Overview

This package is designed to:

1. Process either user data or existing gage data through the online functional flows calculator (documentation).
2. Transform that data and generate functional flow metrics, predicted percentiles, alteration assessments, as well as return plots of the Dimensionless Reference Hydrograph (DRH) and boxplots showing the observed versus predicted percentile values for each metric.
3. Provide functions that follow the CEFF Steps: see Step One, Step Two, and Step Three below.
4. In addition, there are shortcut functions that provide direct access to useful intermediate products, such as the functional flow metric results or alteration assessment data as R dataframes.

It is meant to be used with either a gage ID, or with a timeseries dataframe with a column of flow values and a column of date values and a user-supplied COMID value for the stream segment or latitude and longitude. See Setup and Examples in our getting started guide for more.

Articles

This documentation site has links to function and class documentation at the top under the Reference section and then tutorials and narrative examples in the Articles section. If you’re just getting started, you may be interested in the following:

1. Getting Started Guide
2. Following CEFF Steps
3. Batch Processing of Data

Full Documentation

There are many examples below, including instructions on how to set up and use the core parts of the package. Check the documentation for the classes and functions in this site and especially in the “articles” provided at the top. We also publish a PDF version of this manual.

Known Issues

• In some cases, the package fails to install using devtools. Upgrade your copy of devtools and the installation should proceed without error.
• When providing a timeseries, if the date field is of type date rather than dates as formatted text, the filtering code will trigger an error. In the future, we will enable it to process these values correctly, but the workaround is to do any filtering on data gaps yourself and disable filtering by setting ffc$timeseries_enable_filtering <- TRUE on your FFCProcessor object.

Change Log

Version 0.9.8.3

• [Bugfix] get_predicted_flow_metrics() no longer returns observed metrics, specifically returns only modeled or inferred.

Version 0.9.8.2

• [Bugfix] Log messages weren’t going to the screen when running CEFF steps with an output folder. They once again go to both the screen and the output file. We now have a known issue where when it prints the FFC percentiles to the console, they don’t come out appropriately (due to our logging method) - use the output CSV instead in the meantime.

Version 0.9.8.1

• [Bugfix] Internal stream class data occasionally had multiple records, which would cause bad parameters to be sent to the FFC and a failure in the package. Now checks if there’s more than one stream class record and uses the first one.

Version 0.9.8.0

• [Enhancement] The package now checks to make sure it received a valid COMID from web services, which helps when the web service is down. It prints a warning if the lookup failed.
• [Enhancement] The package now checks to make sure it obtained at least 24 predicted metric records. If it didn’t but received some, then it prints a warning. If it received no records, it prints an error about the COMID
• [Enhancement] Added a new $get_comid_online (default TRUE) flag to FFCProcessor objects. The web service that we use to look up COMIDs for gages has been spotty recently, and we returned the option to do a lookup locally with spatial data. It will still download a large amount of spatial data for NHD segments the first time it runs with the flag set to FALSE, but then future lookups will be much faster. It uses the nhdR package, which is not included as a package requirement, and instead is installed only if you set ffc$get_comid_online = FALSE.

Version 0.9.7.5

• [Update] Included updated data for peak flow metric predictions into package data. To support this, we are temporarily changing the FFCProcessor object to use offline metrics instead of data from the TNC API. If you wish to use the API again, set ffc$predicted_percentiles_online <- TRUE. We will revert it to using online data in the future once the API is updated

Version 0.9.7.4

• [Enhancement] New code that fills NA values in the 10th percentile column of predicted metrics from the TNC API if the 25th percentile column is 0. A warning will be raised if NA values are found in the 10th percentile column. Can be turned off by setting ffc$predicted_percentiles_fill_na_p10 to FALSE.

Version 0.9.7.3

• [Bugfix] Previously, providing a timeseries with a date field that was not named “date” (case sensitive) would fail when building the data frame to send to the FFC. This has been fixed, and any date field name should be usable, so long as it is provided as a parameter, or set on the ffc object before running ffc$set_up.

Version 0.9.7.2

• [Update] Fixes for new versions of the eflows API launched recently. Everyone using this package will need to upgrade to this version or newer to keep using the package.

Version 0.9.7.1

• Added function clean_account to remove all current runs from the online FFC. Helps with broken accounts after recent FFC update. To use, just call clean_account(token) after setting your token value into the variable named token

Version 0.9.7.0

• [Change] Data sent to the FFC is now filtered according to CEFF Tech Team determined rules - water years are dropped if they have more than 7 missing days or more than 2 consecutive missing days (by default). See the documentation for the function filter_timeseries for more info. It applies to both automatically retrieved gage data and user-provided timeseries. It can be disabled by setting timeseries_enable_filtering to FALSe on the FFCProcessor object, but you’re much better off just disabling it by filling gaps in your data yourself if you need to keep all water years.
• [Enhancement] ffcAPIClient now logs both to the console and to a log file in the output folder, including the version of the package and any log messages (some R warnings and errors may not show up in the file yet)
• [Change] The package now stops running if you have fewer than 10 years of data after the filters implemented in this version have run. It warns you, but still runs if you have fewer than 15 years of data. These apply whether the data source is gage data or a provided timeseries. To change this behavior, change the values of fail_years_data and warn_years_data on the FFCProcessor object
• [Enhancement] You can now pass minimum and maximum dates for gage data retrieval. Set the values of gage_start_date and gage_end_date on the FFCProcessor object.

Version 0.9.6.9

• [Bugfix] Fixed issue preventing export of R6 Classes - FFCProcessor and USGSGage should now be available for use as the documentation describes

Version 0.9.6.8

• [Enhancement] Code available for three steps of CEFF process - working on documentation for it still

Version 0.9.6.7

• [Bugfix] Adjusted to change in FFM API from flows.codefornature.org
• [Enhancement] Code available to support first step of CEFF process

Version 0.9.6.6

• [Enhancement] New function force_consistent_naming sets option to convert peak magnitude metrics to use same name format as other magnitude metrics. Peak_2 becomes Peak_Mag_2, etc. Defaults to off to remain aligned with CEFF, but if you need metric names to follow a pattern, that will help. See documentation for usage.
• [Change] Predicted flow metrics now use a character instead of a factor in the metric column.

Version 0.9.6.5

• [Enhancement] ffc_results dataframe now filters out non-metrics (things starting with __ or ending with _Julian)

Version 0.9.6.4

• [Bugfix] Handled a condition where the predicted flow metric API returns duplicate values for some metrics

Version 0.9.6.3

• [Bugfix] Fixed an error where predicted Spring Duration metrics came through as SP_Du

Version 0.9.6.2

• [Bugfix] Fixed error preventing evaluate_alteration from running with warnings about date_format_string.

Version 0.9.6.1

• [Enhancement] Updated plotting to facet each metric with a free Y axis so that all boxplots can be clearly seen. Other minor enhancements to plotting, like titles and X axis labels as well.

Version 0.9.6.0

• [Enhancement] evaluate_alteration family of functions now also returns predicted_wyt_percentiles in addition to the predicted_percentiles. The WYT form includes a wyt column that includes the water year type of the prediction
• [Change] Using TNC’s online API to pull predicted flow metrics instead of internal data by default
• [Change] Under the hood, the code behaves differently - most processing is now being handled in the FFCProcessor class, but more will be moved there

Version 0.9.5.8

• [Change] Updated the rules used to determine alteration to match new rules for CEFF Appendix F - specifically, we now always check that >=50% of observations are within the i80r before declaring something unaltered.

Version 0.9.5.7

• [Enhancement] evaluate_alteration now supports parameter to control plotting (similar to evaluate_gage_alteration) and documentation has been added for the function.

Version 0.9.5.6

• [Enhancement] Added the ability to pull predicted metrics from TNC’s predicted metrics API instead of from internal data. To use it, set online=TRUE when calling get_predicted_flow_metrics. It includes one small difference - in the source field, values marked as obs in the offline data show up as inferred.

Version 0.9.5.5

• [Change] No longer look up gage COMIDs by default due to error-prone nature of lookup near stream junctions. Use force_comid_lookup parameter to evaluate_gage_alteration to enable previous lookup behavior.
• [Enhancement] Added an automatic lookup that corrects bad data from comid lookups and returns the correct COMID. Only used for Jones Bar gage right now, but structure is there for if others are found.

Version 0.9.5.4

• [Breaking Change] Where found, column names have been fully lowercased for consistency, including Metric -> metric and COMID -> comid
• [Breaking Change] Parameter com_id to get_predicted_flow_metrics was renamed comid
• [Enhancement] observed percentiles and predictions both include a result_type field, with observed FFC results containing the value “observed” and prediction percentiles fields containing the value “predicted” to allow for merging of the data frames in some contexts
• [Enhancement] evaluate_gage_alteration now attaches a field gage_id to predicted_percentiles, observed_percentiles, and alteration data frames.
• [Enhancement] observed percentiles now include a comid field to allow for merging and accessing the comid in other contexts
• [Enhancement] evaluate_alteration and evaluate_gage_alteration now includes a fifth key alteration with the assessed flow alteration scores in a data frame

Version 0.9.5.3

• [Breaking Change] Results from evaluate_alteration and evaluate_gage_alteration now use the list key ffc_percentiles instead of simply percentiles to be clear that the percentiles are from the observed FFC results.
• [Change] Changed quantile processing type to the default of type 7 so that observed FFC data are processed into percentiles the same way that the predicted flow metrics were calculated to minimize resulting error.
• [Enhancement] evaluate_alteration and evaluate_gage_alteration now includes a fourth key predicted_percentiles with the predicted flow metric percentile values so they don’t need to be looked up separately.

Version 0.9.5.2

• [Enhancement] Added annual parameter to assess_alteration that runs a year over year analysis.

Version 0.9.5.1

• [Enhancement] New parameter plot (boolean) to evaluate_gage_alteration controls whether the function produces plots or not

Version 0.9.5

• [Enhancement] New assess_alteration function returns a data frame with alteration results - documentation forthcoming.
• [Change] Warning when can’t determine stream segment’s hydrogeomorphic type has been downgraded to a print statement.

Version 0.9.4.2

• [Breaking Change] The client now detects and sends the appropriate parameters to the FFC online for the stream class that it detects based on the COMID. If you are using low-level functions such as get_ffc_results_for_df, then you must provide an argument comid - check the documentation for which functions need it. Further,process-data now requires that the stream parameters be provided to it. I recommend moving to something like get_ffc_results_for_df as process_data may soon be moved to be internal only.

Version 0.9.4.1

• [Enhancement] New code to support sending the correct stream class parameters to the FFC - includes the ability to identify stream classes by COMID, but not yet send the parameters
• [Change] Data loading code made more generic, and potentially faster - multiple calls to get predicted flow metrics should not result in reloading the dataset.

Version 0.9.4

• [Breaking Change] List item $ffc_results_df returned from evaluate_alteration functions changed to $ffc_results for consistency with FFCProcessor object and allowing for more flexibility in the future.
• [Enhancement] Basic alteration assessment capabilities included. Require more testing before use
• [Documentation] Reworking documentation to make best workflows clearer

Version 0.9.3

• [Enhancement] Can now provide a time format string to evaluate_alteration - it will use that to read the values in the time field and reformat them to send to the FFC as needed.
• [Bugfix] FFC results no longer fail to transform if one flow metric is entirely NULL