In turf-reserves/MPAtools: Tools to simulate and analyze no-take Marine Reserves

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title: r params$title

knitr::opts_chunk$set(echo = F, fig.height = 3, warning = F, message = F)

suppressPackageStartupMessages({
  library(ggplot2)
  library(dplyr)
  library(tidyr)
  library(MPAtools)
  library(reshape)
  library(stargazer)
  library(ggExtra)
})

Resumen

Leyenda

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Clase de indicador | Indicador | Valor -------------------|-------------------------|----------------------------------------------------- Bio | Densidad Peces | r knitr::include_graphics(params$summary$Bio$P$Dp) Bio | Riqueza Peces | r knitr::include_graphics(params$summary$Bio$P$Sp) Bio | Biomasa Peces | r knitr::include_graphics(params$summary$Bio$P$Bp) Bio | Nivel Trofico Peces | r knitr::include_graphics(params$summary$Bio$P$NT) Bio | Densidad Iinvertebrados | r knitr::include_graphics(params$summary$Bio$I$Di) Bio | Densidad de langostas | r knitr::include_graphics(params$summary$Bio$O$L) Bio | Densidad de caracol rosa| r knitr::include_graphics(params$summary$Bio$O$C) Bio | Densidad de pargos | r knitr::include_graphics(params$summary$Bio$O$P) Bio | Densidad de pargos | r knitr::include_graphics(params$summary$Bio$O$Pb)

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Peces

Densidad

Np <- density(data = peces, location = params$comunidad) %>%
  mutate(D = D/60)

mpa_plot3(Np, reserve = params$reserva, control = params$control, y.lab = "Densidad (org / m^2)")

stargazer(turfeffect(Np, reserve = params$reserva, control = params$control), dep.var.labels = "Densidad (org / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Riqueza

Sp <- richness(data = peces, location = params$comunidad)
mpa_plot3(Sp, reserve = params$reserva, control = params$control, y.lab = "Riqueza (Sp. / transecto)")

stargazer(turfeffect(Sp, reserve = params$reserva, control = params$control), dep.var.labels = "Riqueza (Sp. / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Biomasa

Bp <- fish_biomass(data = peces, location = params$comunidad)
mpa_plot3(Bp, reserve = params$reserva, control = params$control, y.lab = "Biomasa (Kg / transecto)")

stargazer(turfeffect(Bp, reserve = params$reserva, control = params$control), dep.var.labels = "Biomasa (Kg / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Nivel trofico

NTp <- trophic(data = peces, location = params$comunidad)
mpa_plot3(NTp, reserve = params$reserva, control = params$control, y.lab = "Nivel trofico")

stargazer(turfeffect(NTp, reserve = params$reserva, control = params$control), dep.var.labels = "Nivel trofico", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Densidades por Nivel trofico

NT2 <- peces %>%
  filter(Comunidad == params$comunidad) %>%
  filter(Sitio == params$reserva | Sitio == params$control) %>%
  filter(!is.na(NT)) %>%
  filter(Abundancia > 0) %>%
  mutate(NT = as.factor(floor(NT))) %>%
  group_by(Ano, Zonificacion, Sitio, Transecto, NT) %>%
  summarize(Abundancia = sum(Abundancia)) %>%
  group_by(Ano, Zonificacion, NT) %>%
  summarize(Abundancia = mean(Abundancia))


ggplot(NT2, aes(x = Ano, y = Abundancia, factor = NT, color = NT))+
  geom_point()+
  geom_line()+
  theme_bw()+
  facet_grid(.~Zonificacion)+
  scale_color_brewer(palette = "Set1")+
  labs(x = "Ano", y = "Densidad (org / transecto)")

# # Para zonas de pesca
# NT_P <- NT2 %>%
#   ungroup() %>%
#   filter(Zonificacion == "Pesca") %>%
#   select(-Zonificacion) %>%
#   spread(Ano, Abundancia)
# 
# rows <- unique(NT_P$NT)
# NT_P <- as.data.frame(NT_P[-1])
# rownames(NT_P) <- rows
# pro.NT_P<- prop.table(as.matrix(NT_P),2)
# XsqP <- chisq.test(pro.NT_P)
# print(XsqP)
# 
# # Para zonas de no pesca
# NT_R <- NT2 %>%
#   ungroup() %>%
#   filter(Zonificacion == "No Pesca") %>%
#   select(-Zonificacion) %>%
#   spread(Ano, Abundancia)
# 
# rows <- unique(NT_R$NT)
# NT_R <- as.data.frame(NT_R[-1])
# rownames(NT_R) <- rows
# pro.NT_R<- prop.table(as.matrix(NT_R),2)
# XsqR <- chisq.test(pro.NT_R)
# print(XsqR)

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Invertebrados

Densidades

Ni <- density(data = invertebrados, location = params$comunidad) %>%
  filter(Sitio == params$reserva|
           Sitio == params$control)

mpa_plot3(Ni, reserve = params$reserva, control = params$control, y.lab = "Densidad (org / transecto)")

stargazer(turfeffect(Ni, reserve = params$reserva, control = params$control), dep.var.labels = "Densidad (org / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Especies de interes

Langosta (Panulirus argus)

lang <- filter(invertebrados, GeneroEspecie == "Panulirus argus")

Nlang <- density(lang, location = params$comunidad)

mpa_plot3(Nlang, reserve = params$reserva, control = params$control, y.lab = "Densidad (langostas / transecto)")

stargazer(turfeffect(Nlang, reserve = params$reserva, control = params$control), dep.var.labels = "Densidad (org / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Caracol rosa (Lobatus gigas)

car <- filter(invertebrados, GeneroEspecie == "Strombus gigas")

Ncar <- density(car, location = params$comunidad)

mpa_plot3(Ncar, reserve = params$reserva, control = params$control, y.lab = "Densidad (caracoles / transecto)")

stargazer(turfeffect(Ncar, reserve = params$reserva, control = params$control), dep.var.labels = "Densidad (org / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Pargos (Lutjanus sp.)

Densidad

lutjanus <- peces %>%
  filter(Genero == "Lutjanus")

Nlut <- density(lutjanus, location = params$comunidad)

mpa_plot3(Nlut, reserve = params$reserva, control = params$control, y.lab = "Densidad de pargos (org / transecto)")

stargazer(turfeffect(Nlut, reserve = params$reserva, control = params$control), dep.var.labels = "Densidad (org / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Biomasa

Blut <- fish_biomass(lutjanus, location = params$comunidad)

mpa_plot3(Blut, reserve = params$reserva, control = params$control, y.lab = "Biomasa de pargos (Kg / transecto)")

stargazer(turfeffect(Blut, reserve = params$reserva, control = params$control), dep.var.labels = "Biomasa (Kg / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")

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Referencias

• R Core Team (2015). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

• JJ Allaire, Joe Cheng, Yihui Xie, Jonathan McPherson, Winston Chang, Jeff Allen, Hadley Wickham, Aron Atkins and Rob Hyndman (2016). rmarkdown: Dynamic Documents for R. R package version 0.9.6. https://CRAN.R-project.org/package=rmarkdown

• Hadley Wickham and Romain Francois (2016). dplyr: A Grammar of Data Manipulation. R package version 0.5.0. https://CRAN.R-project.org/package=dplyr

• Hadley Wickham (2016). tidyr: Easily Tidy Data with spread() and gather() Functions. R package version 0.6.0. https://CRAN.R-project.org/package=tidyr

• Hlavac, Marek (2015). stargazer: Well-Formatted Regression and Summary Statistics Tables. R package version 5.2. http://CRAN.R-project.org/package=stargazer

turf-reserves/MPAtools documentation built on June 1, 2019, 2:54 a.m.