Function reference • fftidy

Project Configuration General settings that are used to keep plots consistent.
`bic_proj`	Project UTM crs
`clr_accent`	Highlighter Color
`clr_neighbor`	The basic color scheme for pair_ids
`clr_neighbor_alpha`	The semi-transparent color scheme for pair_ids
`clr_set_base`	The basic color scheme for the sample IDs
`clr_set_light`	The light project color scheme
`clr_set_samples`	The de-saturated project color scheme
`clr_water`	Water Color
`fft_case()`	Project case
`fft_case_inv()`	Inverted project case
`fft_f_width`	Default figure width (double column)
`fft_f_width_half`	Default figure width (single column)
`fft_lwd`	Default plot linewidth
`fft_plot_size`	Default plot size
`fft_text_size`	Default plot font size
`fft_text_size_small`	Small plot font size
`guide_use()`	Helper for Dipteryx density plot guides
`neighbor_ids`	Vector of all neighbor-pair_ids
`sample_ids`	The sample IDs
`sample_ids_short`	Abbreviations of sample IDs
`samples_short`	Reference vector short to long sample ID
`sample_years`	The sample year-class
Data Import Functions for importing FFT tracking data.
`data_extend()`	Extend tracking data with computed metrics
`data_fft()`	Load FFT tracking data
Geo Specific Geographical reference data and operations specific to the project.
`bb`	Define project bounding box
`canal`	Load Panama Canal
`cent_plotter()`	plot all centroids within a tibble-column of sf-objects
`central_point`	Central point (non-sfversion)
`central_point_crs`	Set Projection of Central Point of Area Covered by Tracks
`central_point_sf`	Get central point of area covered by tracks (as sf object)
`crp()`	crop a sf obj to the project bounding box
`dipteryx`	Load Locations of Dipteryx
`gatun`	Load Gatun Lake Outline
`hull_plotter()`	plot all hulls within a tibble-column of sf-objects
`island`	Load Isla Barro Colorado Outline
`merge_sf_columns()`	merge multiple sf columns
`neighboring_samples`	Neighboring groups
`outer_hull`	Get area covered by tracks
`outer_hull_sf`	sf version of area covered by tracks
`pan_detail`	Load clipped Panama Coastline
`sample_as_stars()`	Convert FFT data to Stars object
`sf_raster_empty()`	Initialize empty Stars object
`wgs`	The WGS proj string
Geo General General geographical and operations.
`centroid_of_points()`	combine several sf-points and create a joint centroid
`df_as_sf()`	create the convex hull of a two column tibble with lat long columns (output as sf-obj)
`get_pw_dists()`	given a table with synchronous positions, compute all distances for a specific column-pair (sample-pair)
`hull_tib()`	create the convex hull of a two column tibble with lat long columns (output as tibble)
`tibble_to_sf()` `tibble_to_sf()`	turn a tibble with a lat and long column into a set sf points
`wide_to_distmat()`	transform a wide tibble with pair-wise distances into a distance-matrix
General Helper Functions all kinds of small data processing.
`dtim()`	extract the time of the day from a date-time (as numeric seconds)
`idx_graph()`	convert an igraph-graph into a tidygraph tbl_graph, annotate with the idx (later to become the time-bin), and compute tdiverse node-centralities
`subs()`	subset a list of lists by a common index (the n_th object of each sub-list)
Base Plots Base layers for ggplots.
`p_init()`	initialize a field-trip specific base-plot
`p_init_hull()`	initialize a field-trip specific base-plot (with individuals range)
`p_init_voronoi()`	Base plot for voronoi layers
ctmm related content Functions to modify ctmm results.
`compare_all_models()`	function to compare variogram with all ML model fits (initial close up and total data range)
`compare_n_best_models()`	function to compare variogram with the n best ML model fits (initial close up and total data range)
`fit_ouf()`	function to create and fit a Ornstein-Uhlenbeck-F model to a semi-variance function
`get_akde()`	function for automatizing autocorrelated kernel density estimation
`get_akde_aligned()`	Load ctmm based AKDEs grouped by field season
`get_akde_maual()`	Load ctmm based AKDEs by Sample ID
`get_ci_univ()`	universal function (works for both OU & OUF)
`get_ci_ouf()`	function for OUF specific parameters (tau2)
`get_kriged_occurrence_maual()`	Load ctmm based kriged occurrences by Sample ID
`get_param_estimate()`	Get the parameter estimates from a ctmm fitted model
`get_var_fit_raw()`	Extract a fitted parameter from a ctmm object
`get_var_fit_ou()`	Extract a OU fitted parameter from a ctmm object
`get_var_fit_ouf()`	Extract a OUF fitted parameter from a ctmm object
`m2_to_ha()`	convert SI units (m2 -> ha)
`mod_tab()`	wrapper to get sigma, tauH, tauF, and speed estimates of a model
`parse_cis()`	functions to parse estimated model parameters (mu & tau) from ctmm
`plot_ctm()`	plot two model (original guess and modified) in context of variogram (in right colors)
`plot_svf()`	modified plot.svf from ctmm
`plot_svf_vs_model()`	function to compare variogram with a model fit (initial close up and total data range)
`plot_svfs()`	function to create a variogram plot pair (initial close up and total data range)
`plot_svfs_single()`	function to plot a variogram in the correct color of athe sample
`plot_variogram()`	modified plot.variogram from ctmm
`read_all_ml_fits()`	Load all ctmm fitted models
`s_to_day()`	convert SI units (s -> day)
`separate_mod_tab()`	separate ctmm model estimates from units
`update_model()`	manipulate ctmm model and output new model alongside original for comparison plot
`update_tau()`	manipulate ctmm model tau entry
encounter related content Functions to calcultate pair wise distances and encounters.
`complex_distance()`	Compute pair wise distances within time bins
`on_any_overlap()`	Determine if timepoint x is on any overlap
simulations related content Functions to help with the {ctmm} based simulation of movement tracks.
`back_convert_simulation()`	Convert Simulation results back to data format
`sim_to_sf()`	Convert simulated tracks into a sf-object
`simulate_id()`	Simulate movement track for a particular Sample
accelerometer data related Functions to extract accelerometer data
`assign_overlaps_acc()`	Assign the overlap ID of a timestamp
`xyz_d()`	compute delta XYZ of accelerometer data
`xyz_get()`	get XYZ from accelerometer data
table formating Functions for table formating in rmarkdown
`color_column()`	Color entire column based on sample_id
`styler_id()`	Color cell of of column by sample id
`styler_id_conditional()`	Color table cell based on sample id
`table_theme`	Basic table theme
`table_total()`	Total a Column and ignore NAs

Reference

Project Configuration

Data Import

Geo Specific

Geo General

General Helper Functions

Base Plots

ctmm related content

encounter related content

simulations related content

accelerometer data related

table formating