qra (version 0.2.7)

extractLT: Obtain complete set of LT or LD estimates

Description

When supplied with a model object that has fitted dose-response lines for each of several levels of a factor, extractLT calls the function fieller to calculate lethal time

Usage

extractLT(
  obj,
  a = 1:3,
  b = 4:6,
  link = NULL,
  logscale = FALSE,
  p = 0.99,
  eps = 0,
  offset = 0,
  df.t = NULL
)
extractLTpwr(
  obj,
  a = 1:3,
  b = 1:3,
  link = "fpower",
  logscale = FALSE,
  p = 0.99,
  lambda = 0,
  eps = 0.015,
  offset = 0,
  df.t = NULL
)

Arguments

obj

merMod object, created using lmer() or glmerMod object, created using glmer().

a

Subscripts for intercepts.

b

Subscripts for corresponding slopes.

link

Link function, for use with objects where no link was specified in the function call, but it is required to back-transform a transformation that was performed prior to the function call. Otherwise leave as link=NULL, and the link function will be extracted as family(obj)[['link']]. For a folded power function, with extractLTpwr(), the only available link is fpower, and the exponent lambda must be specified.

logscale

Logical. Specify TRUE, if LT values are to be back-transformed from a logarithmic scale.

p

Target response proportion.

eps

Replace prob by prob+eps before transformation.

offset

Use to undo scaling of time or dose variable. This is passed to the fieller function that extractLT calls.

df.t

Degrees of freedom for a t-distribution approximation for `t` or `z` statistics. If NULL, a conservative (low) value will be used. For linear (but not generalized linear) models and mixed models, approximations are implemented in the afex package. See vignette('introduction-mixed-models', package="afex"), page 19.

lambda

(extractLTpwr only) Power for power function.

Value

Matrix holding LD or LD estimates.

Details

Fixed coefficients from obj must be for intercepts and for slopes. Starting the model formula with 0+ will commonly do what is required. The coefficients fixef(obj)[a] are assumed to specify line intercepts, while fixef(obj)[b] specify the corresponding slopes. These replace the arguments nEsts (subscripts for intercepts were 1:nEsts) and slopeAdd (subscripts for slopes were (nEsts+1):(nEsts+slopeAdd)).

Examples

# NOT RUN {
pcheck <- suppressWarnings(requireNamespace("glmmTMB", quietly = TRUE))
if(pcheck) pcheck & packageVersion("glmmTMB") >= "1.1.2"
if(pcheck){
form <- cbind(Dead,Live)~0+trtGp/TrtTime+(1|trtGpRep)
HawMed <- droplevels(subset(HawCon, CN=="MedFly"&LifestageTrt!="Egg"))
HawMed <- within(HawMed,
                 {trtGp <- factor(paste0(CN,LifestageTrt, sep=":"))
                 trtGpRep <- paste0(CN,LifestageTrt,":",RepNumber)
                 scTime <- scale(TrtTime) })
HawMedbb.cll <- glmmTMB::glmmTMB(form, dispformula=~trtGp+splines::ns(scTime,2),
                                 family=glmmTMB::betabinomial(link="cloglog"),
                                 data=HawMed)
round(qra::extractLT(p=0.99, obj=HawMedbb.cll, link="cloglog",
               a=1:3, b=4:6, eps=0, df.t=NULL)[,-2], 2)} else
message("Example requires `glmmTMB` version >= 1.1.2: not available")

# }