All functions
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PEcAn.DB
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Database functions for PEcAn, the Predictive Ecosystem Analyzer |
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append.covariate()
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Append covariate data as a column within a table |
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arrhenius.scaling.traits()
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Apply Arrhenius scaling to 25 degC for temperature-dependent traits |
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assign.treatments()
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assign.treatments |
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bety2pecan()
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Convert BETY variable names to MsTMIP and subsequently PEcAn standard names |
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betyConnect()
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Connect to bety using current PEcAn configuration |
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build_insert_query()
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Build query to insert R data frame into SQL table |
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check.lists()
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Compares two lists |
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clone_pft()
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Duplicate existing pft with associated priors, species, and cultivars |
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db.close()
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Close database connection |
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db.exists()
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db.exists |
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db.getShowQueries()
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db.getShowQueries |
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db.open()
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Open database connection |
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db.print.connections()
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Debug leaked connections |
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db.query()
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Query database |
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db.showQueries()
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db.showQueries |
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dbHostInfo()
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Database host information |
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db_merge_into()
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Merge local data frame into SQL table |
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dbfile.check()
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Check for a file in the dbfiles tables |
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dbfile.file() dbfile.id()
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Convert between file paths and ids |
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dbfile.input.check()
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Check for a file in the input/dbfiles tables |
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dbfile.input.insert()
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Insert file into tables |
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dbfile.insert()
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Insert file into tables |
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dbfile.posterior.check()
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Check for a file in the input/dbfiles tables |
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dbfile.posterior.insert()
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Insert file into tables |
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default_hostname()
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default_hostname |
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derive.trait()
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Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait. |
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derive.traits()
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Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait. |
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dplyr.count()
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Count rows of a data frame |
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fancy_scientific()
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Convert number to scientific notation pretty expression |
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fetch.stats2se()
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Fetch data and transform stats to SE |
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filter_sunleaf_traits()
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Function to filter out upper canopy leaves |
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get.id()
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get.id |
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get.trait.data()
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Gets trait data from the database |
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get.trait.data.pft()
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Gets trait data from the database |
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get_run_ids()
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Get vector of run IDs for a given workflow ID |
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get_users()
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Get data frame of users and IDs |
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get_var_names()
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Get vector of variable names for a particular workflow and run ID |
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get_workflow_ids()
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Get vector of workflow IDs |
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insert.format.vars()
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Insert Format and Format-Variable Records |
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insert_table()
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Insert R data frame into SQL database |
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load_data_single_run()
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Load data for a single run of the model |
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match_colnames()
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Match names of local data frame to SQL table |
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match_dbcols()
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Match column names and classes between local and SQL table |
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ncdays2date()
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Convert netcdf number of days to date |
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query.covariates()
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Queries covariates from database for a given vector of trait id's |
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query.data()
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Query data and transform stats to SE by calling fetch.stats2se; |
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query.file.path()
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Get file path given id and machine |
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query.format.vars()
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Given input_id, return formats table and table of variables and units |
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query.pft_cultivars()
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Select cultivars associated with a PFT |
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query.pft_species()
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Query species given pft name |
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query.priors()
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Query Priors |
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query.site()
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Given site_id, return site table |
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query.trait.data()
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Extract trait data from database |
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query.traits()
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Query trait data |
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query.yields()
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Query yield data and transform stats to SE by calling fetch.stats2se; |
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rename_jags_columns()
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renames the variables within output data frame trait.data |
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runs()
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Get table of runs corresponding to a workflow |
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search_reference_single()
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Perform crossref search for a single reference |
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search_references()
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Perform crossref search for a list of references |
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take.samples()
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Sample from normal distribution, given summary stats |
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try2sqlite()
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Convert TRY text file to SQLite database |
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var_names_all()
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Get vector of variable names for a particular workflow and run ID |
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workflow()
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Get single workflow by workflow_id |
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workflows()
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list of workflows that exist |