sciCentRverse

Important

This package is intended for internal use within the ABMI Science Centre and serves as a development playground for prototyping, testing, and iterating on cross-project functions and workflows.

Installation

You can install the package directly from GitHub:

devtools::install_github("ABbiodiversity/sciCentRverse")

Functions

The package includes the following utility functions:

Spatial Functions

• add_alberta_flag() - Add Alberta flag to a site data frame using provincial boundaries
• extract_by_year() - Extract raster values by year from spatial features
• parallel_extract_directory() - Parallel extraction of raster data stored in a directory

Time & Processing Functions

• estimate_processing_time() - Estimate total processing time based on subset
• format_time_diff() - Format time difference as days, hours, minutes, and seconds

File I/O Functions

• load_most_recent_data() - Load the most recent .RData file dynamically
• load_rdata_files() - Load .RData files into a list
• read_tifs_to_list() - Read TIF files into a named list
• read_tifs_to_multiband() - Read TIF files into a multiband raster object

Data Manipulation Functions

• select_one_response() - Select a single response column from data
• select_species() - Select a specific species column
• sample_blocks() - Sample a fraction of rows within blocks
• snake_case() - Convert strings to snake_case
• summarize_column_classes() - Generate a data frame of column classes

Configuration Functions

• set_terra_options() - Set Terra options with buffer for memory management

Plotting & Styling Functions

• theme_science() - Minimal theme for scientific plots
• theme_science_map() - Minimal theme for scientific map plots
• style_active_file() - Style the active R file using styler

Camera Methods Functions

• cam_get_op_days() - Get a dataframe of operational days for each camera
• cam_summarise_op_by_season() - Summarise operational days by user-defined seasons
• cam_consolidate_tags() - Consolidate per-image species tags into one row from a WildTrax main report
• cam_obtain_n_gap_class() - Identify "N" gap boundaries where a NONE is found between animal images
• cam_calc_time_by_series() - Calculate time-in-front-of-camera by series (in seconds)
• cam_sum_total_time() - Summarise total time by project, location, species, and season (with op-days)
• cam_extract_model_lookup() - Extract camera models from an image report
• cam_calc_density_by_loc() - Calculate density at each location from seasonal time and EDD

Usage

library(sciCentRverse)

# Example: Convert strings to snake_case
snake_case(c("Normal 1991_2020 AHM", "Normal 1991_2020 bFFP"))

# Example: Format time difference
start_time <- Sys.time()
Sys.sleep(5)
end_time <- Sys.time()
format_time_diff(start_time, end_time)

# Example: Use custom ggplot2 theme
library(ggplot2)
ggplot(mtcars, aes(x = wt, y = mpg)) +
  geom_point() +
  labs(title = "Example Plot", x = "Weight", y = "MPG") +
  theme_science()

Dependencies

The package requires the following R packages:

• dplyr
• sf
• terra
• rnaturalearth
• ggplot2
• glue
• parallel

License

MIT