Man pages for USGS-R/mda.streams
Data Preparation, Access, and Analysis Functions for the Powell Center Continental Stream Metabolism Project
| archive_ts | Archive a timeseries file |
| build_calc_ts_needs | Build and return the table calc_ts_needs |
| build_sysdata | For use in package development only: build R/sysdata.rda |
| calc_mfootdaily_calc3vK | Internal - calculate the metabolic footprint for each day |
| calc_ts_depth_calcDischHarvey | Internal - calculate depth_calcDisch from discharge and... |
| calc_ts_depth_calcDischRaymond | Internal - calculate depth_calcDisch from any data using the... |
| calc_ts_doinit_calcDStart | Internal - calculate doinit_calcDStart from any data |
| calc_ts_dopsat_calcObsSat | Internal - calculate dopsat_calcObsSat from any data |
| calc_ts_dosat_calcGG | Internal - calculate dosat_calcGG from any data |
| calc_ts_par_calcLat | Internal - calculate par_calcLat from any data |
| calc_ts_par_calcLatSw | Internal - calculate par by merging modeled (calcLat) and... |
| calc_ts_par_calcSw | Internal - calculate par from SW data |
| calc_ts_simCopy | Internal - calculate any variable with simNew from any data |
| calc_ts_simNew | Internal - calculate any variable with simNew from any data |
| calc_ts_sitedate_calcLon | Internal - calculate sitedate_calcLon from any data |
| calc_ts_sitetime_calcLon | Internal - calculate sitetime_calcLon from any data |
| calc_ts_suntime_calcLon | Internal - calculate suntime_calcLon from any data |
| calc_ts_veloc_calcDischHarvey | Internal - calculate velocity from discharge and... |
| calc_ts_veloc_calcDischRaymond | Internal - calculate depth_calcDisch from any data using the... |
| calc_ts_with_input_check | Helper to stage_calc_ts for simXxx-style functions |
| choose_data_source | Select the specific data source to use for a given variable... |
| cluster_bundle_packages | Build a zip file of bundled packages |
| combine_dplyr | A function to combine unitted data.frames/tbl_dfs |
| combine_tables | Combine several tables into a single table |
| combine_ts | Combine ts/const variables into a single data.frame |
| condense_by_ply | Condense function called by mm_model_by_ply |
| condense_by_stat | Condense a data.frame to daily resolution |
| config_preds_to_data_column | Get predictions of metabolism or DO from a model |
| config_to_data | Convert config specifications into a data input table |
| config_to_data_column | Read a single column worth of data |
| config_to_metab | Actually run the model as specified by the configuration... |
| config_to_metab_clusterfun | Create a function to pass to cluster nodes |
| config_to_metab_repeat | Acquire data and fit a model repeatedly |
| define_pkg_env | Define a package environment for storing data specific to a... |
| delete_item | Delete a ScienceBase item |
| delete_meta | Delete a metadata item-file combination |
| delete_metab_model | Delete a metab_model item from SB |
| delete_metab_run | Delete a metab_run item from SB |
| delete_sb_file | Delete a single file from a ScienceBase item |
| delete_site | Delete a site and all its files. |
| delete_ts | Delete a time series item and its data |
| download_item_files | Download file[s] to local destination |
| download_meta | Download metadata data to local file destination |
| download_metab_model | Download metabolism model .RData to local file |
| download_metab_run | Download metabolism run data data to local file destination |
| download_ts | Download timeseries data to local file destination |
| format_item | Format an item as a ScienceBase ID or URL, as requested |
| get_config | Download and read a config file from a metab run on SB |
| get_meta | Get metadata (site data) from ScienceBase |
| get_metab_data | Get a data.frame of metabolism input data |
| get_metab_model | Load one or more metab_model objects into R |
| get_metab_prep | Get a data.frame of metabolism input data |
| get_scheme | Get the scheme name for this project |
| get_site_coords | Pull the latitude and longitude of a site from ScienceBase |
| get_sites | A helper to list_sites. Gets site IDS from sciencebase w/... |
| get_ts | Bring one or more timeseries into R and merge them |
| get_var_src_codes | Retrieve the var and src codes for mda.streams |
| get_watershed_WFS | get WFS from site |
| get_watershed_WMS | get WMS from site |
| list_datasets | Get a vector of timeseries dataset names |
| list_metab_models | List the available metab_model objects |
| list_metab_run_files | List the files stored in a metabolism runs |
| list_metab_runs | List the available metabolism runs |
| list_metas | List the available metadata tables |
| list_sites | Get a list of the sites on ScienceBase |
| list_tses | List the timeseries data available for a particular site |
| load_google_sheet | Read in data from a Google Spreadsheet |
| locate_folder | Find a high-level folder on ScienceBase |
| locate_item | Find a folder or other item on ScienceBase |
| locate_meta | Find a metadata object on ScienceBase |
| locate_metab_model | Find a metab_model item on ScienceBase |
| locate_metab_run | Find a metab_run item on ScienceBase |
| locate_site | Find a site folder on ScienceBase |
| locate_ts | Find a timeseries item on ScienceBase |
| locate_ts_meta | Find a timeseries metadata object on ScienceBase |
| login_sb | Log into ScienceBase with your myUSGS credentials |
| make_metab_config | Make a metabolism config file |
| make_metab_model_name | Produce a name unique to a single metab_model |
| make_metab_model_path | Combine the model_name and folder into a file path for a... |
| make_metab_run_title | Combine the date, tag, and strategy of a model_run into a... |
| make_meta_path | Create a standardized file name for specific file contents |
| make_site_name | Translate a site name from database and site number to a... |
| make_ts_archive_path | Create an archive file name for a file on ScienceBase |
| make_ts_name | Translate a timeseries name from mda.streams to ScienceBase |
| make_ts_path | Create a standardized file name for specific file contents |
| make_var_src | Translate a variable and data source into a var_src |
| mda.streams | Functions for managing the Continental Stream Metabolism data... |
| modernize_metab_model | Update a metabolism model from SB to meet current formatting... |
| onAttach | Check whether this package is up to date |
| parse_metab_model_name | Parse a metab_model name |
| parse_metab_model_path | Parse a file path into metab_model information |
| parse_metab_run_title | Parse the title of a metab_model run |
| parse_meta_path | Split a metadata file path into contents |
| parse_site_name | Split site name into siteID (used for NWIS site numbers) |
| parse_ts_archive_name | Split archived file path into its contents |
| parse_ts_name | Translate a timeseries name from ScienceBase to mda.streams |
| parse_ts_path | Split file path into contents |
| parse_var_src | Translate a var_src into a variable and a source |
| post_indy_site | Create a indy site and post a list of timeseries files to it |
| post_meta | Post new metadata file[s] to SB |
| post_metab_model | Post individual metab_model object[s] to SB |
| post_metab_run | Post files to a model run item on SB |
| post_site | Create new site in SB |
| post_styx_site | Create a styx site and post a list of timeseries files to it |
| post_ts | Post a new timeseries file to SB |
| post_watershed | Post a new watershed shape to a site on SB |
| read_config | Read a config file |
| read_meta | Read metadata file for mda.streams into data.frame |
| read_ts | Read timeseries data into a data.frame |
| repair_meta | Repair a meta item that is missing its identifier tags |
| repair_metab_model | Repair a metab_model item that is missing its identifier tags |
| repair_metab_run | Repair a metab_run item that is missing its identifier tags |
| repair_ts | Repair a ts item that is missing its identifier tags |
| sb_renew_login | If needed, renew SB login |
| sb_require_login | Throw error or warning if SB login is inactive |
| search_dataframe | Search within a data.frame for text matches to the... |
| search_metab_models | Search the metab_models |
| search_metab_runs | Search the metab_runs |
| search_sites | Search the sites |
| search_var_src_codes | Search the var_src_codes |
| set_scheme | Set the scheme name of the project |
| stage_calc_ts | stage calculated or modeled data into a time series file |
| stage_indy_site | Generate a list of files to post as a custom ('indy') site |
| stage_ldas_ts | Stage NASA NLDAS or GLDAS data into a time series file |
| stage_meta_basic | Create/modify sites file |
| stage_meta_basic_indy | Get data for Indy (custom/independently collected data) sites |
| stage_meta_basic_nwis | Get data for NWIS sites |
| stage_meta_basic_styx | Get data for Styx (simulated data) sites |
| stage_metab_config | Write a metabolism modeling configuration file |
| stage_metab_model | Stage metabolism model outputs into individual metab_model... |
| stage_metab_ts | Stage metabolism model outputs into ts files |
| stage_meta_dvqcoefs | Create/modify file of depth v discharge scaling relationships |
| stage_meta_indy | Create/modify the meta_indy file |
| stage_meta_manual | Create/modify file of manually-determined site information |
| stage_meta_metabinput | Create/modify the meta_metabinput file |
| stage_meta_nawqahst | Acquire data from the Accumulated and Reach Catchment Land... |
| stage_meta_struct | Create/modify file of interferences within the metabolic... |
| stage_meta_styx | Create/modify the meta_styx file |
| stage_nwis_sitelist | generate nwis site_ids for given p_codes |
| stage_nwis_ts | stage nwis data into a file |
| stage_styx_site | Generate a list of files to post as a styx site |
| summarize_metab_inputs | Summarize a timeseries |
| summarize_metab_model | Summarize a single metabolism model |
| summarize_ts | Summarize a timeseries |
| summarize_ts_files | Get a table of information on ts files for the specified... |
| try_calc_ts | Attempt to stage and post a calc_ts for all available sites |
| ts_has_file | Seek specific file types within a ts sbitem |
| verify_config | Verify that a config file row has the requisite info |
| verify_ts | verify timeseries data.frame format and contents |
| verify_var_src | Check whether a var_src is listed in get_var_src_codes() |
| view_file | Open a file |
| view_folder | Open a folder or a file's folder |
| view_google_map | Get, and by default browse to, a URL to the site location on... |
| warning_table | Describe data changes that will occur on combining multiple... |
| write_config | Write a config file |
| write_ts | Write timeseries data into a compressed file |
