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) })
Leyenda
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)
\clearpage
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$control), dep.var.labels = "Densidad (org / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")
\clearpage
Sp <- richness(data = peces, location = params$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 = "+")
\clearpage
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$control), dep.var.labels = "Biomasa (Kg / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")
\clearpage
NTp <- trophic(data = peces, location = params$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 = "+")
\clearpage
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$NT) # NT_R <- as.data.frame(NT_R[-1]) # rownames(NT_R) <- rows # pro.NT_R<- prop.table(as.matrix(NT_R),2) # XsqR <- chisq.test(pro.NT_R) # print(XsqR)
\clearpage
Ni <- density(data = invertebrados, location = params$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 = "+")
\clearpage
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$control), dep.var.labels = "Densidad (org / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")
\clearpage
car <- filter(invertebrados, GeneroEspecie == "Strombus gigas") Ncar <- density(car, location = params$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 = "+")
\clearpage
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$control), dep.var.labels = "Densidad (org / transecto)", type = "latex", dep.var.caption = "", report = "vc*", single.row = T, omit.stat = c("adj.rsq", "n"), digits = 2, df = F, covariate.labels = c("Ano", "Zona", "**Ano:Zona**", "Constante"), notes = "+p < 0.1, ++p<0.05, +++p<0.001", notes.append = FALSE, star.char = "+")
\clearpage
Blut <- fish_biomass(lutjanus, location = params$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 = "+")
\clearpage
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
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