Nothing
### R code from vignette source 'vignette.Rnw'
###################################################
### code chunk number 1: vignette.Rnw:41-53
###################################################
options(width = 65)
# load necessary packages, assuming they have already been installed on the system
library(waterData)
library(survival)
library(seawaveQ)
# load example data that comes with the package
data(swData)
# show first few rows of water-quality data for Missouri River at Omaha, Nebr.
head(qwMoRivOmaha)
# get a description of the data including definitions of the columns
# by viewing the help documentation
?qwMoRivOmaha
###################################################
### code chunk number 2: vignette.Rnw:62-64
###################################################
# scatter plot showing quantified, estimated, and censored values
cenScatPlot(qwMoRivOmaha, pname = "04035")
###################################################
### code chunk number 3: vignette.Rnw:71-86
###################################################
# scatter plot with many additional plotting arguments
# these options provide a plot closer to the plotting standards
# of the U.S. Geological Survey, however, these plots may not
# meet all U.S. Geological Survey publication requirements
par(las = 1, tcl = 0.5)
cenScatPlot(qwMoRivOmaha, pname = "04035",
site = "06610000 Missouri River at Omaha, Nebraska",
ylabel = "Simazine concentration, in micrograms per liter",
legcex = 0.7, qwcols = c("R", "P"), ylim = c(0,0.1), yaxs = "i",
cex.lab = 0.9, cex.axis = 0.9, xaxs = "i", xaxt = "n",
xlim = c(as.Date("1996-01-01"), as.Date("2004-01-01")))
axdates <- c("1996-01-01", "1998-01-01", "2000-01-01", "2002-01-01",
"2004-01-01")
axis(1, as.Date(axdates), labels = c("1996", "1998", "2000", "2002", "2004"),
cex.axis = 0.9)
###################################################
### code chunk number 4: vignette.Rnw:93-99
###################################################
data(swData)
# show last few rows of water-quality data for Missouri River at Omaha, Nebr.
tail(cqwMoRivOmaha)
# get a description of the data including definitions of the columns
# by viewing the help documentation
?cqwMoRivOmaha
###################################################
### code chunk number 5: vignette.Rnw:108-113
###################################################
data(swData)
MoRivOmaha <- combineData(qwdat = qwMoRivOmaha, cqwdat = cqwMoRivOmaha,
qwcols = c("staid", "dates", "R", "P"))
# view combined data set
head(MoRivOmaha)
###################################################
### code chunk number 6: vignette.Rnw:121-135
###################################################
data(swData)
# associate continuous water-quality data with each sample
# combineData does this for you
modMoRivOmaha <- combineData(qwdat=qwMoRivOmaha, cqwdat=cqwMoRivOmaha)
# then fit model(s)
myfitLinearTrend <- fitswavecav(cdat = modMoRivOmaha, cavdat = cqwMoRivOmaha,
tanm = "myfitLinearTrend",
pnames = c("04035", "04037", "04041"),
yrstart = 1995, yrend = 2003, tndbeg = 1995,
tndend = 2003, iwcav = c("flowa30", "flowa1"),
dcol = "dates", qwcols = c("R", "P"), mclass = 1,
plotfile = FALSE)
###################################################
### code chunk number 7: vignette.Rnw:142-161
###################################################
# get the first element of the list for each model/constituent combination
# the data frame with information about each model/constituent combination
myfitLinearTrend[[1]]
# get the second element of the list for each model/constituent combination
# the survival regression summary for each model/constituent combination
myfitLinearTrend[[2]]
# get the first few lines of the third element of the list
head(myfitLinearTrend[[3]])
# get the first few lines of the fourth element of the list
head(myfitLinearTrend[[4]])
# get the summary of predicted concentrations
myfitLinearTrend[[5]]
# get summary of trend results
myfitLinearTrend[[6]]
###################################################
### code chunk number 8: vignette.Rnw:168-172
###################################################
attributes(myfitLinearTrend[[2]][[1]])
myfitLinearTrend[[2]][[1]]$n
myfitLinearTrend[[2]][[1]]$table
###################################################
### code chunk number 9: vignette.Rnw:201-214
###################################################
data(swData)
# associate continuous water-quality data with each sample
# combineData does this for you
modMoRivOmaha <- combineData(qwdat = qwMoRivOmaha, cqwdat = cqwMoRivOmaha)
# then fit model
myfitRCS <- fitswavecav(cdat = modMoRivOmaha, cavdat = cqwMoRivOmaha,
tanm = "myfitRCS", pnames = c("04035"), yrstart = 1995,
yrend = 2003, tndbeg = 1995, tndend = 2003,
iwcav = c("flowa30", "flowa1"), dcol = "dates",
qwcols = c("R", "P"), mclass = 2, numk = 4,
plotfile = FALSE)
###################################################
### code chunk number 10: vignette.Rnw:219-238
###################################################
# get the first element of the list for each model/constituent combination
# the data frame with information about each model/constituent combination
myfitRCS[[1]]
# get the second element of the list for each model/constituent combination
# the survival regression summary for each model/constituent combination
myfitRCS[[2]]
# get the first few lines of the third element of the list
head(myfitRCS[[3]])
# get the first few lines of the fourth element of the list
head(myfitRCS[[4]])
# get the summary of predicted concentrations
myfitRCS[[5]]
# get summary of trend results
myfitRCS[[6]]
###################################################
### code chunk number 11: vignette.Rnw:242-245
###################################################
attributes(myfitRCS[[2]][[1]])
myfitRCS[[2]][[1]]$n
myfitRCS[[2]][[1]]$table
###################################################
### code chunk number 12: vignette.Rnw:262-269
###################################################
# myfitRCSTrend <- fitswavecav(cdat = modMoRivOmaha, cavdat = cqwMoRivOmaha,
# tanm = "myfitRCSTrend",
# pnames = c("04035", "04037", "04041"),
# yrstart = 1995, yrend = 2003, tndbeg = 1995,
# tndend = 2003, iwcav = c("flowa30", "flowa1"),
# dcol = "dates", qwcols = c("R", "P"), mclass = 2,
# numk = 4, bootRCS = TRUE, nboot = 1000, plotfile=FALSE)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.