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

check_missing_files(): Check for Missing or Empty Files in Conversion Results

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(): Queries data from the trait database and transforms statistics 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_machine_host(): Helper Function to retrieve machine host and machine informations

get_machine_info(): Get machine information from db

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(): Function to query data from database for specific species and convert stat to SE

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(): Function to query yields data from database for specific species and convert stat to SE

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

update_ensemble_writes(): Insert or Update Database Records for New or Modified Input Data

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