Reconstruct a reference grid with a new transformation or simulations

The typical use of this function is to cause EMMs to be computed on a different scale, e.g., the back-transformed scale rather than the linear-predictor scale. In other words, if you want back-transformed results, do you want to average and then back-transform, or back-transform and then average?

Usage

regrid(object, transform = c("response", "mu", "unlink", "none", "pass",
  links), inv.link.lbl = "response", predict.type,
  bias.adjust = get_emm_option("back.bias.adj"), sigma, N.sim,
  sim = mvtnorm::rmvnorm, ...)

Arguments

object

An object of class emmGrid

transform

Character, list, or logical value. If "response", "mu", or TRUE, the inverse transformation is applied to the estimates in the grid (but if there is both a link function and a response transformation, "mu" back-transforms only the link part); if "none" or FALSE, object is re-gridded so that its bhat slot contains predict(object) and its linfct slot is the identity. Any internal transformation information is preserved. If transform = "pass", the object is not re-gridded in any way (this may be useful in conjunction with N.sim).

If transform is a character value in links (which is the set of valid arguments for the make.link function, excepting "identity"), or if transform is a list of the same form as returned by make.links or make.tran, the results are formulated as if the response had been transformed with that link function.

inv.link.lbl

Character value. This applies only when transform is in links, and is used to label the predictions if subsequently summarized with type = "response".

predict.type

Character value. If provided, the returned object is updated with the given type to use by default by summary.emmGrid (see update.emmGrid). This may be useful if, for example, when one specifies transform = "log" but desires summaries to be produced by default on the response scale.

bias.adjust

Logical value for whether to adjust for bias in back-transforming (transform = "response"). This requires a valid value of sigma to exist in the object or be specified.

sigma

Error SD assumed for bias correction (when transform = "response" and a transformation is in effect). If not specified, object@misc$sigma is used, and a warning is issued if it is not found.

N.sim

Integer value. If specified and object is based on a frequentist model (i.e., does not have a posterior sample), then a fake posterior sample is generated using the function sim.

sim

A function of three arguments (no names are assumed). If N.sim is supplied with a frequentist model, this function is called with respective arguments N.sim, object@bhat, and object@V. The default is the multivariate normal distribution.

...

Ignored.

Value

An emmGrid object with the requested changes

Details

The regrid function reparameterizes an existing ref.grid so that its linfct slot is the identity matrix and its bhat slot consists of the estimates at the grid points. If transform is TRUE, the inverse transform is applied to the estimates. Outwardly, when transform = "response", the result of summary.emmGrid after applying regrid is identical to the summary of the original object using type="response". But subsequent EMMs or contrasts will be conducted on the new scale -- which is the reason this function exists.

This function may also be used to simulate a sample of regression coefficients for a frequentist model for subsequent use as though it were a Bayesian model. To do so, specify a value for N.sim and a sample is simulated using the function sim. The grid may be further processed in accordance with the other arguments; or if transform = "pass", it is simply returned with the only change being the addition of the simulated sample.

Note

Another way to use regrid is to supply a regrid argument to ref_grid (either directly of indirectly via emmeans), in which case its value is passed to regrid as transform. This is often a simpler approach if the reference grid has not already been constructed.

Degrees of freedom

In cases where the degrees of freedom depended on the linear function being estimated (e.g., Satterthwaite method), the d.f. from the reference grid are saved, and a kind of “containment” method is substituted in the returned object, whereby the calculated d.f. for a new linear function will be the minimum d.f. among those having nonzero coefficients. This is kind of an ad hoc method, and it can over-estimate the degrees of freedom in some cases. An annotation is displayed below any subsequent summary results stating that the degrees-of-freedom method is inherited from the previous method at the time of re-gridding.

Examples

pigs.lm <- lm(log(conc) ~ source + factor(percent), data = pigs)
rg <- ref_grid(pigs.lm)

# This will yield EMMs as GEOMETRIC means of concentrations:
(emm1 <- emmeans(rg, "source", type = "response"))
#>  source response   SE df lower.CL upper.CL
#>  fish       29.8 1.09 23     27.6     32.1
#>  soy        39.1 1.47 23     36.2     42.3
#>  skim       44.6 1.75 23     41.1     48.3
#> 
#> Results are averaged over the levels of: percent 
#> Confidence level used: 0.95 
#> Intervals are back-transformed from the log scale 
pairs(emm1) ## We obtain RATIOS
#>  contrast    ratio     SE df null t.ratio p.value
#>  fish / soy  0.761 0.0403 23    1  -5.153  0.0001
#>  fish / skim 0.669 0.0362 23    1  -7.428  <.0001
#>  soy / skim  0.879 0.0466 23    1  -2.442  0.0570
#> 
#> Results are averaged over the levels of: percent 
#> P value adjustment: tukey method for comparing a family of 3 estimates 
#> Tests are performed on the log scale 

# This will yield EMMs as ARITHMETIC means of concentrations:
(emm2 <- emmeans(regrid(rg, transform = "response"), "source"))
#>  source response   SE df lower.CL upper.CL
#>  fish       30.0 1.10 23     27.7     32.2
#>  soy        39.4 1.49 23     36.3     42.5
#>  skim       44.8 1.79 23     41.1     48.5
#> 
#> Results are averaged over the levels of: percent 
#> Confidence level used: 0.95 
pairs(emm2)  ## We obtain DIFFERENCES
#>  contrast    estimate   SE df t.ratio p.value
#>  fish - soy     -9.40 1.86 23  -5.051  0.0001
#>  fish - skim   -14.84 2.10 23  -7.071  <.0001
#>  soy - skim     -5.44 2.25 23  -2.424  0.0591
#> 
#> Results are averaged over the levels of: percent 
#> P value adjustment: tukey method for comparing a family of 3 estimates 
# Same result, useful if we hadn't already created 'rg'
# emm2 <- emmeans(pigs.lm, "source", regrid = "response")

# Simulate a sample of regression coefficients
set.seed(2.71828)
rgb <- regrid(rg, N.sim = 200, transform = "pass")
#> Simulating a sample of size 200 of regression coefficients.
emmeans(rgb, "source", type = "response")  ## similar to emm1
#>  source response lower.HPD upper.HPD
#>  fish       29.8      27.7      31.9
#>  soy        39.3      36.5      41.8
#>  skim       44.7      41.7      48.3
#> 
#> Results are averaged over the levels of: percent 
#> Point estimate displayed: median 
#> Results are back-transformed from the log scale 
#> HPD interval probability: 0.95