JM_report.Rmd

---
title: "prelim-analysis-JM"
output: html_document
date: "2024-11-27"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
library(tidyverse)

```


```{r}
lizards <- read.table('FullyLoadedLizards.tsv') %>% 
  select(-c('individuals'))

summary <- lizards %>%
  group_by(species, lighting, tank, substrate) %>% 
  summarise(mean_wt = mean(weight),
            sd_wt = sd(weight))

species_mean_weights <- lizards %>% 
  group_by(species) %>% 
  summarise(species_mean_wt = mean(weight))

```

### Interaction plot for lizards across treatments

```{r}
inter <- summary %>% 
  mutate('all_conditions' = paste(lighting, tank, substrate, sep='-')) %>% 
  mutate('substrate_tank' = paste(substrate, tank, sep='-')) %>% 
  # Normalize the species weights for the interaction plot
  left_join(species_mean_weights, by='species') %>% 
  rename(species_mean_weight = species_mean_wt) %>% 
  mutate(mean_wt_normalized = mean_wt / species_mean_weight) %>% 
  mutate(sd_wt_normalized = sd_wt / species_mean_weight)

```

```{r}
  
inter_plot <- ggplot(data=inter, mapping=aes(x=all_conditions, y=mean_wt_normalized, color=species)) +
  geom_point(size=2) +
  geom_errorbar(aes(ymin = (mean_wt - sd_wt) / species_mean_weight,
                    ymax = (mean_wt + sd_wt) / species_mean_weight),
                width=0.2) +
  labs(title='Full interaction plot all treatment categories') +
  theme_bw() +
  theme(
    axis.text.x=element_text(angle=90, face='bold', size=8),
    axis.title.x = element_blank(),
    legend.position = c(0.95, 0.95),
    legend.title = element_blank(),
    legend.text = element_text(siz=6, face='bold')
  )

(inter_plot)

```
```{r}
inter_lighting_plot <- ggplot(data=inter, mapping=aes(x=substrate_tank, y=mean_wt_normalized, color=species)) +
  facet_wrap(~lighting) +
  geom_point(size=2) +
  geom_line(linewidth=1) +
  geom_errorbar(aes(ymin = (mean_wt - sd_wt) / species_mean_weight,
                    ymax = (mean_wt + sd_wt) / species_mean_weight),
                width=0.2) +
  labs(title='Full interaction plots faceted by lighting') +
  theme_bw() +
  theme(
    axis.text.x=element_text(angle=90, face='bold', size=8),
    axis.title.x = element_blank(),
    legend.position = c(0.95, 0.95),
    legend.title = element_blank(),
    legend.text = element_text(siz=6, face='bold')
  )

(inter_lighting_plot)
```