stat_locs object for active stations in the NERR system.Added keep_qaqcstatus argument to import_local() to retain historical and provisionalplus columns in the output
Added unit testing for most functions
getSunlightTimes() function from suncalc package to estimate metabolic days in metab_day() functionAdded fill argument to plot_summary as option to fill missing values with long term monthly averages or linear interpolation
Added base_size argument for global text size in plot_summary
Fix to annual anomalies in plot_summary as average of monthly sums
Enhancement to qaqc to work if angle brackets not included in qualifier codes
Only required functions from data.table dependency imported
Fix to map_reserve function for updates to ggmap
Added Pacific/Honolulu time zone and 'hee' site code to time_vec function for He'eia reserve
Added colsleft, colsmid, and colsright arguments to plot_summary for separate colors on left, mid, right portions of plot
URL fix to metab_day documentation
Each function is now in its own file instead of grouped by categories (thanks Kim!)
Fix to gas exchange estimate for correct units in ecometab function
Fixing broken URLs in vignette and package documentation
Added collMethd argument to import_local function to specify diel or standard monthly sampling for nutrient samples
Minor fix to swmpr function if trailing white spaces found at end of each qaqc column
Minor fix to help files if searching by concept, e.g., help.search('analyze', package = "SWMPr")
Added informative error message if IP address not registered for using CDMO web services
Added plot_quants function to evaluate trends relative to long-term averages
All numeric columns are forced to numeric atomic vectors on input
Documentation updated to indicate a return value in the calckl function
Fixed bug with comb function if differ argument is incorrect
Added option in qaqc to included additional columns specifying censored values (via cens_id function)
Added plot_wind function for wind roses from weather data
Fixes to decomp_cj function, including grandmean back to output
Added point and line options for overplot
Trailing whitespace in qaqc columns are removed in swmpr argument
Removed dependency to deprecated wq package
Safety stop in import_local if data type not in station code
Removed use of setstep function in ecometab that caused less precise results
Fixed bug with sanity check of depth_val argument in ecometab
Fixed bug with metab_day if original time series was not continuous
Default S3 method added to ecometab
parser now uses xmlTreeParse making CDMO retrieval functions much fasterimport_localqaqc function that treated integer flags the same regardless of signDefault method for smoother was added,
aggremetab can now use moving window smoothing with appropriate changes in plot_metab
timestep argument in setstep. The default value for differ was causing an error.comb that caused error if the input was not a list of objects to combine.comb added so it can be used with non-swmpr objects.setstep added so it can be used with non-swmpr objects.decomp added so it can be used with non-swmpr objects.decomp_cj added so it can be used with non-swmpr objects.overplot function added that allows plotting of multiple variables on the sample plot with different y-axes.qaqc function now uses string matching to keep flags. This is a more flexible approach to keeping desired flags, the previous version used hard coded integers for each flag.plot_summary that returned an error if a cumulative precipitation column was present. This is no longer collected by SWMP but older datasets may have have it included.import_local to handle more flexible text input for the station code. Function doesn't break if the file extension is included and the date is stripped from the station attribute of the imported swmpr object.import_local function can now import files directly from a zipped folder, i.e., it doesn't have to be decompressed first.
SWMPr functions can be searched by concepts - retrieve, organize, analyse, e.g., help.search('retrieve', package = 'SWMPr')
single_param now retreives more than 100 records by using all_params_dtrng internally.all_params now retreives more than 100 records by using all_params_dtrng internally.all_params_dtrng function now retrieves more than 1000 records from the CDMO. In theory, all records for a station can be retrieved but this would take a long time.timestep argument in the setstep function, e.g., "hours". See the help file.