Man pages for USGS-R/mda.streams
Data Preparation, Access, and Analysis Functions for the Powell Center Continental Stream Metabolism Project

archive_tsArchive a timeseries file
build_calc_ts_needsBuild and return the table calc_ts_needs
build_sysdataFor use in package development only: build R/sysdata.rda
calc_mfootdaily_calc3vKInternal - calculate the metabolic footprint for each day
calc_ts_depth_calcDischHarveyInternal - calculate depth_calcDisch from discharge and...
calc_ts_depth_calcDischRaymondInternal - calculate depth_calcDisch from any data using the...
calc_ts_doinit_calcDStartInternal - calculate doinit_calcDStart from any data
calc_ts_dopsat_calcObsSatInternal - calculate dopsat_calcObsSat from any data
calc_ts_dosat_calcGGInternal - calculate dosat_calcGG from any data
calc_ts_par_calcLatInternal - calculate par_calcLat from any data
calc_ts_par_calcLatSwInternal - calculate par by merging modeled (calcLat) and...
calc_ts_par_calcSwInternal - calculate par from SW data
calc_ts_simCopyInternal - calculate any variable with simNew from any data
calc_ts_simNewInternal - calculate any variable with simNew from any data
calc_ts_sitedate_calcLonInternal - calculate sitedate_calcLon from any data
calc_ts_sitetime_calcLonInternal - calculate sitetime_calcLon from any data
calc_ts_suntime_calcLonInternal - calculate suntime_calcLon from any data
calc_ts_veloc_calcDischHarveyInternal - calculate velocity from discharge and...
calc_ts_veloc_calcDischRaymondInternal - calculate depth_calcDisch from any data using the...
calc_ts_with_input_checkHelper to stage_calc_ts for simXxx-style functions
choose_data_sourceSelect the specific data source to use for a given variable...
cluster_bundle_packagesBuild a zip file of bundled packages
combine_dplyrA function to combine unitted data.frames/tbl_dfs
combine_tablesCombine several tables into a single table
combine_tsCombine ts/const variables into a single data.frame
condense_by_plyCondense function called by mm_model_by_ply
condense_by_statCondense a data.frame to daily resolution
config_preds_to_data_columnGet predictions of metabolism or DO from a model
config_to_dataConvert config specifications into a data input table
config_to_data_columnRead a single column worth of data
config_to_metabActually run the model as specified by the configuration...
config_to_metab_clusterfunCreate a function to pass to cluster nodes
config_to_metab_repeatAcquire data and fit a model repeatedly
define_pkg_envDefine a package environment for storing data specific to a...
delete_itemDelete a ScienceBase item
delete_metaDelete a metadata item-file combination
delete_metab_modelDelete a metab_model item from SB
delete_metab_runDelete a metab_run item from SB
delete_sb_fileDelete a single file from a ScienceBase item
delete_siteDelete a site and all its files.
delete_tsDelete a time series item and its data
download_item_filesDownload file[s] to local destination
download_metaDownload metadata data to local file destination
download_metab_modelDownload metabolism model .RData to local file
download_metab_runDownload metabolism run data data to local file destination
download_tsDownload timeseries data to local file destination
format_itemFormat an item as a ScienceBase ID or URL, as requested
get_configDownload and read a config file from a metab run on SB
get_metaGet metadata (site data) from ScienceBase
get_metab_dataGet a data.frame of metabolism input data
get_metab_modelLoad one or more metab_model objects into R
get_metab_prepGet a data.frame of metabolism input data
get_schemeGet the scheme name for this project
get_site_coordsPull the latitude and longitude of a site from ScienceBase
get_sitesA helper to list_sites. Gets site IDS from sciencebase w/...
get_tsBring one or more timeseries into R and merge them
get_var_src_codesRetrieve the var and src codes for mda.streams
get_watershed_WFSget WFS from site
get_watershed_WMSget WMS from site
list_datasetsGet a vector of timeseries dataset names
list_metab_modelsList the available metab_model objects
list_metab_run_filesList the files stored in a metabolism runs
list_metab_runsList the available metabolism runs
list_metasList the available metadata tables
list_sitesGet a list of the sites on ScienceBase
list_tsesList the timeseries data available for a particular site
load_google_sheetRead in data from a Google Spreadsheet
locate_folderFind a high-level folder on ScienceBase
locate_itemFind a folder or other item on ScienceBase
locate_metaFind a metadata object on ScienceBase
locate_metab_modelFind a metab_model item on ScienceBase
locate_metab_runFind a metab_run item on ScienceBase
locate_siteFind a site folder on ScienceBase
locate_tsFind a timeseries item on ScienceBase
locate_ts_metaFind a timeseries metadata object on ScienceBase
login_sbLog into ScienceBase with your myUSGS credentials
make_metab_configMake a metabolism config file
make_metab_model_nameProduce a name unique to a single metab_model
make_metab_model_pathCombine the model_name and folder into a file path for a...
make_metab_run_titleCombine the date, tag, and strategy of a model_run into a...
make_meta_pathCreate a standardized file name for specific file contents
make_site_nameTranslate a site name from database and site number to a...
make_ts_archive_pathCreate an archive file name for a file on ScienceBase
make_ts_nameTranslate a timeseries name from mda.streams to ScienceBase
make_ts_pathCreate a standardized file name for specific file contents
make_var_srcTranslate a variable and data source into a var_src
mda.streamsFunctions for managing the Continental Stream Metabolism data...
modernize_metab_modelUpdate a metabolism model from SB to meet current formatting...
onAttachCheck whether this package is up to date
parse_metab_model_nameParse a metab_model name
parse_metab_model_pathParse a file path into metab_model information
parse_metab_run_titleParse the title of a metab_model run
parse_meta_pathSplit a metadata file path into contents
parse_site_nameSplit site name into siteID (used for NWIS site numbers)
parse_ts_archive_nameSplit archived file path into its contents
parse_ts_nameTranslate a timeseries name from ScienceBase to mda.streams
parse_ts_pathSplit file path into contents
parse_var_srcTranslate a var_src into a variable and a source
post_indy_siteCreate a indy site and post a list of timeseries files to it
post_metaPost new metadata file[s] to SB
post_metab_modelPost individual metab_model object[s] to SB
post_metab_runPost files to a model run item on SB
post_siteCreate new site in SB
post_styx_siteCreate a styx site and post a list of timeseries files to it
post_tsPost a new timeseries file to SB
post_watershedPost a new watershed shape to a site on SB
read_configRead a config file
read_metaRead metadata file for mda.streams into data.frame
read_tsRead timeseries data into a data.frame
repair_metaRepair a meta item that is missing its identifier tags
repair_metab_modelRepair a metab_model item that is missing its identifier tags
repair_metab_runRepair a metab_run item that is missing its identifier tags
repair_tsRepair a ts item that is missing its identifier tags
sb_renew_loginIf needed, renew SB login
sb_require_loginThrow error or warning if SB login is inactive
search_dataframeSearch within a data.frame for text matches to the...
search_metab_modelsSearch the metab_models
search_metab_runsSearch the metab_runs
search_sitesSearch the sites
search_var_src_codesSearch the var_src_codes
set_schemeSet the scheme name of the project
stage_calc_tsstage calculated or modeled data into a time series file
stage_indy_siteGenerate a list of files to post as a custom ('indy') site
stage_ldas_tsStage NASA NLDAS or GLDAS data into a time series file
stage_meta_basicCreate/modify sites file
stage_meta_basic_indyGet data for Indy (custom/independently collected data) sites
stage_meta_basic_nwisGet data for NWIS sites
stage_meta_basic_styxGet data for Styx (simulated data) sites
stage_metab_configWrite a metabolism modeling configuration file
stage_metab_modelStage metabolism model outputs into individual metab_model...
stage_metab_tsStage metabolism model outputs into ts files
stage_meta_dvqcoefsCreate/modify file of depth v discharge scaling relationships
stage_meta_indyCreate/modify the meta_indy file
stage_meta_manualCreate/modify file of manually-determined site information
stage_meta_metabinputCreate/modify the meta_metabinput file
stage_meta_nawqahstAcquire data from the Accumulated and Reach Catchment Land...
stage_meta_structCreate/modify file of interferences within the metabolic...
stage_meta_styxCreate/modify the meta_styx file
stage_nwis_sitelistgenerate nwis site_ids for given p_codes
stage_nwis_tsstage nwis data into a file
stage_styx_siteGenerate a list of files to post as a styx site
summarize_metab_inputsSummarize a timeseries
summarize_metab_modelSummarize a single metabolism model
summarize_tsSummarize a timeseries
summarize_ts_filesGet a table of information on ts files for the specified...
try_calc_tsAttempt to stage and post a calc_ts for all available sites
ts_has_fileSeek specific file types within a ts sbitem
verify_configVerify that a config file row has the requisite info
verify_tsverify timeseries data.frame format and contents
verify_var_srcCheck whether a var_src is listed in get_var_src_codes()
view_fileOpen a file
view_folderOpen a folder or a file's folder
view_google_mapGet, and by default browse to, a URL to the site location on...
warning_tableDescribe data changes that will occur on combining multiple...
write_configWrite a config file
write_tsWrite timeseries data into a compressed file
USGS-R/mda.streams documentation built on May 9, 2019, 8:36 p.m.