install.packages(c("AICcmodavg", "bbmle", "betapart", "buildmer", "corrplot", "gbm", "glmmTMB", "modEvA", "sjstats", "spdep"))
(12611-943)/1261
(1261-943)/1261
(3396-2553)/3396
(1167-880)/1167
library(plyr)
library(rgeos)
library(rgdal)
library(ggplot2)
library(gridExtra)
library(maps)
# theme -------------------------------------------------------------------
theme_nothing2 <- function (base_size = 12, base_family = "") {
theme_grey(base_size = base_size, base_family = base_family) %+replace%
theme(rect = element_rect(fill = "transparent",
colour = NA,
color = NA,
size = 0,
linetype = 0),
line = element_blank(),
plot.title = element_text(size=14, face='italic',hjust = 0.5),
axis.text = element_blank(),
axis.title = element_blank(),
panel.background = element_blank(), axis.ticks.length = grid::unit(0,"lines"), legend.position = "none",
panel.spacing = grid::unit(c(0,0, 0, 0), "lines"),
plot.margin = grid::unit(c(0.1,0.1, 0.1,0.1), "lines"))
}
# load master table -------------------------------------------------------
setwd("~/OneDrive - Universidade de Lisboa/Documents/Exotic data paper/Final files/to submit/DataS1")
setwd("C:/Users/Fernando/OneDrive - Universidade de Lisboa/Documents/Exotic data paper/NeoBiota/2nd submission/DataS1")
dir()
master.yes <- read.csv("Citizen science.csv", head=T)
master.no <- read.csv("All records.csv", head=T)
head(master.no)
names(master.yes)
library(reshape)
master.yesx <- melt(master.yes[,-156], id.vars = "UTM")
head(master.yesx)
master.yesx <- master.yesx[master.yesx$value==1,]
class <- strsplit(master.yesx$variable, "_")[[1]][1]
master.yesx$variable
class <- strsplit(as.character(master.yesx$variable), "_")[[1]][1]
class
class <- strsplit(as.character(master.yesx$variable), "_")
class
master.yesx$species <- NA
i=1
sp.name <- strsplit(master.yesx$variable[i], "_")[[1]][2]
sp.name <- strsplit(as.character(master.yesx$variable)[i], "_")[[1]][2]
sp.name
sp.name <- gsub("[.]"," ",sp.name)
sp.name
for(i in 1:nrow(master.yesx)){
sp.name <- strsplit(as.character(master.yesx$variable)[i], "_")[[1]][2]
sp.name <- gsub("[.]"," ",sp.name)
master.yesx$species[i] <- sp.name
}
write.csv(master.yesx, "CitizenScience.csv", head=F)
write.csv(master.yesx, "CitizenScience.csv")
library(readxl)
myd <- read_excel("Data.xlsx", sheet = 1)
head(myd)
names(myd)
names(master.yesx)
all.x=T)
myd2 <- merge(myd, master.yesx, by.x=c("Scientific name", "UTM"),
by.y=c("species", "UTM"),
all.x=T)
head(myd)
names(myd)
names(master.yesx)
myd2 <- merge(myd, master.yesx[,c(1,4)], by.x=c("Scientific name", "UTM"),
by.y=c("species", "UTM"),
all.x=T)
myd2 <- merge(myd, master.yesx[,c(1,3,4)], by.x=c("Scientific name", "UTM"),
by.y=c("species", "UTM"),
all.x=T)
head(myd2)
names(myd2)
names(myd2)[10]
names(myd2)[10] = "Citizen science"
