Package index • PEcAn.DB

All functions
`append.covariate()`	Append covariate data as a column within a table
`arrhenius.scaling.traits()`	Apply Arrhenius scaling to 25 degC for temperature-dependent traits
`assign.treatments()`	assign.treatments
`bety2pecan()`	Convert BETY variable names to MsTMIP and subsequently PEcAn standard names
`betyConnect()`	Connect to bety using current PEcAn configuration
`check.lists()`	Compares two lists
`clone_pft()`	Duplicate existing pft with associated priors, species, and cultivars
`convert_input()`	Convert between formats, reusing existing files where possible
`db.close()`	Generic function to close a database connection
`db.exists()`	Test connection to database
`db.getShowQueries()`	db.getShowQueries
`db.open()`	Open a database connection
`db.print.connections()`	Debug leaked connections
`db.query()`	Generic function to query database
`db.showQueries()`	db.showQueries
`dbHostInfo()`	Database host information
`db_merge_into()`	Merge local data frame into SQL table
`dbfile.check()`	List files associated with a container and machine exist in `dbfiles` table
`dbfile.file()` `dbfile.id()`	Convert between file paths and ids
`dbfile.input.check()`	Check for a file in the input/dbfiles tables
`dbfile.input.insert()`	Insert file into tables
`dbfile.insert()`	Insert file into tables
`dbfile.move()`	Move files to new location
`dbfile.posterior.check()`	Check for a file in the input/dbfiles tables
`dbfile.posterior.insert()`	Insert file into tables
`default_hostname()`	default_hostname
`derive.trait()`	Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.
`derive.traits()`	Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.
`dplyr.count()`	Count rows of a data frame
`fancy_scientific()`	Convert number to scientific notation pretty expression
`fetch.stats2se()`	Fetch data and transform stats to SE
`filter_sunleaf_traits()`	Function to filter out upper canopy leaves
`get.id()`	get.id
`get.trait.data()`	Get trait data from the database.
`get.trait.data.pft()`	Get trait data from the database for a single PFT
`get_postgres_envvars()`	Look up Postgres connection parameters from environment variables
`get_run_ids()`	Get vector of run IDs for a given workflow ID
`get_users()`	Get data frame of users and IDs
`get_var_names()`	Get vector of variable names for a particular workflow and run ID
`get_workflow_ids()`	Get vector of workflow IDs
`insert.format.vars()`	Insert Format and Format-Variable Records
`insert_table()`	Insert R data frame into SQL database
`load_data_single_run()`	Load data for a single run of the model
`match_colnames()`	Match names of local data frame to SQL table
`match_dbcols()`	Match column names and classes between local and SQL table
`met_inputs()`	Retrieve available met inputs for the given site, model, and hostname
`ncdays2date()`	Convert netcdf number of days to a datetime
`pft.add.spp()`	Associate species with a PFT.
`query.covariates()`	Queries covariates from database for a given vector of trait id's
`query.data()`	Query data and transform stats to SE by calling `fetch.stats2se`;
`query.file.path()`	Get file path given id and machine
`query.format.vars()`	Look up names and units of input variables from a format id or input id
`query.pft_cultivars()`	Select cultivars associated with a PFT
`query.pft_species()`	Query species given pft name
`query.priors()`	Query Priors
`query.site()`	Given site_id, return site table
`query.trait.data()`	Extract trait data from database
`query.traits()`	Query trait data
`query.yields()`	Query yield data and transform stats to SE by calling `fetch.stats2se`;
`query_pfts()`	Retrieve PFT ID, name, and type from BETY
`query_priors()`	Query priors using prepared statements
`runs()`	Get table of runs corresponding to a workflow
`search_reference_single()`	Perform crossref search for a single reference
`search_references()`	Perform crossref search for a list of references
`stamp_started()` `stamp_finished()`	Stamp start and stop times of runs
`symmetric_setdiff()`	Symmetric set difference of two data frames
`take.samples()`	Sample from normal distribution, given summary stats
`try2sqlite()`	Convert TRY text file to SQLite database
`var_names_all()`	Get vector of variable names for a particular workflow and run ID
`workflow()`	Get single workflow by workflow_id
`workflows()`	list of workflows that exist

Reference

All functions