Package 'reformulas'

Detect whether there are any 'specials' in a formula term

Description

Detect whether there are any 'specials' in a formula term

Usage

anySpecial(term, specials = findReTrmClasses(), fast = FALSE)

Arguments

term	formula term
specials	values to detect
fast	(logical) use quick (syntactic) test for presence of specials?

Value

logical value

Examples

## should only detect s as the head of a function, s(...)
anySpecial(~diag(1))
anySpecial(~diag)
anySpecial(~diag[[1]])
anySpecial(~diag[1])
anySpecial(~s)
anySpecial(~s(hello+goodbye,whatever))

---

Expand terms with '||' notation into separate '|' terms

Description

From the right hand side of a formula for a mixed-effects model, expand terms with the double vertical bar operator into separate, independent random effect terms.

Usage

expandDoubleVerts(term)

Arguments

term	a mixed-model formula

Value

the modified term

See Also

formula, model.frame, model.matrix.

Other utilities: mkReTrms(), nobars(), subbars()

---

apply operator expansion (e.g. a/b -> a + a:b) to a formula term

Description

apply operator expansion (e.g. a/b -> a + a:b) to a formula term

Usage

expandGrpVar(f)

Arguments

f	a language object (an atom of a formula)

Examples

expandGrpVar(quote(x*y))
expandGrpVar(quote(x/y))

---

list of specials – taken from enum.R

Description

list of specials – taken from enum.R

Usage

findReTrmClasses()

---

Format columns corresponding to std. dev. and/or variance.

Description

Format columns corresponding to std. dev. and/or variance.

Usage

format_sdvar(
  reStdDev,
  use.c = "Std.Dev.",
  formatter = format,
  digits = max(3, getOption("digits") - 2),
  ...
)

format_corr(x, maxdim = Inf, digits = 2, maxlen = 10, ...)

get_sd(x, ...)

Arguments

reStdDev	a vector of standard deviations.
use.c	a character vector indicating which scales to include.
formatter	formatting function.
digits	digits for format
...	additional parameters
x	a square numeric matrix
maxdim	maximum number of rows/columns to display
maxlen	maximum number of rows to display

---

Format the 'VarCorr' Matrix of Random Effects

Description

"format()" the VarCorr matrix of the random effects – for print()ing and show()ing

Usage

formatVC(
  varcor,
  digits = max(3, getOption("digits") - 2),
  corr_digits = max(2, digits - 2),
  maxdim = 10,
  comp = "Std.Dev.",
  formatter = format,
  useScale = attr(varcor, "useSc"),
  ...
)

Arguments

varcor	a VarCorr (-like) matrix with attributes.
digits	the number of significant digits for standard deviations and variances.
corr_digits	the number of significant digits for correlations.
maxdim	maximum dimensions (numbers of standard deviations/variances and number of rows of correlation matrices) to report per random effects term.
comp	character vector of length one or two indicating which columns out of "Variance" and "Std.Dev." should be shown in the formatted output.
formatter	the function to be used for formatting the standard deviations and or variances (but not the correlations which (currently) are always formatted as "0.nnn".
useScale	whether to report a scale parameter (e.g. residual standard deviation).
...	optional arguments for formatter(*) in addition to the first (numeric vector) and digits.

Value

a character matrix of formatted VarCorr entries from varcor.

---

get grouping variable symbols/names

Description

get grouping variable symbols/names

Usage

get_grpvars(formula, return_val = c("char", "symbol"))

Arguments

formula	a formula
return_val	return character string or raw symbol?

Examples

form <- Reaction ~ Days + (Days | group / Subject)
get_grpvars(form)
get_grpvars(form, return_val = "symbol")

---

Is f1 nested within f2?

Description

Does every level of f1 occur in conjunction with exactly one level of f2? The function is based on converting a triplet sparse matrix to a compressed column-oriented form in which the nesting can be quickly evaluated.

Usage

isNested(f1, f2)

Arguments

f1	factor 1
f2	factor 2

Value

TRUE if factor 1 is nested within factor 2

Examples

if (requireNamespace("lme4")) {
   data("Pastes", package = "lme4")
   with(Pastes, isNested(cask, batch))   ## => FALSE
   with(Pastes, isNested(sample, batch))  ## => TRUE
}

---

Create list of structures needed for models with random effects

Description

From the result of findbars applied to a model formula and and the evaluation frame, create the model matrix, etc. associated with random-effects terms. See the description of the returned value for a detailed list.

Usage

mkReTrms(
  bars,
  fr,
  drop.unused.levels = TRUE,
  reorder.terms = TRUE,
  reorder.vars = FALSE,
  calc.lambdat = TRUE,
  sparse = NULL
)

Arguments

bars	a list of parsed random-effects terms
fr	a model frame in which to evaluate these terms
drop.unused.levels	(logical) drop unused factor levels?
reorder.terms	arrange random effects terms in decreasing order of number of groups (factor levels)?
reorder.vars	arrange columns of individual random effects terms in alphabetical order?
calc.lambdat	(logical) compute Lambdat and Lind components? (At present these components are needed for lme4 machinery but not for glmmTMB, and may be large in some cases; see Bates et al. 2015
sparse	(logical) set up sparse model matrices?

Details

Lambdat, Lind, theta, lower are likely to be useful only for lme4; the other terms can be generally useful for constructing mixed-effect models

Value

a list with components

Zt	transpose of the sparse model matrix for the random effects
Ztlist	list of components of the transpose of the random-effects model matrix, separated by random-effects term
Lambdat	transpose of the sparse relative covariance factor
Lind	an integer vector of indices determining the mapping of the elements of the theta to the "x" slot of Lambdat
theta	initial values of the covariance parameters
lower	lower bounds on the covariance parameters
flist	list of grouping factors used in the random-effects terms
cnms	a list of column names of the random effects according to the grouping factors
Gp	a vector indexing the association of elements of the conditional mode vector with random-effect terms; if nb is the vector of numbers of conditional modes per term (i.e. number of groups times number of effects per group), Gp is c(0,cumsum(nb)) (and conversely nb is diff(Gp))
nl	names of the terms (in the same order as Zt, i.e. reflecting the reorder.terms argument)
ord	an integer vector giving the relationship between the order of the terms in the formula and the terms in the final object (which are ordered by the number of levels in the grouping variable, if reorder.terms is TRUE)

References

Bates D, Mächler M, Bolker B, Walker S (2015). "Fitting Linear Mixed-Effects Models Using lme4." Journal of Statistical Software, 67(1), 1-48. doi:10.18637/jss.v067.i01

See Also

Other utilities: expandDoubleVerts(), nobars(), subbars()

Examples

## (silly/impractical formula, for illustration only)
form <- mpg ~ 1 + (1|gear) + (factor(cyl)|gear) + (1 + hp | carb)
fr <- model.frame(subbars(form), data = mtcars)
rterms <- mkReTrms(findbars(form), fr)
names(rterms)
## block sizes (latent variables per block) of each term
(nperblock <- lengths(rterms$cnms))
## latent variables per term
(nperterm <- diff(rterms$Gp))
with(rterms, identical(unname(nl*nperblock), nperterm))
## illustrate reordering of terms
dd <- expand.grid(a = 1:7, b = 1:3, c = 1:5, d = 1:9)
dd$y <- 1
form2 <- y ~ 1 + (1|a) + (1|b) + (1|c) + (1|d)
rterms2 <- mkReTrms(findbars(form2), dd, reorder.terms = TRUE)
## reorder elements into original formula order
with(rterms2, cnms[order(ord)])
## reorder splitForm output to match mkReTrms components
ss <- splitForm(form2)
ss$reTrmFormulas[rterms2$ord]

---

Drop 'specials' from a formula

Description

Drop 'specials' from a formula

Usage

no_specials(term, specials = c("|", "||", "s"))

Arguments

term	a term or formula or list thereof
specials	function types to drop

Value

a call or language object (or list) with specials removed

Examples

no_specials(findbars_x(~ 1 + s(x) + (f|g) + diag(x|y)))
no_specials(~us(f|g))
no_specials(~us(f|g, extra_arg))

---

Omit terms separated by vertical bars in a formula

Description

Remove the random-effects terms from a mixed-effects formula, thereby producing the fixed-effects formula.

Usage

nobars(term)

nobars_(term)

Arguments

term	the right-hand side of a mixed-model formula

Value

the fixed-effects part of the formula

Note

This function is called recursively on individual terms in the model, which is why the argument is called term and not a name like form, indicating a formula.

See Also

formula, model.frame, model.matrix.

Other utilities: expandDoubleVerts(), mkReTrms(), subbars()

Examples

nobars(Reaction ~ Days + (Days|Subject)) ## => Reaction ~ Days

---

Remove all random slopes from a formula, while retaining random intercepts.

Description

Remove all random slopes from a formula, while retaining random intercepts.

Usage

randint(form)

Arguments

form

A formula

Value

The new formula

Examples

f <- ~ 1 + a  + b + (a | f) + (1 + a | g) + (a + b | h ) + (1 + a + b | i)
randint(f)

---

extract right-hand side of a formula

Description

extract right-hand side of a formula

Usage

RHSForm(form, as.form = FALSE)

Arguments

form	a formula object
as.form	(logical) return a formula (TRUE) or as a call/symbolic object (FALSE) ?

Value

a language object

Examples

RHSForm(y ~ x + (1|g))

---

"Substitute bars"

Description

Substitute the '+' function for the '|' and '||' function in a mixed-model formula. This provides a formula suitable for the current model.frame function.

Usage

subbars(term)

Arguments

term	a mixed-model formula

Value

the formula with all | and || operators replaced by +

Note

This function is called recursively on individual terms in the model, which is why the argument is called term and not a name like form, indicating a formula.

See Also

formula, model.frame, model.matrix.

Other utilities: expandDoubleVerts(), mkReTrms(), nobars()

Examples

subbars(Reaction ~ Days + (Days|Subject)) ## => Reaction ~ Days + (Days + Subject)

---