Confidence Estimation of Environmental State Classifications

Description

This package can be used to estimate the confidence of state classifications (e.g., with the classification ‘bad’, ‘moderate’, ‘good’) produced using environmental indicators and associated targets. The implementation closely follows Baggelaar et al. (2010) where the confidence intervals for the estimated multiyear averages are derived by assuming a Student's t distribution for the errors. For more information about the package see the package-vignette (type: vignette("confidence") at the R-prompt to view the vignette.).

Author(s)

Willem M.G.M. van Loon and Dennis J.J. Walvoort

References

Baggelaar, P., O. van Tongeren, R. Knoben, and W. van Loon, 2010. Rapporteren van de betrouwbaarheid van KRW-beoordelingen (in Dutch, English translation: Reporting the confidence of WFD-assessments). H2O 16: 21–25

See Also

conf and the package vignette mentioned above.

Annual Average 1,2-dichloroethane Concentration

Description

Annual arithmetic average concentration of 1,2-dichloroethane (DCA) in a specific water body (\mu g/l), based on Baggelaar et al., (2010)

Details

The columns represent the following information:

OBJECTID

water body code

PAR

parameter, in this case 1,2-dichloroethane

color

colors in density function

DATE

year

VALUE

annual arithmetic average concentration

TARGET

target according to the European Water Framework Directive

UNIT

measurement unit (\mu g/l)

Source

Baggelaar, P., O. van Tongeren, R. Knoben, & W. van Loon, 2010. Rapporteren van de betrouwbaarheid van KRW-beoordelingen. H2O 16, p.21–25

Annual Average Environmental Quality Ratio for Macrofauna.

Description

Annual artithmetic average environmental quality ratio's (EQR) for Macrofauna in a specific water body, based on Baggelaar et al., (2010)

Details

The columns represent the following information:

OBJECTID

water body code

PAR

parameter, in this case EQR

color

colors in density function

DATE

year

VALUE

annual arithmetic average EQR

TARGET

target EQR

transfrom

applied transform

Source

Baggelaar, P., O. van Tongeren, R. Knoben, & W. van Loon, 2010. Rapporteren van de betrouwbaarheid van KRW-beoordelingen. H2O 16, p.21–25

Back-transformations Performs inverse log or logit transformations.

Description

Back-transformations

Performs inverse log or logit transformations.

Usage

backtransform(x, type = c("identity", "log", "logit", "none", NA_character_))

Arguments

Value

backtransformed value

Perform Confidence Run

Description

This function starts the 'confidence tool'. The results will be stored in a subdirectory in the current working directory. See details section below.

Usage

conf(x = NULL, tmpdir = tempfile(pattern = "confidence"), browse = TRUE)

Arguments

Details

This function will create a subdirectory

• in the same directory as x, in case x is a filename or

• in the current working directory (see getwd), in case x is a data.frame.

The computer should have write permission to this directory, if not an error message will be raised. The subdirectory contains an HTML-report with all analysis results. For convenience, the results are also stored in CSV-format (tables) and png-format (figures) for further processing.

See Also

confidence and the package vignette (vignette("confidence")).

Check Confidence data

Description

This function checks data.frames to be used by the confidence package. The format has been specified in Van Loon (2014) and should contain the following columns:

• OBJECTID: water body code, e.g., NL89_os;

• PAR: parameter, e.g., Cadmium;

• DATE: date according to ISO 8601 (YYYY-mm-dd) for point values or year YYYY for annual means;

• VALUE: numerical value.

• TARGET: target value for the European Water Framework Directive;

• UNIT: measurement unit of PAR. This unit should be the same for all records with the same PAR and is the same for both VALUE and TARGET;

• transform: data transformation, i.e., log, logit, NA.

Usage

conf_input(x)

Arguments

Details

The function performs the following tasks:

• checks availablitity of required columns (case insensitive);

• make column names case-insensitive;

• removes redundant spaces;

• checks on missing values in required columns;

• checks if DATE-field adheres to ISO 8601 (YYYY-mm-dd) or YYYY;

• checks mixtures of annual averages and point values for a each year;

• checks if measurement units are the same for a specific OBJECTID-PAR-pair;

• checks if TARGET-value is the same for a specific OBJECTID-PAR-pair;

• checks if transform is one of log, logit, NA in transform column;

• checks that the EQR-column contains identical values fo each OBJECTID-PAR combination.

Value

data.frame that has passed all checks

Simulated Metal Contents

Description

A data set with two time-series of simulated metal contents. These data have mainly been used to test the package. Users may find this dataset convenient as an example to construct their own data sets. The columns represent the following information:

OBJECTID

water body code, e.g., NL89_os

PAR

parameter, e.g., Cadmium

color

colors in density function

DATE

date according to ISO 8601 (YYYY-mm-dd) for point values or year YYYY for annual means

VALUE

numerical value

TARGET

e.g., the target value for the European Water Framework Directive

UNIT

measurement unit of PAR. This unit should be the same for all records with the same PAR and is the same for both VALUE and TARGET

transform

data transformation, i.e., log, logit, NA

Multi-Year Average

Description

Estimates the multi-year average of environmental properties and associated confidence intervals.

Usage

mya(x, ...)

Arguments

Value

a data.frame with the following columns:

MYA:

the multi-year arithmetic average;

PROB_LTT:

the probability that MYA is less than the target value specified;

PROB_GTT:

the probability that MYA is greater than the target value specified;

q05:

the lowerbound of the 90% confidence interval of MYA;

q95:

the upperbound of the 90% confidence interval of MYA.

See Also

conf

Sanitize Text to Give Proper Filenames

Description

Sanitize Text to Give Proper Filenames

Usage

sanitize(x)

Arguments

Value

sanitized character vector

Remove Redundant Spaces

Description

This function removes redundant spaces from character vectors

Usage

strip_spaces(x)

Arguments

Value

character vector without trailing or multiple spaces

Examples

stopifnot(confidence:::strip_spaces(" Hello  World  ") == "Hello World")

Transformations Performs log or logit transformations.

Description

Transformations

Performs log or logit transformations.

Usage

transform(x, type = c("identity", "log", "logit", "none", NA_character_))

Arguments

Value

transformed value

Internal Functions For Writing HTML

Description

Internal Functions For Writing HTML

Usage

write_html(x, ...)

Arguments