Fit three models to pesticide degradation data

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Documentation for package ‘xxDeg’ version 0.8.13

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xxDeg-package Compute and plot representative half-lives from pesticide degradation studies.
arrayRead Convert a 2-D character array, such as obtained from RExcel, to a vector of strings and a data frame
BadFit This function sets up a class for a failed curve fit. It is a list with those elements needed by other functions, but with all values set to NA
clipread Read the clipboard (or other file) into a list consisting of a data frame and a header.
coef.FitEmpty A coef function for the FitEmpty class.
coef.opdfopfit A coef function for for the opdfopfit class, which is returned by the fit.dfop function in cases where the nls function fails to fit the dfop model, but the optim function succeeds
coef.opiorefit A coef function for for the opiorefit class, which is returned by the fit.iore function in cases where the nls function fails to fit the iore model, but the optim function succeeds
dataTableGrob Generates a grob of a table listing a two column data frame
deg.vp Sets up a Grid viewport with appropriate spacing for axis labels
degfit A function for fitting degradation functions to data. Based on ead.plot, but does not include plotting, instead returning a list consisting of the original data and objects for each fit.
degLegend Generate a legend for the degradation plot
degplot A function for plotting the results of a list of curve fits
fit.dfop ##' A function for fitting a dual exponential to data using 'nls'
fit.iore A function for fitting an nth order rate equation to data using 'nls'
fit.loglmsfo A function which fits an exponential curve to data by taking the log of the dependent variable and using linear regression
fit.sfo Calculate curve fits to pesticide degradation study data
fitandplot A convenience function to read in data from the clipboard or a file, fit it and plot the results.
fitsummary.other Generate a 1 row data frame with the values from the rightmost column of table in the summary plot
fitsummary2DF Convert the results of 'summarizeFits' to a data frame
focus.chisq Apply the chi squared test as described by FOCUS
fomc2iore This function converts parameters from FOMC to IORE
GUS This is a function for generating a density plot of all possible GUS scores for a set of DT50 and KOC values
GUSplot Runs the GUS function from data on the clipboard
iore Calculates the IORE function and gradient for use by nls
iore2fomc This function converts parameters from IORE to FOMC
iore_g Calculates the IORE function and gradient for use by nls. Always includes The gradient
logLik.opiorefit This is a method logLik method for class opiorefit. It is basically copied from logLik.nls, except that it ignores weights (since there will be no weights).
mainPlot A function for making a grob for the main plot, which consists of one set of data point and any number of fits.
myspline A function which fits a natural spline with k knots to data
parameterstats This function runs the summary function on all fits in fits and returns data frame made by concatenating the parameters or coefficients elements returned by R's summary() function
predict.FitEmpty A predict function for the FitEmpty class.
predict.opdfopfit A predict function for for the opdfopfit class, which is returned by the fit.dfop function in cases where the nls function fails to fit the dfop model, but the optim function succeeds.
predict.opiorefit A predict function for for the opiorefit class, which is returned by the fit.iore function in cases where the nls function fails to fit the iore model, but the optim function succeeds.
residPlot A function for drawing the residual plot. The plot has the y-axis on the right, and only optionally has an x-axis.
residuals.FitEmpty A residuals function for the FitEmpty class. Returns NA values
residuals.opdfopfit A residuals function for for the opdfopfit class, which is returned by the fit.dfop function in cases where the nls function fails to fit the dfop model, but the optim function succeeds.
residuals.opiorefit A residuals function for for the opiorefit class, which is returned by the fit.iore function in cases where the nls function fails to fit the iore model, but the optim function succeeds.
summarizeFits Extracts summary values from a list of fits
summary.FitEmpty A summary method for the FitEmpty class.
summaryTable Generates a grob for a summary table, including DT50, DT90 and fitted parameters
xxDeg Compute and plot representative half-lives from pesticide degradation studies.