P_hastatus_Consistentlong-distance_foragingflights/11.Figure_S4_gh.Rmd at main · livingingroups/P_hastatus_Consistentlong-distance_foragingflights · GitHub

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---
title: "Switching behavior dry and wet season"
author: "Camila Calderon"
date: "2024-07-222"
output: html_document
---
## Load libraries

```{r setup, warning=FALSE, message=FALSE}
library(ggplot2)
library(patchwork)
library(ggmap)
library(tidyverse)
library(ggnewscale)
library(ggsn)
```

## Load data

```{r}
load(file="~/ownCloud/PhDLife/P.hastatus/Thesis/Paper1/BiologyLetters/data/Phyllostomus_HMMbehaviors.RData")
```

## Select bats with switching behavior in colony 1 during the dry early season 2022 and colony 2 during the wet season 2023

```{r, results=FALSE}
# select bats in Bocas march 2022 with area switching
bats <- bats_behaviors %>%
  filter(tag_local_identifier=="PH_TS_046"| tag_local_identifier=="PH_TS_039")%>%
  filter(ID!="PH_TS_039_2022-03-16")

bats_aj_2023 <- bats_behaviors %>%
  filter(tag_local_identifier=="PHYL9" |tag_local_identifier=="PHYL27"|tag_local_identifier=="PHYL28")

# make a data frame with the locations of the colonies
colonies <- data.frame(colonies=c("lagruta", "ajcave"), location_lat=c( 9.396448,9.440312), location_long=c(-82.271541, -82.274955))

```

## Plot switching in map

```{r}
# plot using stamen map from Bocas
register_stadiamaps("3a58670b-0653-4668-bb0c-f9e5454596e7")

# create a bounding box
e <- make_bbox(location_long, location_lat, data = bats_behaviors)

# plot colony 1 switching
gruta_switching  <- get_stadiamap(e, zoom = 13, maptype = "stamen_toner_lite") %>% ggmap()+
  coord_sf(crs = "+proj=lonlat", expand = FALSE)+
  scale_x_continuous(breaks = c(-82.50, -82.40, -82.30, -82.20))+
  geom_path(aes(x=location_long, y=location_lat, color=as.factor(date)),data=bats)+
  labs(color="date")+
  new_scale_color()+
  new_scale_fill()+
  geom_point(data=colonies[colonies$colonies=="lagruta",], aes(x=location_long, y=location_lat, shape=colonies, size=5, fill=colonies, color=colonies))+
  scale_shape_manual(values = c(21), guide="none")+
  scale_color_manual(values = "black", guide="none")+
  scale_fill_manual(values = alpha("black", 0.6), guide="none")+
  theme_bw()+
 annotation_scale(location = "bl", line_width = 1, height = unit(0.5, "cm"), pad_x= unit(0.5, "cm"), pad_y= unit(0.5, "cm"), text_cex = 2)+
  guides(color = "none", size="none", alpha="none", fill="none")+
  facet_wrap(.~tag_local_identifier, nrow=2)+
  theme(legend.position="bottom")+
  theme_linedraw()+
  theme(legend.position="none",
        axis.text.x = element_text(size = 14),
        axis.text.y = element_text(size = 14),
        axis.title.x = element_text(size = 24),
        axis.title.y = element_text(size = 24),
        strip.text = element_blank())+
  xlab("Longitude")+
  ylab("Latitude")

gruta_switching

# plot colony 2 switching
ajcave_switching <- get_stadiamap(e, zoom = 13, maptype = "stamen_toner_lite") %>% ggmap()+
  coord_sf(crs = "+proj=lonlat", expand = FALSE)+
  scale_x_continuous(breaks = c(-82.50, -82.40, -82.30, -82.20))+
  geom_path(aes(x=location_long, y=location_lat, color=as.factor(date)),data=bats_aj_2023)+
  labs(color="date")+
  new_scale_color()+
  new_scale_fill()+
  geom_point(data=colonies[colonies$colonies=="ajcave",], aes(x=location_long, y=location_lat, shape=colonies, size=5, fill=colonies, color=colonies))+
  scale_shape_manual(values = c(22), guide="none")+
  scale_color_manual(values = "black", guide="none")+
  scale_fill_manual(values = alpha("black", 0.6), guide="none")+
  theme_bw()+
  annotation_scale(location = "bl", line_width = 1, height = unit(0.5, "cm"), pad_x= unit(0.5, "cm"), pad_y= unit(0.5, "cm"), text_cex = 2)+
  guides(color = "none", size="none", alpha="none", fill="none")+
  facet_wrap(.~tag_local_identifier, nrow=3)+
  theme_linedraw()+
  theme(legend.position="none",
        axis.text.x = element_text(size = 14),
        axis.text.y = element_text(size = 14),
        axis.title.x = element_text(size = 24),
        axis.title.y = element_text(size = 24),
        strip.text = element_blank())+
  xlab("Longitude")+
  ylab("Latitude")

ajcave_switching

# compile plots for figure S4
((gruta_switching | ajcave_switching) + plot_layout(axis_titles = "collect")+ plot_annotation(tag_levels = "A") &
    theme(plot.tag  = element_text(face = 'bold', size=24), axis.title = element_text(face = 'bold', size=24), axis.title.x = element_text(size = 24), axis.title.y=element_text(size=24), axis.text.x=element_text(size=18), axis.text.y=element_text(size=18)))

# save figure
ggsave(file="~/ownCloud/PhDLife/P.hastatus/Thesis/Paper1/BiologyLetters/figures/FigS4.pdf", width=15, height = 10, dpi=300)
```