Package index • harsat

Primary functions

These are the functions you’re likely to need for any assessment. For most standard assessments, these will be all you need.

read_data(): Read HARSAT data

tidy_data(): Tidy the data

create_timeseries(): Create a time series

run_assessment(): Assess timeseries for trends and status

update_assessment(): Update timeseries assessments

check_assessment(): Check whether the assessments have converged

write_summary_table(): Write assessment summary to a csv file

plot_assessment(): Graphical summaries of an assessment

report_assessment(): Reports the assessment of individual time series

All functions

add_stations(): Add stations to contaminant data from an ICES extraction

apply_subset(): Apply subsetting to a time series

check_assessment(): Check whether the assessments have converged

check_convergence_lmm(): Checks convergence of an assessment model

convert_reftable(): Add OSPAR_subregion to simplified sediment threshold reference table

convert_units(): Converts units, e.g., from mg/kg to ug/kg

create_timeseries(): Create a time series

cstm.VDS.environment(): Detects the environment from the call

ctsm.VDS.loglik.calc(): ctsm.VDS.loglik.calc

ctsm.VDS.p.calc(): ctsm.VDS.p.calc

ctsm.VDS.varlist: ctsm.VDS.varlist

ctsm.projection(): Calculates a polar projection

ctsm_TBT_convert(): Convert tin concentrations

ctsm_convert_basis(): Basis and matrix information and basis conversion

ctsm_get_determinands(): Get the determinands to be assessed

ctsm_get_info(): Gets data from the standard reference tables

ctsm_uncrt_plot_data(): Generates a relative uncertainty plot

get_AC: Access function map

get_AC_biota_OSPAR(): Gets OSPAR threshold values for biota

get_basis_biota_OSPAR(): Gets the OSPAR biota target basis

get_basis_default(): The default function for generating a basis

get_station_code(): Get station code from station name

get_timeseries(): Extracts timeSeries

harsat harsat-package: harsat: Harmonized Regional Seas Assessment Tool

`$`: TEFs for selected groups of compounds

label_normaliser(): Text representation of normaliser information for plots and reports

label_unit(): Text representation of units for plots and reports

locate_information_file(): Find the path for an information file

make_key(): Make key for annotating assessment plots

normalise_biota_HELCOM(): Normalises biota concentrations, HELCOM vwersion

normalise_sediment_HELCOM(): Normalises sediment concentrations, HELCOM version

normalise_sediment_OSPAR(): Normalises sediment concentrations, OSPAR version

ordinal_theta_cl(): Calculates confidence limits for imposex time series

ordinal_theta_est(): Estimates cut-points in ordinal model (imposex assessments)

parallel_objects(): Identifies functions needed for parallel processing in run_assessment

plot_assessment(): Graphical summaries of an assessment

pretty_unit(): Pretty representation of units for plots and reports

read_ICES_file(): Reads an ICES extraction

read_contaminants(): Reads contaminant data

read_data(): Read HARSAT data

read_stations(): Reads station dictionary

report_assessment(): Reports the assessment of individual time series

report_file_digest(): Generates and logs a file digest

run_assessment(): Assess timeseries for trends and status

run_control_default() experimental: Default control parameters for run_assessment

run_control_modify(): Modifies control parameters for run_assessment

safe_read_file(): Reads an input file, given a particular encoding, and possibly additional hints

subset_assessment(): Subsets an assessment object

tidy_data(): Tidy the data

update_assessment(): Update timeseries assessments

write_summary_table(): Write assessment summary to a csv file