Sea Turtle Nest Disturbance

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library(ggplot2)
library(readxl)
library(dplyr)

## Warning: package 'dplyr' was built under R version 4.2.3

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(lubridate)

## 
## Attaching package: 'lubridate'

## The following objects are masked from 'package:base':
## 
##     date, intersect, setdiff, union

# Set working directory
setwd("D:/YPI Office/R Analysis/Monitoring Penyu")

# Read data from the 'SMP' sheet
data <- read_excel("Pemantauan Penyu CALK.xlsx", sheet = "SMP")

## New names:
## • `` -> `...32`
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## • `` -> `...35`
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# Create Year and Quarter columns
data <- data %>%
  mutate(`Patrol Start Date` = as.Date(`Patrol Start Date`),
         Year = year(`Patrol Start Date`),
         Quarter = paste0("Q", quarter(`Patrol Start Date`), "-", Year))

# Summarize number of disturbances per quarter and predator type
rekap <- data %>%
  filter(!is.na(Predator)) %>%
  group_by(Quarter, Predator) %>%
  summarise(Count = n(), .groups = "drop")

# Calculate total and percentage per quarter
total_per_quarter <- rekap %>%
  group_by(Quarter) %>%
  summarise(Total = sum(Count), .groups = "drop")

rekap_percent <- rekap %>%
  left_join(total_per_quarter, by = "Quarter") %>%
  mutate(Percent = round((Count / Total) * 100, 2))

# Order the quarters chronologically
quarter_levels <- c("Q1-2024", "Q2-2024", "Q4-2024", "Q1-2025")
rekap_percent$Quarter <- factor(rekap_percent$Quarter, levels = quarter_levels)

# Calculate average percentage per predator category
avg_percent_per_predator <- rekap_percent %>%
  group_by(Predator) %>%
  summarise(AveragePercent = round(mean(Percent), 2))

Sea Turtle Disturbance Percentage

# Plot 1: Trend of disturbance percentage per quarter (smooth line)
ggplot(rekap_percent, aes(x = Quarter, y = Percent, color = Predator, group = Predator)) +
  geom_point(size = 3) +
  geom_smooth(method = "loess", se = FALSE, size = 1.2) +
  scale_y_continuous(labels = function(x) paste0(x, "%"), limits = c(0, 100)) +
  labs(title = "Trend of Sea Turtle Nest Disturbance Percentage per Quarter",
       x = "Quarter",
       y = "Disturbance Percentage (%)",
       color = "Predator Category") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

## `geom_smooth()` using formula = 'y ~ x'

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : span too small.  fewer data values than degrees of freedom.

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at 0.985

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 1.015

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 4.0602

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : span too small.  fewer data values than degrees of freedom.

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at 0.985

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 2.015

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 0

## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 4.0602

Average Sea Turtle Nest Disturbance by Years

# Plot 2: Average disturbance percentage by predator (pie chart)
ggplot(avg_percent_per_predator, aes(x = "", y = AveragePercent, fill = Predator)) +
  geom_col(width = 1, color = "white") +
  coord_polar(theta = "y") +
  labs(title = "Average Sea Turtle Nest Disturbance Percentage by Predator",
       fill = "Predator Category") +
  theme_void() +
  geom_text(aes(label = paste0(AveragePercent, "%")),
            position = position_stack(vjust = 0.5),
            color = "white", size = 5)

Sea Turtle Nest Disturbance

Hendra Budaya Hadikusuma

2025-06-18

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Conclusion