[!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()