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Update for renamed smwr pacakges
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‎.gitignore

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src-i386
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src-x64
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.Rbuildignore

‎DESCRIPTION

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Package: rloadest
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Type: Package
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Title: River Load Estimation
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Version: 0.3.0
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Date: 2014-08-08
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Version: 0.4.0
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Date: 2015-02-27
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Author: Dave Lorenz, Rob Runkel, Laura De Cicco
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Maintainer: Dave Lorenz <[email protected]>
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Description: Collection of functions to make constituent load estimations
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based on the LOADEST program.
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License: File LICENSE
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Depends:
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R (>= 3.0.0),
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USGSwsGraphs,
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USGSwsStats,
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USGSwsQW
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smwrGraphs,
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smwrStats,
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smwrQW
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Imports:
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stats
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Suggests:
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USGSwsBase
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smwrBase,
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dataRetrieval
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LazyLoad: yes
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LazyData: yes

‎NAMESPACE

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# Generated by roxygen2 (4.0.1): do not edit by hand
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# Generated by roxygen2 (4.0.2): do not edit by hand
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S3method(coef,loadReg)
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S3method(fitted,loadReg)
@@ -27,9 +27,9 @@ export(predLoad)
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export(resampleUVdata)
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export(selBestModel)
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export(selBestSubset)
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import(USGSwsGraphs)
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import(USGSwsQW)
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import(USGSwsStats)
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import(smwrGraphs)
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import(smwrQW)
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import(smwrStats)
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importFrom(stats,logLik)
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importFrom(stats,makepredictcall)
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importFrom(stats,step)

‎R/loadReg.R

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@@ -20,10 +20,10 @@
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#'flow column.
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#' @param dates character string indicating the name of the
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#'date column.
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#' @param flow.units character string describing the flow units.
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#' @param flow.units character string describing the flow units. See \bold{Details}.
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#' @param conc.units character string describing the concentration
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#'unit.
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#' @param load.units character string describing the load unit.
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#'unit. See \bold{Details}.
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#' @param load.units character string describing the load unit. See \bold{Details}.
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#' @param time.step character string describing the time step of
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#'the calibration data. Must be one of "instantaneous," "2 hours," "3 hours,"
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#'"4 hours," "6 hours," "12 hours," or "day." The default is "day."
@@ -45,7 +45,7 @@
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#' station="Illinois River at Marseilles, Ill.")
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#'print(app1.lr)
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#'
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#' @import USGSwsQW
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#' @import smwrQW
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#' @export
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loadReg <- function(formula, data, subset, na.action, flow, dates,
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flow.units="cfs", conc.units="", load.units="kg",
@@ -62,6 +62,12 @@ loadReg <- function(formula, data, subset, na.action, flow, dates,
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"8 hours", "12 hours", "day"))
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call <- match.call()
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m <- match.call(expand.dots = FALSE)
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Terms <- attr(m, "terms")
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## Make sure that the formula is a formula and not a symbol--this
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# improves output and subsequent formula references
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if (typeof(call$formula) == "symbol") {
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call$formula <- formula(Terms)
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}
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## remove components not needed for model.frame
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m$flow <- m$dates <- m$flow.units <- m$conc.units <- NULL
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m$load.units <- m$time.step <- m$station <- NULL
@@ -246,6 +252,11 @@ loadReg <- function(formula, data, subset, na.action, flow, dates,
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lfit$xlevels <- xlevels
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class(lfit) <- "censReg"
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## Construct the evaluation data frame
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## Capture errors
256+
if(lfit$IERR > 0L) {
257+
lfit$AIC <- lfit$SPPC <- Inf
258+
lfit$LLR <- -Inf
259+
}
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MEC <- data.frame(model=model.no, AIC=lfit$AIC, SPCC=lfit$SPPC)
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retval <- list(station=station, constituent=ynam,
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flow=flow, dates=dates, Qadj=Qadj,

‎R/plot.loadReg.R

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#'# Produce the full suite of diagnostic plots
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#'plot(app1.lr)
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#'}
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#' @import USGSwsGraphs
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#' @import smwrGraphs
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#' @export
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#' @method plot loadReg
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plot.loadReg <- function(x, which='All', set.up=TRUE, span=1.0, ...) {

‎R/predConc.R

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#'are not permitted in any column in \code{newdata}. Observations with
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#'missing values \code{NAs} must be removed before prediction. Columns that
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#'are not needed for prediction that contain missing values can be removed
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#'before removing all rows with missing values.
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#'before removing all rows with missing values. The maximum number of rows
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#'permitted in \code{newdata} is 176000.
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#' @param by the time frame for estimates. See \code{Details}.
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#' @param allow.incomplete compute loads for periods withing
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#'missing values or incomplete record? See \code{Details}.
@@ -47,6 +48,8 @@ predConc <- function(fit, newdata, by="day",
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## By options and other preliminary code
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if(any(is.na(newdata)))
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stop("newdata contains missing values, remove before prediction")
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if(nrow(newdata) > 176000L)
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stop("newdata has too many rows, the size limit is 176000")
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ByOpt <- c("unit", "day")
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Qadj <- fit$Qadj
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Tadj <- fit$Tadj
@@ -194,7 +197,7 @@ predConc <- function(fit, newdata, by="day",
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## Preserve flow for later
195198
Flow <- newdata[[flow]]
196199
if(time.step == "day") {
197-
KDate <- as.Date(newdata[[dates]])
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KDate <- as.Date(as.POSIXlt(newdata[[dates]]))
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KDays <- seq(nrow(model.inp))
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KinAll <- KDays
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## Exclude NAs and presumably 0 flows
@@ -204,7 +207,7 @@ predConc <- function(fit, newdata, by="day",
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} else {
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Kin <- seq(nrow(model.inp))
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Kin <- Kin[is.finite(rowSums(model.inp))]
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KDate <- as.Date(newdata[[dates]])
210+
KDate <- as.Date(as.POSIXlt(newdata[[dates]]))
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Kdy <- as.integer(KDate)
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KDate <- unique(KDate)
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Kdy <- Kdy - Kdy[1L] + 1L # make relative to first day (Index)

‎R/predLoad.R

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#'the prediction intervals, computed from the SEP.
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#'
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#' @param fit the output from \code{loadReg}.
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#' @param newdata a data frame of the prediction variables. MIssing values
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#' @param newdata a data frame of the prediction variables. Missing values
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#'are not permitted in any column in \code{newdata}. Observations with
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#'missing values \code{NAs} must be removed before prediction. Columns that
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#'are not needed for prediction that contain missing values can be removed
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#'before removing all rows with missing values.
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#'before removing all rows with missing values. The maximum number of rows
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#'permitted in \code{newdata} is 176000.
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#' @param load.units a character string indicating the units of the
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#'predicted loads/fluxes. By default, uses the value specified in
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#'\code{loadReg}. See \code{\link{loadReg}} for a complete list of options.
@@ -64,6 +65,8 @@ predLoad <- function(fit, newdata, load.units=fit$load.units, by="total",
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## By options and other preliminary code
6566
if(any(is.na(newdata)))
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stop("newdata contains missing values, remove before prediction")
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if(nrow(newdata) > 176000L)
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stop("newdata has too many rows, the size limit is 176000")
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ByOpt <- c("unit", "day", "month", "water year", "calendar year", "total")
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load.units
6972
seopt <- match.arg(seopt, c("exact", "approximate"))
@@ -222,7 +225,7 @@ predLoad <- function(fit, newdata, load.units=fit$load.units, by="total",
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## Preserve flow for later
223226
Flow <- newdata[[flow]]
224227
if(time.step == "day") {
225-
KDate <- as.Date(newdata[[dates]])
228+
KDate <- as.Date(as.POSIXlt(newdata[[dates]]))
226229
KDays <- seq(nrow(model.inp))
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KinAll <- KDays
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## Exclude NAs and presumably 0 flows
@@ -232,7 +235,7 @@ predLoad <- function(fit, newdata, load.units=fit$load.units, by="total",
232235
} else {
233236
Kin <- seq(nrow(model.inp))
234237
Kin <- Kin[is.finite(rowSums(model.inp))]
235-
KDate <- as.Date(newdata[[dates]])
238+
KDate <- as.Date(as.POSIXlt(newdata[[dates]]))
236239
Kdy <- as.integer(KDate)
237240
KDate <- unique(KDate)
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Kdy <- Kdy - Kdy[1L] + 1L # make relative to first day (Index)

‎R/print.loadReg.R

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#' @note The printed output includes the call, the coefficent table, the
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#'estimated residual standard error, the log-likelihood of the model and
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#'null model with the attained p-value, and the computational method.
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#' NEED more details about what is printed and the difference in output due to arguments
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#' @seealso \code{\link{loadReg}}
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#' @keywords utilities
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#'
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## Print the results of the input data and model evaluation.
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## to nearly match the output from LOADEST if brief is FALSE
3233
load.only
34+
## Catch errors/warnings
35+
if(x$lfit$IERR == -201L) {
36+
warning("Excessive censoring, greater than 80%")
37+
} else if(x$lfit$IERR == -202L) {
38+
warning("Excessive censoring, fewer than 3 uncensored values for each parameter")
39+
} else if(x$lfit$IERR == 1L) {
40+
stop("Too many parameters")
41+
} else if(x$lfit$IERR == 2L) {
42+
stop("Too many observations")
43+
} else if(x$lfit$IERR == 201L) {
44+
stop("Excessive censoring, greater than 90%")
45+
} else if(x$lfit$IERR == 202L) {
46+
stop("Excessive censoring, fewer than 1.5 uncensored values for each parameter")
47+
} else if(x$lfit$IERR == 203L) {
48+
stop("Variance of uncensored values is 0")
49+
} else if(x$lfit$IERR > 0L) {
50+
stop("\nFatal error in censReg, error code: ", x$IERR, "\n")
51+
}
3352
if(brief)
3453
cat("*** Load Estimation ***\n\n")
3554
else {

‎R/rloadest-package.R

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#' \tabular{ll}{
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#' Package: \tab LOADEST\cr
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#' Type: \tab Package\cr
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#' Version: \tab 0.3.0\cr
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#' Date: \tab 2014-08-08\cr
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#' License: \tab GPL 2\cr
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#' Version: \tab 0.4.0\cr
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#' Date: \tab 2015-02-27\cr
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#' License: \tab File\cr
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#' LazyLoad: \tab yes\cr
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#' }
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#'

‎R/rmse.loadReg.R

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#' flow = "FLOW", dates = "DATES", conc.units="mg/L",
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#' station="Illinois River at Marseilles, Ill.")
2020
#'rmse(app1.lr)
21-
#' @import USGSwsStats
21+
#' @import smwrStats
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#' @export
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#' @method rmse loadReg
2424
rmse.loadReg <- function(x, model=c("load", "concentration"), ...) {

‎R/selBestModel.R

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}
6565
}
6666
options(warn)
67+
## But warn if fewer N than 70
68+
if(model$lfit$NOBSC < 70L)
69+
warning("Selected model may be over fit: only ",
70+
model$lfit$NOBSC, " observations.")
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## Replace model.eval with complete list
6872
retval$model.eval <- model.eval
6973
return(retval)

‎R/selBestSubset.R

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m$dist <- "lognormal"
9292
k <- if(criterion == "AIC") 2 else log(nrow(df))
9393
m <- eval(m)
94-
best <- step(m, scope=min.formula, direction="both", trace=0, k=k)
94+
## Warn if fewer N than 10*potential params
95+
if(m$NOBSC < 10L * (m$NPAR - 1L))
96+
warning("Selected model may be over fit: only ",
97+
m$NOBSC, " observations for ", m$NPAR, " possible parameters.")
98+
best <- step(m, scope=min.formula, direction="both", trace=0, k=k)
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# retain the step wise model selections
96100
model.eval <- best$anova
97101
names(model.eval)[[6L]] <- criterion # Fix this to represent what was really done
98-
# No build the load model
102+
# Now build the load model
99103
m <- call
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m[[1L]] <- as.name("loadReg")
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m$min.formula <- m$criterion <- NULL

‎R/vif.loadReg.R

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#' station="Illinois River at Marseilles, Ill.")
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#'vif(app1.lr, app1.calib)
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#' @keywords regression
18-
#' @import USGSwsStats
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#' @import smwrStats
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#' @export
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#' @method vif loadReg
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vif.loadReg <- function(model, ...) {

‎demo/BatchLoad.r

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# ** End of user input **
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# Set the required libraries
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library(dataRetrieval)
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library(rloadest)
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# Loop for each station
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# Get the flow and water-quality data--use temporary dataset
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# names that can be overwritten to manipulate and then save
2930
# in the names provided above.
30-
Qtmp <- renCol(readNWIS(sta, begin.date=Start, end.date=End))
31+
Qtmp <- renameNWISColumns(readNWISdv(sta, "00060", startDate=Start, endDate=End))
3132
QWtmp <- importNWISqw(sta, params=Params, begin.date=Start,
3233
end.date=End, use.pnames=TRUE)
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# Make sure that the recorded values are daily averages

‎inst/doc/app3.pdf

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‎man/AICc.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{AICc}
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\alias{AICc}
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\title{Akaike's An Information Criterion with Correction}

‎man/Atrazine.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\docType{data}
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\name{Atrazine}
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\alias{Atrazine}

‎man/LOADEST-package.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\docType{package}
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\name{LOADEST-package}
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\alias{LOADEST-package}
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\tabular{ll}{
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Package: \tab LOADEST\cr
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Type: \tab Package\cr
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Version: \tab 0.3.0\cr
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Date: \tab 2014-08-08\cr
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License: \tab GPL 2\cr
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Version: \tab 0.4.0\cr
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Date: \tab 2015-02-27\cr
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License: \tab File\cr
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LazyLoad: \tab yes\cr
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}
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}

‎man/c2load.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{c2load}
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\alias{c2load}
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\title{Loads}

‎man/center.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{center}
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\alias{center}
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\title{Centered Linear Terms}

‎man/coef.loadReg.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{coef.loadReg}
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\alias{coef.loadReg}
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\title{Extract Model Coefficients}

‎man/dailyAg.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{dailyAg}
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\alias{dailyAg}
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\title{Daily Mean}

‎man/fitted.loadReg.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{fitted.loadReg}
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\alias{fitted.loadReg}
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\title{Extract Model Fitted Values}

‎man/loadConvFactor.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{loadConvFactor}
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\alias{loadConvFactor}
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\title{Unit Conversion}

‎man/loadReg.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{loadReg}
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\alias{loadReg}
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\title{Load Estimation}
@@ -21,12 +21,12 @@ flow column.}
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\item{dates}{character string indicating the name of the
2222
date column.}
2323

24-
\item{flow.units}{character string describing the flow units.}
24+
\item{flow.units}{character string describing the flow units. See \bold{Details}.}
2525

2626
\item{conc.units}{character string describing the concentration
27-
unit.}
27+
unit. See \bold{Details}.}
2828

29-
\item{load.units}{character string describing the load unit.}
29+
\item{load.units}{character string describing the load unit. See \bold{Details}.}
3030

3131
\item{time.step}{character string describing the time step of
3232
the calibration data. Must be one of "instantaneous," "2 hours," "3 hours,"

‎man/loadReport.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{loadReport}
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\alias{loadReport}
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\title{Create Load Report}

‎man/loadStats.Rd

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% Generated by roxygen2 (4.0.1): do not edit by hand
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% Generated by roxygen2 (4.0.2): do not edit by hand
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\name{loadStats}
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\alias{loadStats}
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\title{Summary Statistics}

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