NEWS.md

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

0.10.0

• by default, login_sb now attempts to access a 'stream_metab' secret in a default vault using the secret package. The GitHub version of secret is recommended

0.9.24

• update stage_meta_basic to include new NHDPlusV2 COMIDs from Ted and the Network Linked Data Index (NLDI)

0.9.20

• accommodate NAs in parse_metab_model_path, _name, and _title

0.9.15

• added par_calcLatSw to build_calc_ts_needs

0.9.14

• added par_calcLatSw option to stage_calc_ts to compute the merger of modeled and observed light

0.9.12+ to 0.9.13

• config_to_data now converts instantaneous discharge (disch) from cfs, as on ScienceBase, to cms, as required by streamMetabolizer

• list_sites, list_datasets, and list_tses now accept a with_ts_uploaded_after argument

• minor improvements to get_ts, build_calc_ts_needs (again), and stage_calc_ts in support of the ongoing data re-pull in the stream_metab_usa project

0.9.12

• updates throughout to accommodate changes to package dependencies (dplyr and tibble)

• new: login_sb now looks for username and password in a stream_metab profile file if that file exists (outside the project directory)

• stage_calc_ts now tracks and reports on input data provenance for truly calculated (src == calc[XYZ]) variables

• minor improvements to build_calc_ts_needs, get_site_coords, summarize_ts_files, stage_nwis_ts, stage_ldas_ts, stage_nwis_sitelist in support of the ongoing data re-pull in the stream_metab_usa project

• new: cluster_bundle_packages builds a zip file of bundled package and dependency sources for use in cluster computing

0.9.7

• new: make_metab_config is like stage_metab_config but more suited to interactive use (less typing required)

• new: get_metab_prep is a shortcut to config_to_data(stage_metab_config()), with less typing required

• new: get_metab_data is a shortcut to get_metab_prep(out='data', simplify_out=TRUE)

• faster: choose_data_source takes shortcuts in locating a metabolism model when possible

0.9.6.3

• locate_ts and locate_site are now much more efficient in special cases of looking up many items at a time

• view_google_map can now open several tabs at a time

• summarize_metab_model works with the newest streamMetabolizer models

• parse_ts_path now accommodates archived ts files even when rownames are requested

• re-modernized modernize_metab_model

• smarter default filename for get_config

0.9.6.2

• include CI bounds in metab estBest timeseries files

0.9.6.1

• date column name update in modernize_metab_model

• now looks to ScienceBase for the table of var_src codes, units, etc.

• minor documentation updates

0.9.6

• new: try_calc_ts, which combines stage_calc_ts and post_ts in a fault-tolerant loop that only tries the sites that have the prerequisite data and haven't already been posted in the desired time window and format

• new: delete_sb_files, which deletes a single file from a single item (in an optionally vectorized way). permits corrections of mis-postings even in multi-file items such as metab_models and tses

• new: summarize_ts_files, which quickly returns a table of ts files, their upload dates, and other inventory information

• faster: repair_ts, which now runs locate_ts not twice but once whenever possible

• bugfixes and robustness improvements to stage_calc_ts and ts_has_file

0.9.5

• config_to_metab_repeat now works better with Bayesian models and arbitrary model 'strategy' fields

• simulation pipeline (data -> DO simulation model -> metabolism fitting model) is up to date with recent package changes

• updates for querying ScienceBase with sbtools 0.18.0

• more internal functions seek .Rds timeseries data; external functions (get_ts, etc.) still seek .tsv by default for backward compatibility

0.9.4

• moving toward system-wide use of binary (.Rds) timeseries files rather than text (.tsv) - allows greater precision and censoring information in stored data

• now using gO2 and mgO2 for units of oxygen variables

• stage_nldas_ts has been updated in response to changes in how NLDAS data are served

• updates for querying ScienceBase with sbtools 0.16.0

• stage_calc_ts for stage_styx_site are back up to date

0.9.3

• Now automatically checks for available updates when you attach the package

0.9.2

• complex requests to get_ts() are about 7 times faster now if accompanied by update to streamMetabolizer v0.9.3

0.9.1

• read_ts, write_ts, post_ts, and download_ts now support either .tsv or .Rds versions of data (Jordan Read)

• get_ts is now much smarter about requests for multiple timeseries whose temporal resolutions and/or extents are different (e.g., merging daily and 15-minute data) (Lindsay Carr)

0.9.0

Changes

• file downloads are faster and more internally streamlined (0.8.17)

• get_metab_model now posts a modernized model to SB when practical (0.8.16)

• make get_sites private (0.8.15)

0.8.14

Status

This package is not ready for use by many, but it does currently have functions for:

• downloading and preparing (staging) data from outside websites

• posting staged data to ScienceBase as tab-separated (.tsv) tables with data units

• modifying or deleting data on ScienceBase

• synthesizing data for model testing, and posting such data to ScienceBase

• querying and modifying the table of variables and their units, sources, and definitions

• querying, locating, downloading, and merging data from ScienceBase

• finding site information including metadata and maps

• creating metabolism model configuration files

• using metabolism model configuration files to build input datasets from ScienceBase

• running metabolism models based on configuration files - once per row or many times per row - locally or on a cluster

• posting model config files and results to ScienceBase

• retrieving posted models and modernizing to meet current streamMetabolizer formatting standards

• summarizing the availability of input data

• summarizing the quality of fitted models (but some of this logic might move to streamMetabolizer)

USGS-R/mda.streams documentation built on June 3, 2023, 8:43 a.m.