Function reference • MATSS

Creating a Research Compendium
`create_MATSS_compendium()`	Create a research compendium for MATSS
Drake Plans Functions to help build Drake plans
`build_analyses_plan()`	Generate a Drake Plan for Analyses
`build_datasets_plan()`	Generate a Drake Plan for Datasets
`build_bbs_datasets_plan()`	Generate a Drake Plan for BBS Datasets
`build_biotime_datasets_plan()`	Generate a Drake Plan for Biotime Datasets
`build_gpdd_datasets_plan()`	Generate a Drake Plan for GPDD Datasets
`build_retriever_datasets_plan()`	Generate a Drake Plan for retriever datasets
`analysis_wrapper()`	Create a function that replicates an analysis for all time series in a dataset
`collect_analyses()`	Collect Analyses Together into a Tibble
Configure Data Path Functions to configure the data path for storing downloaded datasets
`get_default_data_path()`	What is the default data path?
`check_default_data_path()`	Check if a default data path is set
`use_default_data_path()`	Manage the default path for downloading MATSS Data into
Rdataretriever Functions that use Rdataretriever to download and import data
`install_retriever_data()` `import_retriever_data()` `download_datasets()`	Download data from the data retriever
Get Data Functions to load datasets
`get_biotime_data()`	Get a cleaned BioTime dataset
`get_biotime_dataset_ids()` `prepare_biotime_data()`	Return BioTime dataset ids for individual loading
`get_bbs_route_region_data()`	Get cleaned BBS data
`get_cowley_lizards()`	Read in the cowley lizard community data from a txt file Import cowley lizard data from data files
`get_cowley_snakes()`	Read in the cowley snake community data from a txt file Import cowley snake data from data files
`get_gpdd_data()`	Create GPDD population time-series data
`get_jornada_data()`	get Jornada rodent data
`get_karoo_data()`	get Karoo ungulate data Import and clean Karoo abundance from data files
`get_kruger_data()`	get Kruger National Park ungulate data Import and clean Kruger National Park abundance from data files
`get_maizuru_data()`	get the maizuru community data
`get_mtquad_data()`	get Montana plant quad time-series data
`get_portal_rodents()`	get portal rodent data Import Portal rodent data using portalr functions. Currently returns rodent data formatted appropriately for LDA analysis.
`get_sdl_data()`	Create Sonoran desert lab time-series data
`get_sgs_data()`	get Shortgrass Steppe rodent data
`process_biotime_dataset()`	Process an individual BioTime dataset
`correct_biotime_dataset()`	Correct and clean specific datasets
Analysis Methods Functions to compute analyses
`ts_summary()`	Summarize a time series dataset
`summarize_df()` `summarise_df()`	Compute summaries and autocorrelation for each variable
`summarize_vec()` `summarise_vec()`	Summarize a univariate vector
`richness()`	Count non-0 entries
`temp_autocor()`	Interpolate observations
`interpolate_obs()`	Interpolate observations
Data Checking, Filtering, and Processing Functions to check datasets, extract components, and preprocess them
`check_data_format()`	Check data format
`get_times_from_data()`	extract the times from a formatted data structure
`get_effort_from_data()`	extract the effort from a formatted data structure
`normalize_obs()` `normalize_times()` `normalize_effort()`	Normalize observations, effort, or times
`to_numeric_vector()`	Extract a numeric vector
`prepare_bbs_ts_data()`	Prepare BBS population time-series data
`process_bbs_route_region_data()`	Process the BBS data for an individual route and region
`filter_bbs_ts()`	Filter BBS to specified time series period and number of samples
`filter_bbs_species()`	Filter poorly sampled BBS species
`combine_bbs_subspecies()`	Combine subspecies into their common species
Datasets Description of the built-in datasets
`MATSS`	Macroecological Analayses of Time Series Structure
`analysis_wrapper()`	Create a function that replicates an analysis for all time series in a dataset
`append_data_citations()`	Generate a vector of citations.
`append_retriever_citation()`	Append citation info to a formatted dataset
`build_analyses_plan()`	Generate a Drake Plan for Analyses
`build_bbs_datasets_plan()`	Generate a Drake Plan for BBS Datasets
`build_biotime_datasets_plan()`	Generate a Drake Plan for Biotime Datasets
`build_datasets_plan()`	Generate a Drake Plan for Datasets
`build_gpdd_datasets_plan()`	Generate a Drake Plan for GPDD Datasets
`build_references_plan()`	Generate a Drake Plan for dataset references
`build_retriever_datasets_plan()`	Generate a Drake Plan for retriever datasets
`check_data_format()`	Check data format
`check_default_data_path()`	Check if a default data path is set
`collect_analyses()`	Collect Analyses Together into a Tibble
`combine_bbs_subspecies()`	Combine subspecies into their common species
`correct_biotime_dataset()`	Correct and clean specific datasets
`create_MATSS_compendium()`	Create a research compendium for MATSS
`dragons`	dragons dataset
`filter_bbs_species()`	Filter poorly sampled BBS species
`filter_bbs_ts()`	Filter BBS to specified time series period and number of samples
`get_bbs_route_region_data()`	Get cleaned BBS data
`get_biotime_data()`	Get a cleaned BioTime dataset
`get_biotime_dataset_ids()` `prepare_biotime_data()`	Return BioTime dataset ids for individual loading
`get_cowley_lizards()`	Read in the cowley lizard community data from a txt file Import cowley lizard data from data files
`get_cowley_snakes()`	Read in the cowley snake community data from a txt file Import cowley snake data from data files
`get_default_data_path()`	What is the default data path?
`get_effort_from_data()`	extract the effort from a formatted data structure
`get_gpdd_data()`	Create GPDD population time-series data
`get_jornada_data()`	get Jornada rodent data
`get_karoo_data()`	get Karoo ungulate data Import and clean Karoo abundance from data files
`get_kruger_data()`	get Kruger National Park ungulate data Import and clean Kruger National Park abundance from data files
`get_maizuru_data()`	get the maizuru community data
`get_mtquad_data()`	get Montana plant quad time-series data
`get_portal_rodents()`	get portal rodent data Import Portal rodent data using portalr functions. Currently returns rodent data formatted appropriately for LDA analysis.
`get_sdl_data()`	Create Sonoran desert lab time-series data
`get_sgs_data()`	get Shortgrass Steppe rodent data
`get_times_from_data()`	extract the times from a formatted data structure
`has_integer_times()`	Check if a dataset has integer times
`has_missing_samples()`	Check for missing samples
`install_retriever_data()` `import_retriever_data()` `download_datasets()`	Download data from the data retriever
`interpolate_missing_samples()`	Impute missing samples using linear interpolation
`interpolate_obs()`	Interpolate observations
`invoke()`	Invoke an analysis on a dataset
`is_equitimed()`	Check that the times of a dataset are evenly sampled
`make_equitimed()`	Insert rows if necessary so that time series are evenly sampled
`make_integer_times()`	Add a time variable with integer values for evenly sampled data
`normalize_obs()` `normalize_times()` `normalize_effort()`	Normalize observations, effort, or times
`prepare_bbs_ts_data()`	Prepare BBS population time-series data
`prepare_datasets()`	Prepare datasets for usage
`print(<matssdata>)`	Print a time series dataset
`print(<matsssummary>)`	Print a time series summary
`process_bbs_route_region_data()`	Process the BBS data for an individual route and region
`process_biotime_dataset()`	Process an individual BioTime dataset
`richness()`	Count non-0 entries
`summarize_df()` `summarise_df()`	Compute summaries and autocorrelation for each variable
`summarize_vec()` `summarise_vec()`	Summarize a univariate vector
`summary(<matssdata>)`	Summarize a time series dataset
`temp_autocor()`	Interpolate observations
`to_numeric_vector()`	Extract a numeric vector
`ts_summary()`	Summarize a time series dataset
`use_default_data_path()`	Manage the default path for downloading MATSS Data into

Reference

Creating a Research Compendium

Drake Plans

Configure Data Path

Rdataretriever

Get Data

Analysis Methods

Data Checking, Filtering, and Processing

Datasets