Package index • rivRmon

Generating surfer plots

Functions for creating physical and chemical surfer style profile plots for the Swan and Canning rivers

canning_surfR(): Reads in external data, combines with internal datasets and produces Canning River surfer plots

swan_surfR(): Reads in external data, combines with internal datasets and produces Swan River surfer plots

plot_metric(): Reads in external sonde data, combines with internal data sets and produces a single surfer plot of a user defined metric.

Annual report data compilation and cleaning

Functions for reading in original WIN downloads and creating data for annual reporting

canning_WIN_report_data(): Function to read and format water quality data obtained from the WIR water portal for use in annual reporting for the Canning River

swan_WIN_report_data(): Function to read and format water quality data obtained from the WIR water portal for use in annual reporting for the Swan River

Annual report plot and table generation

Convenience functions that produce all plots and tables for a specific river for the annual report

canning_reportR(): Function to create all of the plots and tables for the annual Canning River report.

swan_reportR(): Function to create all of the plots and tables for the annual Swan River report.

Plots and tables for specific groupings of metrics - Canning river

Functions for creating plots and tables for the annual report for specific groupings of metrics that share common display parameters

ann_rep_chla_c(): Function for annual Canning River report plots and tables for chlorophyl a.

ann_rep_doc_c(): Function for annual Canning River report plots and tables for dissolved organic carbon.

ann_rep_grp1_c(): Function for annual Canning River report plots and tables for group 1 metrics.

ann_rep_grp3_c(): Function for annual Canning River report plots and tables for group 3 metrics

ann_rep_secchi_c(): Function for annual Canning River report plots and tables for secchi depth.

ann_rep_si_c(): Function for annual Canning River report plots and tables for silica.

Plots and tables for specific groupings of metrics - Swan river

Functions for creating plots and tables for the annual report for specific groupings of metrics that share common display parameters

ann_rep_chla_s(): Function for annual Swan River report plots and tables for chlorophyl a.

ann_rep_grp1_s(): Function for annual Swan River report plots and tables for group 1 metrics

ann_rep_grp2_s(): Function for annual Swan River report plots and tables for group 2 metrics

ann_rep_grp3_s(): Function for annual Swan River report plots and tables for group 3 metrics

ann_rep_secchi_s(): Function for annual Swan River report plots and tables for secchi depth.

Functions to visualise phytoplankton summaries

Functions that create summaries and plot phytoplankton barcharts by site

phyto_groupR(): Creates summary phytoplankton data for plotting

phyto_plotR(): Creates barcharts from phytoplankton summary data

Internal helper functions

Internal helper functions with various outcomes

data_finder(): Finds filepath to specific river data

dynamic_ylim(): Helper function to calculate sensible y axis limits from the data

get_legend(): Helper function for extracting legend from a plot

just_nums(): Creates correct suffix for day of month

phyto_finder(): Creates file paths to raw phytoplankton xlsx spreadsheets

sonde_reader(): Reads in sonde data from various model formats and creates tidy data

sonde_reader_metric(): Reads in sonde data and formats specifically for use for plotting single metrics

surfer_cols(): Creates correct colour palette for measured metric

Oxy KPI

Functions to aid in generating and visualising dissolved oxygen KPI’s.

oxy_wranglR(): Reads in curated Oxy KPI sonde data and exports cummulative Oxy KPI plots and stats for the purpose of weekly updates.

HAB Tables

Functions to produce conditionally formatted pptx files for HAB reporting

hab_groupR(): Creates summary HAB data for conditionally formatted table export

hab_tablR(): Creates conditionally formatted table as a pptx file from summary HAB data

mngt_response_triggers: Management Response Triggers

LIMs Data

Functions to parse and summarise weekly LIMs data

lims_parsR(): Creates summary LIMs data for interim reporting

Under development

Functions in development stage for future work incorporating CKAN and BIOSYS.

CKAN_canning_surfR(): CKAN version. Reads in external data, combines with internal datasets and produces Canning River surfer plots

CKAN_swan_surfR(): CKAN version. Reads in external data, combines with internal datasets and produces Swan River surfer plots