Package index • drc

Core Functions

Main functions for dose-response analysis

drm(): Fitting dose-response models
ED(): Estimating effective doses
EDcomp(): Comparison of relative potencies between dose-response curves
compParm(): Comparison of parameters
mselect(): Dose-response model selection
drmc(): Sets control arguments

Model Functions

Available dose-response model families

LL.2() l2(): Two-parameter log-logistic function
LL.3() l3(): Three-parameter log-logistic function
LL.3u() l3u(): Three-parameter log-logistic function with upper limit fixed
LL.4() l4(): Four-parameter log-logistic function
LL.5() l5(): Five-parameter log-logistic function
LL2.2(): Two-Parameter Log-Logistic Model with log(ED50) as Parameter
LL2.3(): Three-Parameter Log-Logistic Model with log(ED50) and Lower Limit at 0
LL2.3u(): Three-Parameter Log-Logistic Model with log(ED50) and Fixed Upper Limit
LL2.4(): Four-Parameter Log-Logistic Model with log(ED50) as Parameter
LL2.5(): Five-Parameter Generalised Log-Logistic Model with log(ED50) as Parameter
W1.2() w2(): Two-parameter Weibull type 1 model
W1.3() w3(): Three-parameter Weibull type 1 model
W1.3u(): Three-parameter Weibull type 1 model with upper limit fixed
W1.4() w4(): Four-parameter Weibull type 1 model
W2.2(): Two-parameter Weibull (type 2) model
W2.3(): Three-parameter Weibull (type 2) model
W2.3u(): Three-parameter Weibull (type 2) model with upper limit fixed
W2.4(): Four-parameter Weibull (type 2) model
W2x.3(): Three-parameter Weibull type 2 model with lag time
W2x.4(): Four-parameter Weibull type 2 model with lag time
G.2(): Two-parameter Gompertz model
G.3(): Three-parameter Gompertz model
G.3u(): Three-parameter Gompertz model with upper limit fixed
G.4(): Four-parameter Gompertz model
G.aparine: Herbicide applied to Galium aparine
GiantKelp: Measurements of germination tubes for Giant Kelp
LN.2(): Two-parameter log-normal dose-response model
LN.3(): Three-parameter log-normal dose-response model
LN.3u(): Three-parameter log-normal model with upper limit fixed
LN.4(): Four-parameter log-normal dose-response model
BC.4(): Four-parameter Brain-Cousens hormesis model
BC.5(): Five-parameter Brain-Cousens hormesis model
CRS.4a() deprecated: Cedergreen-Ritz-Streibig Model with Lower Limit Fixed at 0 and Alpha = 1 (Deprecated)
CRS.4b() deprecated: Cedergreen-Ritz-Streibig Model with Lower Limit Fixed at 0 and Alpha = 0.5 (Deprecated)
CRS.4c() deprecated: Cedergreen-Ritz-Streibig Model with Lower Limit Fixed at 0 and Alpha = 0.25 (Deprecated)
CRS.5(): Wrapper for 5-parameter Cedergreen-Ritz-Streibig Model
CRS.5a() deprecated: Cedergreen-Ritz-Streibig Five-Parameter Model with Alpha = 1 (Deprecated)
CRS.5b() deprecated: Cedergreen-Ritz-Streibig Five-Parameter Model with Alpha = 0.5 (Deprecated)
CRS.5c() deprecated: Cedergreen-Ritz-Streibig Five-Parameter Model with Alpha = 0.25 (Deprecated)
CRS.6(): Generalised Cedergreen-Ritz-Streibig Model for Hormesis
UCRS.4a(): U-shaped CRS model with lower limit 0 (alpha=1)
UCRS.4b(): U-shaped CRS model with lower limit 0 (alpha=0.5)
UCRS.4c(): U-shaped CRS model with lower limit 0 (alpha=0.25)
UCRS.5a(): U-shaped CRS five-parameter model (alpha=1)
UCRS.5b(): U-shaped CRS five-parameter model (alpha=0.5)
UCRS.5c(): U-shaped CRS five-parameter model (alpha=0.25)
NEC.2(): Two-parameter NEC model
NEC.3(): Three-parameter NEC model
NEC.4(): Four-parameter NEC model
L.3(): Three-parameter logistic model
L.4(): Four-parameter logistic model
L.5(): Five-parameter generalized logistic model
AR.2(): Two-parameter asymptotic regression model
AR.3(): Three-parameter shifted asymptotic regression model
EXD.2(): Two-parameter exponential decay model
EXD.3(): Three-parameter exponential decay model
MM.2(): Two-parameter Michaelis-Menten function
MM.3(): Three-parameter Michaelis-Menten function
FPL.4(): Four-parameter fractional polynomial-logistic model
ml3a() deprecated: Alias for CRS.4a (Deprecated)
ml3b() deprecated: Alias for CRS.4b (Deprecated)
ml3c() deprecated: Alias for CRS.4c (Deprecated)
ml4a() deprecated: Alias for CRS.5a (Deprecated)
ml4b() deprecated: Alias for CRS.5b (Deprecated)
ml4c() deprecated: Alias for CRS.5c (Deprecated)
uml3a(): Alias for UCRS.4a
uml3b(): Alias for UCRS.4b
uml3c(): Alias for UCRS.4c
uml4a(): Alias for UCRS.5a
uml4b(): Alias for UCRS.5b
uml4c(): Alias for UCRS.5c
bcl3(): Alias for BC.4
bcl4(): Alias for BC.5
baro5(): The Baroreflex Five-Parameter Dose-Response Model
braincousens(): The Brain-Cousens hormesis models
cedergreen(): Cedergreen-Ritz-Streibig Model
ucedergreen(): U-shaped Cedergreen-Ritz-Streibig model
fplogistic(): Fractional polynomial-logistic dose-response model
gammadr(): Gamma Dose-Response Model
gaussian(): Normal (Gaussian) biphasic dose-response model
gompertz(): Gompertz dose-response or growth curve model
gompertzd(): Derivative of the Gompertz function
lgaussian(): Log-normal (log-Gaussian) biphasic dose-response model
llogistic(): The log-logistic function
llogistic2(): Five-Parameter Log-Logistic Model with log(ED50) as Parameter
lnormal(): Log-normal dose-response model
logistic(): The general asymmetric five-parameter logistic model
threephase(): Three-Phase Dose-Response Model
twophase(): Two-Phase Dose-Response Model
weibull1(): The four-parameter Weibull type 1 model
weibull2(): The four-parameter Weibull (type 2) model
weibull2x(): Five-parameter Weibull type 2 model with lag time
yieldLoss(): Calculating yield loss parameters
arandaordaz(): Asymptotic Regression Model

Effective Dose Estimation

Functions for estimating effective doses and comparisons

ED(<drc>): Estimating effective doses
ED_robust(): Robust Calculation of Effective Doses (ED)
CIcomp(): Classical combination index for effective doses
CIcompX(): Calculation of combination index for binary mixtures
comped(): Comparison of effective dose values
maED(): Estimation of ED values using model-averaging
maED_robust(): Robust Calculation of Model-Averaged Effective Doses
isobole(): Creating isobolograms
NEC(): No Effect Concentration (NEC) dose-response model
MAX(): Maximum mean response
PR(): Expected or predicted response
relpot(): Relative potency function

Diagnostics and Model Selection

Model diagnostics and helper functions

modelFit(): Assessing the model fit
Rsq(): R-squared for dose-response models
rss(): Residual sum of squares for dose-response models
rdrm(): Simulating a dose-response curve
anova(<drc>): ANOVA for dose-response model fits
lin.test(): Lack-of-fit test for the mean structure based on cumulated residuals
mr.test(): Mizon-Richard test for dose-response models
neill.test(): Neill's lack-of-fit test for dose-response models
noEffect(): Testing if there is a dose effect at all
backfit(): Calculation of backfit values from a fitted dose-response model
boxcox(<drc>): Transform-both-sides Box-Cox transformation
searchdrc(): Search through a range of initial parameter values to obtain convergence
simDR(): Simulating ED values under various scenarios
simFct(): Simulation of dose-response data and ED estimation
plotFACI(): Plot combination index as a function of fraction affected
getInitial(): Showing starting values used
getMeanFunctions(): Display available dose-response models

S3 Methods

Methods for drc model objects

coef(<drc>): Extract Model Coefficients
confint(<drc>): Confidence Intervals for Model Parameters
cooks.distance(<drc>): Cook's distance for nonlinear dose-response models
estfun(<drc>): Estimating function for the sandwich estimator
fitted(<drc>): Extract fitted values from model
hatvalues(<drc>): Model diagnostics for nonlinear dose-response models
logLik(<drc>): Extracting the log likelihood
plot(<drc>): Plotting fitted dose-response curves
predict(<drc>): Prediction
print(<drc>): Printing key features
print(<summary.drc>): Printing summary of non-linear model fits
residuals(<drc>): Extracting residuals from the fitted dose-response model
summary(<drc>): Summarising non-linear model fits
update(<drc>): Updating and re-fitting a model
vcov(<drc>): Calculating variance-covariance matrix for objects of class 'drc'
bread(<drc>): Bread for the sandwich estimator

Datasets

Example datasets for dose-response analysis

acidiq: Acifluorfen and diquat tested on Lemna minor.
aconiazide: Weight change in rats after exposure to a medical drug
acute.inh: Acute inhalation
algae: Volume of algae as function of increasing concentrations of a herbicide
arbovirus: arbovirus
auxins: Effect of technical grade and commercially formulated auxin herbicides
barley: Barley
bees: bees
blackgrass: Seedling Emergence of Blackgrass (Alopecurus myosuroides)
broccoli: The Effects of Drought Stress on Leaf Development in a Brassica oleracea population
C.dubia: Offsprings resulting from a toxicity test
CadmiumDaphnia: Cadmium Daphnia Data
carbendazim: Damage of lymphocyte cells
chickweed: Germination of common chickweed (Stellaria media)
chlorac: chlorac
chlordan: Chlordan
ctb: CellTiter-Blue Cell Viability Assay Data
Cyp17: Cyp17 expression data
Daphnia: Daphnia
daphnids: Daphnia test
decontaminants: Performance of decontaminants used in the culturing of a micro-organism
deguelin: Deguelin applied to chrysanthemum aphis
earthworms: Earthworm toxicity test
echovirus: Infections as response to exposure with Echovirus 12
Eryngium.sparganophyllum: Germination of Eryngium sparganophyllum
etmotc: Effect of erythromycin on mixed sewage microorganisms
finney71: Example from Finney (1971)
fluoranthene: Death of fathead minnow larvae after exposure to fluoranthene
germination: Germination of three crops
GiantKelp: Measurements of germination tubes for Giant Kelp
glymet: Glyphosate and metsulfuron-methyl tested on algae.
guthion: guthion
H.virescens: Mortality of tobacco budworms
heartrate: Heart rate baroreflexes for rabbits
leaflength: Leaf length of barley
lemna: Lemna
lepidium: Dose-response profile of degradation of agrochemical using lepidium
lettuce: Hormesis in lettuce plants
liver.tumor: Liver tumor incidence
M.bahia: Effect of an effluent on the growth of mysid shrimp
mdra: 3T3 mouse fibroblasts and NRU assay
mecter: Mechlorprop and terbythylazine tested on Lemna minor
metals: Data from heavy metal mixture experiments
methionine: Weight gain for different methionine sources
mixture(): Fitting binary mixture models
multi2(): Multistage Dose-Response Model with Quadratic Terms
nasturtium: Dose-response profile of degradation of agrochemical using nasturtium
nfa: Network Formation Assay Data
nicotine: nicotine
O.mykiss: Test data from a 21 day fish test
P.promelas: Effect of sodium pentachlorophenate on growth of fathead minnow
RScompetition: Competition between two biotypes
red.fescue: Red fescue
ryegrass: Effect of ferulic acid on growth of ryegrass
ryegrass2: Ryegrass
S.alba: Potency of two herbicides
S.alba.comp: Potency of two herbicides
S.capricornutum: Effect of cadmium on growth of green alga
secalonic: Root length measurements
selenium: Data from toxicology experiments with selenium
spinach: Inhibition of photosynthesis
TCDD: Liver tumor incidence
terbuthylazin: The effect of terbuthylazin on growth rate
ursa(): Universal Response Surface Approach (URSA) for Drug Interaction
vinclozolin: Vinclozolin from AR in vitro assay