ED.drc.RdED estimates effective concentration or doses for one or more specified absolute or relative response levels.
# S3 method for drc ED(object, respLev, interval = c("none", "delta", "fls", "tfls", "inv"), clevel = NULL, level = ifelse(!(interval == "none"), 0.95, NULL), reference = c("control", "upper"), type = c("relative", "absolute"), lref, uref, bound = TRUE, od = FALSE, vcov. = vcov, display = TRUE, pool = TRUE, logBase = NULL, multcomp = FALSE, intType = "confidence", ...)
| object | an object of class 'drc'. |
|---|---|
| respLev | a numeric vector containing the response levels. |
| interval | character string specifying the type of confidence intervals to be supplied. The default is "none". See Details below for more explanation. |
| clevel | character string specifying the curve id in case on estimates for a specific curve or compound is requested. By default estimates are shown for all curves. |
| level | numeric. The level for the confidence intervals. The default is 0.95. |
| reference | character string. Is the upper limit or the control level the reference? |
| type | character string. Whether the specified response levels are absolute or relative (default). |
| lref | numeric value specifying the lower limit to serve as reference. |
| uref | numeric value specifying the upper limit to serve as reference (e.g., 100%). |
| bound | logical. If TRUE only ED values between 0 and 100% are allowed. FALSE is useful for hormesis models. |
| od | logical. If TRUE adjustment for over-dispersion is used. |
| vcov. | function providing the variance-covariance matrix. |
| display | logical. If TRUE results are displayed. Otherwise they are not (useful in simulations). |
| pool | logical. If TRUE curves are pooled. Otherwise they are not. This argument only works for models with independently fitted curves as specified in |
| logBase | numeric. The base of the logarithm in case logarithm transformed dose values are used. |
| multcomp | logical to switch on output for use with the package multcomp (which needs to be activated first). Default is FALSE (corresponding to the original output). |
| intType | string specifying the type of interval to use with the predict method in case the type of confidence interval chosen with the argument "type" is "inverse regression." |
| ... | see the details section below. |
There are several options for calculating confidence intervals through the argument interval. The option "delta" results in asymptotical Wald-type confidence intervals (using the delta method and the normal or t-distribution depending on the type of response). The option "fls" produces (possibly skewed) confidence intervals through back-transformation from the logarithm scale (only meaningful in case the parameter in the model is log(ED50) as for the llogistic2) models. The option "tfls" is for transforming back and forth from log scale (experimental). The option "inv" results in confidence intervals obtained through inverse regression.
For hormesis models (braincousens and cedergreen), the additional
arguments lower and upper may be supplied. These arguments specify the lower and upper limits
of the bisection method used to find the ED values. The lower and upper limits need to be smaller/larger
than the EDx level to be calculated. The default limits are 0.001 and 1000 for braincousens and
0.0001 and 10000 for cedergreen and ucedergreen, but this may need to be modified
(for cedergreen the upper limit may need to be increased and for ucedergreen
the lower limit may need to be increased). Note that the lower limit should not be set to 0 (use instead
something like 1e-3, 1e-6, ...).
An invisible matrix containing the shown matrix with two or more columns, containing the estimates
and the corresponding estimated standard errors and possibly lower and upper confidence limits.
Or, alternatively, a list with elements that may be plugged directly into parm
in the package multcomp (in case the argument multcomp is TRUE).
backfit, isobole, and maED use ED for specific calculations involving estimated ED values.
The related function EDcomp may be used for estimating differences and ratios of ED values,
whereas compParm may be used to compare other model parameters.
## Fitting 4-parameter log-logistic model ryegrass.m1 <- drm(ryegrass, fct = LL.4()) ## Calculating EC/ED values ED(ryegrass.m1, c(10, 50, 90))#> #> Estimated effective doses #> #> Estimate Std. Error #> e:1:10 1.46371 0.18677 #> e:1:50 3.05795 0.18573 #> e:1:90 6.38864 0.84510## first column: the estimates of ED10, ED50 and ED90 ## second column: the corresponding estimated standard errors ### How to use the argument 'ci' ## Also displaying 95% confidence intervals ED(ryegrass.m1, c(10, 50, 90), interval = "delta")#> #> Estimated effective doses #> #> Estimate Std. Error Lower Upper #> e:1:10 1.46371 0.18677 1.07411 1.85330 #> e:1:50 3.05795 0.18573 2.67053 3.44538 #> e:1:90 6.38864 0.84510 4.62580 8.15148## Comparing delta method and back-transformed ## confidence intervals for ED values ## Fitting 4-parameter log-logistic ## in different parameterisation (using LL2.4) ryegrass.m2 <- drm(ryegrass, fct = LL2.4()) ED(ryegrass.m1, c(10, 50, 90), interval = "fls")#> #> Estimated effective doses #> #> Estimate Lower Upper #> e:1:10 4.3219 2.9274 6.3809 #> e:1:50 21.2840 14.4476 31.3553 #> e:1:90 595.0468 102.0842 3468.5164ED(ryegrass.m2, c(10, 50, 90), interval = "delta")#> #> Estimated effective doses #> #> Estimate Std. Error Lower Upper #> e:1:10 0.380975 0.127602 0.114802 0.647147 #> e:1:50 1.117746 0.060737 0.991051 1.244442 #> e:1:90 1.854518 0.132282 1.578584 2.130453### How to use the argument 'bound' ## Fitting the Brain-Cousens model lettuce.m1 <- drm(weight ~ conc, data = lettuce, fct = BC.4()) ### Calculating ED[-10] # This does not work #ED(lettuce.m1, -10) ## Now it does work ED(lettuce.m1, -10, bound = FALSE) # works#> #> Estimated effective doses #> #> Estimate Std. Error #> e:1:-10 1.8646 1.0163ED(lettuce.m1, -20, bound = FALSE) # works#> #> Estimated effective doses #> #> Estimate Std. Error #> e:1:-20 0.96333 1.23014## The following does not work for another reason: ED[-30] does not exist #ED(lettuce.m1, -30, bound = FALSE)