Man pages for alfcrisci/bmdModeling
Benchmark dose modeling

averageResponseCalculate the weighted average of estimated response values
bindModelResultsBind results of one/several fitted model(s) into one summary...
bmr1Target function for optimization if ces.ans = 1
bmr2Target function for optimization if ces.ans = 2
bmr3Target function for optimization if ces.ans = 3
bootstrapBmdEstimate lower and upper bound for model-averaged bmd using...
calculateWeightsCalculate weights based on fitted models' aic
f.basics.catcompute basic statistics of a categorical model the value for parameter b, from values of other... value for parameter b for continuous response
f.boot.conOne bootstrap run for continuous response
f.catMain function for calculations with categorical response type
f.ced.catDetermine values for the CED; categorical model
f.ced.conDetermine values for the CED; continuous response
f.cedlines.binPlot dotted lines for the determined CED value for...
f.cedlines.conPlot dotted lines for the determined CED value for continous...
f.ced.pctCalculate CI based on bootstrap estimates and confidence...
f.check.ccCheck whether the parameter value for c is too close to CES
f.check.nonneg.numCheck whether the data frame columns are numeric and can be...
f.CIWrapper function for calculating CI around parameter...
f.conMain function for calculations with continuous response type
f.constr.conDefine lower and upper bounds for the model parameters;...
f.controlDefine control parameters for nlminb(), which minimizes the...
f.convergedDetermine convergence type of the minimization algorithm
f.dtype6.mnCompare model fitted with and without alfa
f.executeCalculate values for the response variable given the response...
f.expect.binCalculate expected response values, for categorical response
f.expect.catcomputed expected value for categorical model
f.expect.conCalculate expected response values, for continuous response
f.hit.constrCheck whether any of the MLEs for the parameters hit the...
filterBestCovariatesRetain model with smallest AIC per family when considering...
findBestModelFind the best model given a table of fitted models results
findBootstrapBoundsFind the lower and upper bound for bmd based on parametric...
f.iniDefine default parameter values needed in the proast...
f.inv.binreturn the CED value for a set of parameters, CES and ces.ans
f.inv.conDetermine value for the CED; continuous response
fitAllCovariatesFit all covariate combinations for model parameters in given...
fitAllModelsFit all model families for the continuous or quantal response
fitSingleModelFit single model for the continuous or quantal response
f.lik.catCalculate likelihood for categorical response
f.lik.conCalculate likelihood for continuous response
f.lines.catplot lines for categorical model
f.lines.conPlot the curve of the estimated model
f.lines.frqPlot the lines
f.LL.binCalculate confidence intervals for each of the plotted points... Add values to e.g. response y to avoid log of 0
f.mm4.catFit the model for a categorical response
f.mm4.conFit the model for a continuous response
f.mm6.catCalculate the CED values for a continuous response
f.mm6.conCalculate the CED values for a continuous response
f.mm7.conMain function for bootstrap method for calculating CI of CED
f.model.bbchange model.ans
f.nested.conCalculations for nested factors (clustered response data)
f.nlminbMinimization of the log-likelihood function the number of group ?
f.PCalculate p-value for likelihood test
f.parsConstruct regression parameter matrix
f.plot.allWrapper function for plotting the results of proast
f.plot.conPlot the predicted response values (points) and estimated CIs
f.plot.frqPlot the predicted response values (points) and estimated CIs
f.proastMain function to perform proast analysis
f.profile.allProfile likelihood method to calculate confidence intervals
f.remove.NAsRemove NAs from a given data frame for all listed column...
f.resid.conCalculate residuals: difference of observed and expected...
f.scanLoad file in proast data format
f.split.parsplit the vector of parameters
f.start.binDefine initial parameter values for the chosen model, binary...
f.start.catDefine initial parameter values for the chosen model,...
f.start.conDefine initial parameter values for the chosen model,...
f.start.lm.conFit linear model for continuous response
f.text.parDefine character vector with all parameter names th.lvm?
f.uniroot.BMDratiocompute the root of the BMD ratio?
f.uniroot.probitcompute the value for the parameter b for a probit function
getModelNamesIndex in Proast and full names of the fitted models
getModelParametersObtain the available model parameters for a given model...
makeForestPlotForest plot for estimated bmd, bmdl and bmdu values per...
matchWithResultsFind which fitted models' results match the listed model and...
optimizeBmdEstimate the model-averaged BMD using numeric optimization...
pasteToVectorPaste elements of vector into string vector (for testing)
plotAverageModelPlot for the model-averaged response values and bmd
printerPrint for debugging
runBmdRun the BmdModeling Application
summaryModelsSummarize the results of all fitted models for continuous or...
testConstraintsTest function for defining parameter constraints
testCovariatesTest function for including covariates
testStartingValuesTest function for defining starting values
alfcrisci/bmdModeling documentation built on May 28, 2019, 12:32 a.m.