,2),
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
             col.names = c("Estimate","SE","Z","p value"),
    caption="Table S7. Effect sizes, error estimates (SE), z and p values for fixed effects in the treatment + seagrass structure model for invertebrate abundance.")%>%
  column_spec(1:4, width_max = "1.5cm")%>%
  kableExtra::kable_styling( font_size=7, full_width = F)
```

\clearpage
\captionsetup[table]{labelformat=empty}

```{r invspr}
ispr<-data.frame(ispr.treat.sum$coefficients$cond)
row.names(ispr)<-c("Intercept (Live sponge)",
                 "Control",
                 "Structure",
                 "+1 month",
                 "+12 months",
                 "Control : +1 month",
                 "Structure : +1 month",
                 "Control : +12 months",
                 "Structure : +12 months")
knitr::kable(round(ispr,2),
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
    col.names = c("Estimate","SE","Z","p value"),
    caption="Table S8. Effect sizes, error estimates (SE), z and p values for fixed effects in the treatment only model for invertebrate taxa richness.")%>%
  column_spec(1:4, width_max = "1.5cm")%>%
  kableExtra::kable_styling( font_size=7, full_width = F)
```

\captionsetup[table]{labelformat=empty}

```{r invspralg}
ispr2<-data.frame(ispr.alg.sum$coefficients$cond)
row.names(ispr2)<-c("Intercept",
                 "+1 month",
                 "+12 months",
                 "Macroalgal abundance")
knitr::kable(round(ispr2,2),
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
    col.names = c("Estimate","SE","Z","p value"),
    caption="Table S9. Effect sizes, error estimates (SE), z and p values for fixed effects in the macroalgal abundance model for invertebrate taxa richness.")%>%
  column_spec(1:4, width_max = "1.5cm")%>%
  kableExtra::kable_styling( font_size=7, full_width = F)
```

\captionsetup[table]{labelformat=empty}

```{r fishcv}
fish.cv.sum$treatment<-c("Control","Structure","Live sponge")
colnames(fish.cv.sum)<-c("Treatment","Mean vector length","sd of vector length","Vectors longer than 0","Mean vector angle","rho","sd of vector angle")
fish.cv.sum<-fish.cv.sum%>%select(-rho)
knitr::kable(fish.cv.sum,
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
    caption="Table S10. Summary of individual plot vectors representing changes in the fish community in species space over the 1 year experiment.")%>%
  column_spec(2:6, width_max = "1.5cm")%>%
  kableExtra::kable_styling(latex_options = "scale_down",font_size=10,full_width = F)
```

\captionsetup[table]{labelformat=empty}

```{r invcv}
inv.cv.sum$treatment<-c("Control","Structure","Live sponge")
colnames(inv.cv.sum)<-c("Treatment","Mean vector length","sd of vector length","Vectors longer than 0","Mean vector angle","rho","sd of vector angle")
inv.cv.sum<-inv.cv.sum%>%select(-rho)
kable(inv.cv.sum,
             # format = "latex",
             booktabs=T,
             # escape = FALSE,
    caption="Table S10. Summary of individual plot vectors representing changes in the invertebrate community in species space over the 1 year experiment.")%>%
  column_spec(2:6, width_max = "1.5cm") %>%
  kableExtra::kable_styling(latex_options = "scale_down",font_size=10,full_width = F)
```

\clearpage

```{r fishcvplot, echo=FALSE, fig.align='left', out.width="60%", message=FALSE, warning=FALSE}
knitr::include_graphics("fish_compositional_vector_plot.jpg")

```

Figure S3. Vectors representing how experimental plots moved in fish species space over the 1 year experiment decomposed into their lengths (A) and angles (Control: B, Structure: C, Live Sponge: D).

<!-- \clearpage -->

```{r invcvplot, echo=FALSE, fig.align='left', out.width="60%", message=FALSE, warning=FALSE}
knitr::include_graphics("invert_compositionalvectors_plot.jpg")

```

Figure S4. Vectors representing how experimental plots moved in invertebrate species space over the 1 year experiment decomposed into their lengths (A) and angles (Control: B, Structure: C, Live Sponge: D).