seawaveQ (version 1.0.0)

fitswavecav: Fit seasonal wave and continuous ancillary data for trend analysis

Description

Function to prepare data and fit the seawaveQ model.

Usage

fitswavecav(cdat, cavdat, tanm = "trend1", pnames,
    yrstart = 0, yrend = 0, tndbeg = 0, tndend = 0,
    iwcav = c("none"), dcol = "dates",
    qwcols = c("R", "P"), mclass = 1)

Arguments

cdat

is the concentration data

cavdat

is the continuous (daily) ancillary data

tanm

is a character identifier that names the trend analysis run. It is used to label output files.

pnames

are the parameters (water-quality constituents) to analyze (omit the the starting character, for example for sulfate data indicated by P00945, enter "00945").

yrstart

is the starting year of the analysis (treated as January 1 of that year). Zero means the start date will be determined by the start date of cavdat, the continuous ancillary data.

yrend

is the ending year of the analysis (treated as December 31 of that year). Zero means the end date will be determined by the end date of cavdat, the continuous ancillary data.

tndbeg

is the beginning (in whole or decimal years) of the trend period. Zero means the begin date will be the beginning of the concentration data, cdat.

tndend

is the end of the trend (treated as December 31 of that year). Zero means the end date will be the end of the concentration data, cdat.

iwcav

is a character vector indicating which continuous ancillary variables to include, if none are used for analysis, use iwcav=c("none").

dcol

is the column name for the dates, should be the same for both cdat and cavdat

qwcols

is a character vector with the beginning of the column headers for remarks code (default is R), and beginning of column headers for concentration data (default is P for parameter).

mclass

has not been implemented yet but will provide additional model options.

Value

• a pdf file containing plots of the data and modeled concentration, a text file containing a summary of the survival regression call for each model selected, and a list. The first element of the list is a data frame described under format. The second element of the list is the summary of the survival regression call. The third element is the observed concentration data (censored and uncensored). The fourth element is the concentration data predicted by the model. The fifth element provides summary statistics for the predicted concentrations.

format

The data frame returned has one row for each parameter analyzed and the number of columns depend on the number of continuous ancillary variables used. The general format is as follows: lll{ pname character Parameter analyzed mclass numeric Currently a value of 1 jmod numeric The choice of pulse input function, an integer 1--14. hlife numeric the model half-life in months, an integer, 1 to 4 months cmaxt numeric the decimal season of maximum concentration scl numeric the scale factor from the survreg.object loglik numeric the log-likelihood for the model cint numeric coefficient for model intercept cwave numeric coefficient for the seasonal wave ctnd numeric coefficient for the trend component of model c[alphanumeric] numeric 0 or more coefficients for the continuous ancillary variables seint numeric standard error for the intercept sewave numeric standard error for the seasonal wave setnd numeric standard error for the trend se[alphanumeric] numeric 0 or more standard errors for the continuous ancillary variables pvaltnd numeric the p-value for the trend line }

Details

Fits the seawaveQ model (Vecchia and others, 2008) using a seasonal wave and continuous ancillary variables (streamflow anomalies and other continuous variables such as conductivity or sediment) to model water quality.

References

Ryberg, K.R., Vecchia, A.V., Martin, J.D., and Gilliom, R.J., 2010, Trends in pesticide concentrations in urban streams in the United States, 1992--2008: U.S. Geological Survey Scientific Investigations Report 2010-5139, 101 p. (Also available at http://pubs.usgs.gov/sir/2010/5139/.)

U.S. Geological Survey, 2013a, National Water Information System: Web Interface, accessed Febaruary 26, 2013, at http://waterdata.usgs.gov.

U.S. Geological Survey, 2013b, Parameter code definition: National Water Information System: Web Interface, accessed Febaruary 26, 2013, at http://nwis.waterdata.usgs.gov/usa/nwis/pmcodes.

Vecchia, A.V., Martin, J.D., and Gilliiom, R.J., 2008, Modeling variability and trends in pesticide concentrations in streams: Journal of the American Water Resources Association, v. 44, no. 5, p. 1308-1324, http://dx.doi.org/10.1111/j.1752-1688.2008.00225.x.

See Also

The functions that fitswavecav calls internally: prepData and fitMod.

Examples

data(swData)
modMoRivOmaha<-combineData(qwdat=qwMoRivOmaha, cqwdat=cqwMoRivOmaha)
myfit1 <- fitswavecav(cdat=modMoRivOmaha, cavdat=cqwMoRivOmaha,
tanm="myfit1", pnames=c("04035", "04037", "04041"), yrstart=1995,
yrend=2003, tndbeg=1995, tndend=2003, iwcav=c("flowa30","flowa1"),
dcol="dates", qwcols=c("R","P"))
 myfit2 <- fitswavecav(cdat=modMoRivOmaha, cavdat=cqwMoRivOmaha,
tanm="myfit2", pnames=c("04035", "04037", "04041"), yrstart=1995,
yrend=2003, tndbeg=1995, tndend=2003, iwcav=c("seda30","seda1"),
dcol="dates", qwcols=c("R","P"))
myfit3 <- fitswavecav(cdat=modMoRivOmaha, cavdat=cqwMoRivOmaha,
tanm="myfit3", pnames=c("04035", "04037", "04041"), yrstart=1995,
yrend=2003, tndbeg=1995, tndend=2003, iwcav=c("flowa30","flowa1",
"seda30", "seda1"), dcol="dates", qwcols=c("R","P"))
# trend model results
myfit1[[1]]
# example regression call
myfit1[[2]][[1]]
# first few lines of observed concentrations
head(myfit1[[3]])
# first few lines of predicted concentrations
head(myfit1[[4]])
# summary statistics for predicted concentrations
head(myfit1[[5]])