# trying to figure out why the plot tells me my columns are different lengths
```{r}
# Using sapply to calculate the length of each column in the data frame
column_lengths <- sapply(data, length)

# Print the column lengths
print(column_lengths)

```

```{r}
# Convert the results to a data frame for a more readable output
column_lengths_df <- data.frame(column = names(data), length = column_lengths)

# Print the data frame with column lengths
print(column_lengths_df)

```

```{r}

#data1 is the first transformation where we move data to longer format vice the current one.
#name this something you can easily recall, for me that is data2
#data1<- data %>% 
  pivot_longer(cols = 16:43, 
               names_to = "Species", 
               values_to = "Count")

# this didn't give me what i was looking for. the sections aren't ID'd and the Count column isn't summing instances across section, so I tried to do this instead:

# this was a failed attempt and changes the format - will remove when cleaning document.
#data2 <- melt(data, id.vars = "section", variable.name = "species", value.name = "count")


```
# Return here to fix this output/ purpose
```{r}

# this didn't work - must separate by section to make this valuable
# how to break it down per section. Pulled this code from old class code and changed the names.

data2 <- data1 %>%
  gather(key = "Section", value = "Species", -Species)

#sr <- data3 %>%
  group_by('Section') %>%
  summarise(SR = unique(Species))

print(sr)
```


# Attempting to visualize the presence/ absence data
```{r}

# Convert the presence-absence data to a readable table and then converting the factors so we can count/ quantify the values

pa1 <- pa %>%
  pivot_longer(cols = 5:32,
               names_to = "species",
               values_to = "presence_absence") %>%
mutate(species = factor(species, levels = unique(species)))

```

```{r}

paSummary <- pa1 %>%
  group_by(SECTION, species, presence_absence) %>%
  tally(name = "count")

```

# Plot
```{r}

ggplot(paSummary, aes(x = SECTION, y = count, fill = presence_absence)) +
  geom_bar(stat = "identity") +
  labs(title = "Stacked Bar Plot of Presence/Absence Counts by Section",
       x = "Section Number",
       y = "Count",
       fill = "Presence/Absence") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))


# Summarize the occurrences for each category
behavior_summary <- aggregate(Occurrence ~ Category, data = seal, sum)

# Reorder the Category levels to match your desired order
behavior_summary$Category <- factor(behavior_summary$Category, levels = c("Land", "Water", "Other", "Human Disturbance", "Land + Water"))

# Calculate the percentage for each category
behavior_summary$Percentage <- behavior_summary$Occurrence / sum(behavior_summary$Occurrence) * 100

# Create the pie chart with custom colors and percentages positioned closer to the edge
ggplot(behavior_summary, aes(x = "", y = Occurrence, fill = Category)) +
  geom_bar(stat = "identity", width = 1) +
  coord_polar("y") +
  geom_text(aes(x = 1.15, label = paste0(round(Percentage), "%")), 
            position = position_stack(vjust = 0.5), 
            size = 3, 
            fontface = "bold",
            color = "black",
            show.legend = FALSE) + # Percentage at the end of pie slices
  scale_fill_manual(values = custom_colors) +  # Use custom colors
  theme_void() +
  labs(title = "Proportion of Seal Behaviors",
       fill = "Category") +
  theme(legend.position = "right")
```

# adding and removing large files to speed up analysis
## DO NOT ADD- Something isn't working - Updated 9.23.24 - add back the prep files from my desktop work
```{r}

#Example syntax: dadaFs <- readRDS("dadaFs.rds")

dadaFs<- readRDS("dadaFs.rds")
errF<- readRDS("errF.rds")
filtFs<- readRDS("filtFs.rds")
fnFs<- readRDS("fnFs.rds")
fnFs_filtered<- readRDS("fnFs_filtered.rds")
#saveRDS(derepFs, "derepFs.rds")

# save- reverse 
dadaRs<- readRDS("dadaRs.rds")
errR<- readRDS("errR.rds")
filtRs<- readRDS( "filtRs.rds")
fnRs<- readRDS("fnRs.rds")
fnRs_filtered<- readRDS( "fnRs_filtered.rds")
#saveRDS(derepRs, "derepRs.rds")

```

# move large files from memory to free up space to move forward - come back to add reverse files when finished
```{r}
# save- forward 
saveRDS(dadaFs, "dadaFs.rds")
saveRDS(derepFs, "derepFs.rds")
saveRDS(errF, "errF.rds")
saveRDS(filtFs, "filtFs.rds")
saveRDS(fnFs, "fnFs.rds")
saveRDS(fnFs_filtered, "fnFs_filtered.rds")

# save- reverse 
saveRDS(dadaRs, "dadaRs.rds")
saveRDS(derepRs, "derepRs.rds")
saveRDS(errR, "errR.rds")
saveRDS(filtRs, "filtRs.rds")
saveRDS(fnRs, "fnRs.rds")
saveRDS(fnRs_filtered, "fnRs_filtered.rds")

# Remove from memory
rm(dadaFs)
rm(derepFs)
rm(errF)
rm(filtFs)
rm(fnFs)
rm(fnFs_filtered)
gc()

# Reload (when needed)
#dadaFs <- readRDS("dadaFs.rds")

```