## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup, echo=TRUE, eval=FALSE, results='hold', warning=FALSE, include=TRUE----
# 
# library(pannotator)
# 
# options(shiny.port = httpuv::randomPort(), shiny.launch.browser = .rs.invokeShinyWindowExternal, shiny.maxRequestSize = 9000 * 1024^2)
# 
# run_app()
# 
# # Optional: launch with a project-specific YAML file
# # run_app(projectSettingsFile = "C:/path/to/project.yml")

## ----echo=TRUE, eval=FALSE, results='hold', warning=FALSE, include=TRUE-------
# 
# library(mapview)
# library(sf)
# 
# 
# df_annotation <- readRDS("C:/user_1_annotations.rds") # read in the .rds file
# df_annotation <- st_as_sf(df_annotation, wkt = "geometry",crs = 4326) #define
# #the geometry
# 
# df_annotation$dd2 <- as.numeric(df_annotation$dd2) # dd2 = -999 where crowns
# # have not been assessed for health (NA); range = 0 for no live leaves (entirely
# # dead) to 100 for entire crown healthy with green leaves
# 
# df_annotation <- subset(df_annotation, dd2 > -1 ) # select only records where
# # Allocasuarina crowns have been assessed for health; that is, excluding NA records
# 
# 
# mapviewOptions(basemaps = c("Esri.WorldImagery"),
#                vector.palette = colorRampPalette(c("red","orange", "yellow", "green")),
#                layers.control.pos = "topright")
# 
# 
# mapview(df_annotation, zcol = "dd2 ", na.rm = TRUE)
# 

## ----echo=TRUE, eval=FALSE, results='hold', warning=FALSE, include=TRUE-------
# # read in the species data file #
# 
# species_data <- read.csv("Calibration_species.csv", stringsAsFactors = FALSE)
# 
# # confirm that there are 79 plots of species data
# cat("The number of rows in the dataframe is", nrow(species_data), "\n")
# 
# 
# # now determine the relationship between plot-level species counts in the field survey versus camera survey counts. abline adds a linear model to the plot   #
# 
# plot(species_data$No_Field_species, species_data$No_Camera_species,
#      main = "Plot-level species richness",
#      xlab = "No. of species (Field Survey)",
#      ylab = "No. of species (Camera Survey)",
#      pch = 16,  # Use filled circles as data points
#      col = "black",  # Set point color
#      ylim = c(0, 8),  # Set y-axis limits
#      xlim = c(0, 8))  # Set x-axis limits
# abline(lm(No_Camera_species ~ No_Field_species, data = species_data), col = "red")
# 
# # view the linear model statistics #
# model <- lm(No_Camera_species ~ No_Field_species, data = species_data)
# 
# model_summary <- summary(model)
# print(model_summary)
# 

