R/formula.utilities.R

In statnet.common: Common R Scripts and Utilities Used by the Statnet Project Software

#  File R/formula.utilities.R in package statnet.common, part of the
#  Statnet suite of packages for network analysis, https://statnet.org .
#
#  This software is distributed under the GPL-3 license.  It is free,
#  open source, and has the attribution requirements (GPL Section 7) at
#  https://statnet.org/attribution .
#
#  Copyright 2007-2024 Statnet Commons
################################################################################
###################################################################
## This file has utilities whose primary purpose is examining or ##
## manipulating ERGM formulas.                                   ##
###################################################################

#' @title Functions for Querying, Validating and Extracting from Formulas
#'
#' @description A suite of utilities for handling model formulas of the style used in Statnet packages.
#'
#' @name formula.utilities
NULL

#' @describeIn formula.utilities
#' 
#' \code{append_rhs.formula} appends a list of terms to the RHS of a
#' formula. If the formula is one-sided, the RHS becomes the LHS, if
#' \code{keep.onesided==FALSE} (the default).
#' 
#' @param object formula object to be updated or evaluated
#' @param newterms a [`term_list`] object, or any list of terms (names
#'   or calls) to append to the formula, or a formula whose RHS terms
#'   will be used; its `"sign"` attribute vector can give the sign of
#'   each term (`+1` or `-1`), and its `"env"` attribute
#'   vector will be used to set its environment, with the first
#'   available being used and subsequent ones producing a warning.
#' @param keep.onesided if the initial formula is one-sided, keep it
#'   whether to keep it one-sided or whether to make the initial
#'   formula the new LHS
#' @param env an environment for the new formula, if `object` is
#'   `NULL`
#' @param \dots Additional arguments. Currently unused.
#' @return \code{append_rhs.formula} each return an updated formula
#'   object; if `object` is `NULL` (the default), a one-sided formula
#'   containing only the terms in `newterms` will be returned.
#' @examples
#' 
#' ## append_rhs.formula
#' 
#' (f1 <- append_rhs.formula(y~x,list(as.name("z1"),as.name("z2"))))
#' (f2 <- append_rhs.formula(~y,list(as.name("z"))))
#' (f3 <- append_rhs.formula(~y+x,structure(list(as.name("z")),sign=-1)))
#' (f4 <- append_rhs.formula(~y,list(as.name("z")),TRUE))
#' (f5 <- append_rhs.formula(y~x,~z1-z2))
#' (f6 <- append_rhs.formula(NULL,list(as.name("z"))))
#' (f7 <- append_rhs.formula(NULL,structure(list(as.name("z")),sign=-1)))
#'
#' fe <- ~z2+z3
#' environment(fe) <- new.env()
#' (f8 <- append_rhs.formula(NULL, fe)) # OK
#' (f9 <- append_rhs.formula(y~x, fe)) # Warning
#' (f10 <- append_rhs.formula(y~x, fe, env=NULL)) # No warning, environment from fe.
#' (f11 <- append_rhs.formula(fe, ~z1)) # Warning, environment from fe
#'
#' \dontshow{
#' stopifnot(f1 == (y~x+z1+z2))
#' stopifnot(f2 == (y~z))
#' stopifnot(f3 == (y+x~-z))
#' stopifnot(f4 == (~y+z))
#' stopifnot(f5 == (y~x+z1-z2))
#' stopifnot(f6 == (~z))
#' stopifnot(f7 == (~-z))
#' stopifnot(f8 == (~z2+z3), identical(environment(f8), environment(fe)))
#' stopifnot(f9 == (y~x+z2+z3), identical(environment(f9), globalenv()))
#' stopifnot(f10 == (y~x+z2+z3), identical(environment(f10), environment(fe)))
#' stopifnot(f11 == (z2+z3~z1), identical(environment(f11), environment(fe)))
#' }
#'
#' @export
append_rhs.formula <- function(object = NULL, newterms, keep.onesided = FALSE, env = if(is.null(object)) NULL else environment(object)){
  force(env)
  if(is.null(object)) keep.onesided <- TRUE

  if(inherits(newterms,"formula")) newterms <- list_rhs.formula(newterms)

  for(i in seq_along(newterms)){
    newterm <- newterms[[i]]
    termsign <- if(NVL(attr(newterms, "sign")[i], +1)>0) "+" else "-"
    if(length(object)==0){
      if(termsign == "-") newterm <- call(termsign, newterm)
      object <- as.formula(call("~", newterm))
    }else if(length(object)==3) object[[3L]]<-call(termsign,object[[3L]],newterm)
    else if(keep.onesided) object[[2L]]<-call(termsign,object[[2L]],newterm)
    else object[[3L]]<- if(termsign=="+") newterm else call(termsign,newterm)

    NVL(env) <- termenv <- attr(newterms, "env")[[i]]
    if(!is.null(termenv) && !identical(env, termenv))
      warning(sQuote(paste0("newterms[[",i,"]]")), " has an environment that differs from the specified environment or another term's environment.")
  }

  environment(object) <- env
  object
}

#' @describeIn formula.utilities
#' 
#' \code{append.rhs.formula} has been renamed to \code{append_rhs.formula}.
#' @export
append.rhs.formula<-function(object,newterms,keep.onesided=FALSE){
  .Deprecate_once("append_rhs.formula")
  append_rhs.formula(object,newterms,keep.onesided)
}

#' @describeIn formula.utilities
#'
#' \code{filter_rhs.formula} filters through the terms in the RHS of a
#' formula, returning a formula without the terms for which function
#' `f(term, ...)` is `FALSE`. Terms inside another term (e.g.,
#' parentheses or an operator other than + or -) will be unaffected.
#'
#'
#' @examples
#' ## filter_rhs.formula
#' (f1 <- filter_rhs.formula(~a-b+c, `!=`, "a"))
#' (f2 <- filter_rhs.formula(~-a+b-c, `!=`, "a"))
#' (f3 <- filter_rhs.formula(~a-b+c, `!=`, "b"))
#' (f4 <- filter_rhs.formula(~-a+b-c, `!=`, "b"))
#' (f5 <- filter_rhs.formula(~a-b+c, `!=`, "c"))
#' (f6 <- filter_rhs.formula(~-a+b-c, `!=`, "c"))
#' (f7 <- filter_rhs.formula(~c-a+b-c(a),
#'                           function(x) (if(is.call(x)) x[[1]] else x)!="c"))
#' 
#'
#' \dontshow{
#' stopifnot(f1 == ~-b+c)
#' stopifnot(f2 == ~b-c)
#' stopifnot(f3 == ~a+c)
#' stopifnot(f4 == ~-a-c)
#' stopifnot(f5 == ~a-b)
#' stopifnot(f6 == ~-a+b)
#' stopifnot(f7 == ~-a+b)
#' }
#'
#' @param f a function whose first argument is the term and whose
#'   additional arguments are forwarded from `...` that returns either
#'   `TRUE` or `FALSE`, for whether that term should be kept.
#' @export
filter_rhs.formula <- function(object, f, ...){
  rhs <- ult(object)
  SnD <- function(x){
    if(!f(x, ...)) return(NULL)
    if(is(x, "call")){
      op <- x[[1L]]
      if(! as.character(op)%in%c("+","-")) return(x)
      else if(length(x)==2){
        arg <- SnD(x[[2L]])
        if(is.null(arg)) return(NULL)
        else return(call(as.character(op), arg))
      }else if(length(x)==3){
        arg1 <- SnD(x[[2L]])
        arg2 <- SnD(x[[3L]])
        if(is.null(arg2)) return(arg1)
        else if(is.null(arg1)){
          if(as.character(op)=="+") return(arg2)
          else return(call(as.character(op), arg2))
        }
        else return(call(as.character(op), arg1, arg2))
      }else stop("Unsupported type of formula passed.")
    }else return(x)
  }

  rhs <- SnD(rhs)
  ult(object) <- rhs
  object
}


#' @describeIn formula.utilities
#'
#' \code{nonsimp_update.formula} is a reimplementation of
#' \code{\link{update.formula}} that does not simplify.  Note that the
#' resulting formula's environment is set as follows. If
#' \code{from.new==FALSE}, it is set to that of object. Otherwise, a new
#' sub-environment of object, containing, in addition, variables in new listed
#' in from.new (if a character vector) or all of new (if TRUE).
#' 
#' @param new new formula to be used in updating
#' @param from.new logical or character vector of variable names. controls how
#' environment of formula gets updated.
#' @return 
#' \code{nonsimp_update.formula} each return an
#' updated formula object
#' @importFrom stats as.formula
#' @export
nonsimp_update.formula<-function (object, new, ..., from.new=FALSE){
  old.lhs <- if(length(object)==2) NULL else object[[2L]]
  old.rhs <- if(length(object)==2) object[[2L]] else object[[3L]]
  
  new.lhs <- if(length(new)==2) NULL else new[[2L]]
  new.rhs <- if(length(new)==2) new[[2L]] else new[[3L]]
  
  sub.dot <- function(c, dot){
    if(is.name(c) && c==".")  dot # If it's a dot, return substitute.
    else if(is.call(c)) as.call(c(list(c[[1L]]), lapply(c[-1], sub.dot, dot))) # If it's a call, construct a call consisting of the call and each of the arguments with the substitution performed, recursively.
    else c # If it's anything else, just return it.
  }
  
  deparen<- function(c, ops = c("+","*")){
    if(is.call(c)){
      if(as.character(c[[1L]]) %in% ops){
        op <- as.character(c[[1L]])
        if(length(c)==2 && is.call(c[[2L]]) && c[[2L]][[1L]]==op)
          return(deparen(c[[2L]], ops))
        else if(length(c)==3 && is.call(c[[3L]]) && c[[3L]][[1L]]==op){
          if(length(c[[3L]])==3)
            return(call(op, call(op, deparen(c[[2L]],ops), deparen(c[[3L]][[2L]],ops)), deparen(c[[3L]][[3L]],ops)))
          else
            return(call(op, deparen(c[[2L]],ops), deparen(c[[3L]][[2L]],ops)))
        }
      }
      return(as.call(c(list(c[[1L]]), lapply(c[-1], deparen, ops)))) # If it's a non-reducible call, construct a call consisting of the call and each of the arguments with the substitution performed, recursively.
    }else return(c)
  }
  

  # This is using some argument alchemy to handle the situation in
  # which object is one-sided but new is two sided with a dot in the
  # LHS. quote(expr=) creates a missing argument object that gets
  # substituted in place of a dot. The next statement then checks if
  # the resulting LHS *is* a missing object (as it is when the
  # arguments are ~a and .~.) removes the LHS if it is.
  out <- if(length(new)==2) call("~", deparen(sub.dot(new.rhs, old.rhs)))
         else if(length(object)==2) call("~", deparen(sub.dot(new.lhs, quote(expr=))), deparen(sub.dot(new.rhs, old.rhs)))
         else call("~", deparen(sub.dot(new.lhs, old.lhs)), deparen(sub.dot(new.rhs, old.rhs)))
  if(identical(out[[2]], quote(expr=))) out <- out[-2]

  #  a new sub-environment for the formula, containing both
  # the variables from the old formula and the new.
  
  if(identical(from.new,FALSE)){ # The new formula will use the environment of the original formula (the default).
    e <- environment(object)
  }else{
    # Create a sub-environment also containing variables from environment of new.
    e <- new.env(parent=environment(object))

    if(identical(from.new,TRUE)) from.new <- setdiff(ls(pos=environment(new), all.names=TRUE), "...") # If TRUE, copy all of them but the dots (dangerous!).

    for(name in from.new)
      assign(name, get(name, pos=environment(new)), pos=e)
  }

  as.formula(out, env = e)
}

#' @describeIn formula.utilities
#' 
#' \code{nonsimp.update.formula} has been renamed to \code{nonsimp_update.formula}.
#' @export
nonsimp.update.formula<-function (object, new, ..., from.new=FALSE){
  .Deprecate_once("nonsimp_update.formula")
  nonsimp_update.formula(object, new, ..., from.new=from.new)
}

#' A helper class for list of terms in an formula
#'
#' Typically generated by [list_rhs.formula()], it contains, in
#' addition to a list of [call()] or similar objects, attributes
#' `"sign"` and `"env"`, containing, respectively a vector of
#' signs that the terms had in the original formula and a list of
#' environments of the formula from which the term has been
#' extracted. Indexing and concatenation methods preserve these.
#'
#' @param x a list of terms or a term; a `term_list`
#' @param sign a vector specifying the signs associated with each term (`-1` and `+1`)
#' @param env a list specifying the environments, or NULL
#' @param i list index
#' @param ... additional arguments to methods
#'
#' @seealso [list_rhs.formula()], [list_summands.call()]
#'
#' @examples
#'
#' e1 <- new.env()
#' f1 <- a~b+c
#' environment(f1) <- e1
#' f2 <- ~-NULL+1
#'
#' (l1 <- list_rhs.formula(f1))
#' (l2 <- list_rhs.formula(f2))
#'
#' (l <- c(l1,l2))
#' \dontshow{
#' stopifnot(identical(c(unclass(l)), alist(b, c, NULL, 1)))
#' stopifnot(identical(attr(l, "sign"), c(1,1,-1,1)))
#' stopifnot(identical(attr(l, "env"), rep(list(e1, globalenv()), each=2)))
#' }
#'
#' (l <- c(l2[1], l1[2], l1[1], l1[1], l2[2]))
#' \dontshow{
#' stopifnot(identical(c(unclass(l)), alist(NULL, c, b, b, 1)))
#' stopifnot(identical(attr(l, "sign"), c(-1,1,1,1,1)))
#' stopifnot(identical(attr(l, "env"), list(globalenv(), e1, e1, e1, globalenv())))
#' }
#'
#' @export
term_list <- function(x, sign = +1, env = NULL){
  if(!is.list(x)) x <- list(x)
  if(!is.list(env)) env <- list(env)
  structure(x,
            sign = rep(sign, length.out=length(x)),
            env = rep(env, length.out=length(x)),
            class = "term_list")
}

#' @rdname term_list
#' @export
as.term_list <- function(x, ...) UseMethod("as.term_list")

#' @rdname term_list
#' @export
as.term_list.term_list <- function(x, ...) x

#' @rdname term_list
#' @export
as.term_list.default <- function(x, sign = +1, env = NULL, ...) term_list(x, sign=sign, env=env)

#' @rdname term_list
#' @export
c.term_list <- function(x, ...){
  xl <- c(list(as.term_list(x)), lapply(list(...), as.term_list))
  structure(
    c(unclass(x), ...),
    sign = unlist(lapply(xl, attr, "sign"), use.names=FALSE),
    env = unlist(lapply(xl, attr, "env"), recursive=FALSE, use.names=FALSE),
    class = "term_list"
  )
}

#' @rdname term_list
#' @export
`[.term_list` <- function(x, i, ...){
  term_list(NextMethod(), sign = attr(x, "sign")[i], env = attr(x, "env")[i])
}

#' @rdname term_list
#' @export
print.term_list <- function(x, ...){
  signstr <- ifelse(attr(x, "sign")>=0, "+", "-")
  envstr <- sapply(attr(x, "env"), format)
  termstr <- lapply(lapply(x, format), paste0, collapse="\n")

  cat("Term List:\n")
  cat(paste(signstr, termstr, envstr, collapse="\n"))
  cat("\n")
}

.recurse_summation <- function(x, sign){
  if(length(x)==1)
    term_list(x, sign)
  else if(length(x)==2 && x[[1L]]=="+")
    .recurse_summation(x[[2L]],sign)
  else if(length(x)==2 && x[[1L]]=="-")
    .recurse_summation(x[[2L]],-sign)
  else if(length(x)==3 && x[[1L]]=="+")
    c(.recurse_summation(x[[2L]],sign),
      .recurse_summation(x[[3L]],sign))
  else if(length(x)==3 && x[[1L]]=="-")
    c(.recurse_summation(x[[2L]],sign),
      .recurse_summation(x[[3L]],-sign))
  else if(length(x[[1]]) && x[[1L]]=="(")
    .recurse_summation(x[[2L]], sign)
  else
    term_list(x, sign)
}


#' @describeIn formula.utilities
#'
#' \code{term.list.formula} is an older version of \code{list_rhs.formula} that required the RHS call, rather than the formula itself.
#'
#' @param rhs,sign Arguments to the deprecated `term.list.formula`.
#' 
#' @export
term.list.formula<-function(rhs, sign=+1){
  .Deprecate_once("list_rhs.formula")
  .recurse_summation(rhs, sign)
}

#' @describeIn formula.utilities
#'
#' \code{list_summands.call}, given an unevaluated call or expression
#' containing the sum of one or more terms, returns an object of class [`term_list`] with the
#' terms being summed, handling \code{+} and \code{-} operators and
#' parentheses, and keeping track of whether a term has a plus or a
#' minus sign.
#'
#' @return \code{list_summands.call} returns an object of type
#'   [`term_list`]; its `"env"` attribute is set to a list of
#'   `NULL`s, however.
#' 
#' @export
list_summands.call<-function(object){
  .recurse_summation(object, sign=+1)
}


#' @describeIn formula.utilities
#'
#' \code{list_rhs.formula} returns an object of type [`term_list`],
#' containing terms in a given formula, handling \code{+} and \code{-}
#' operators and parentheses, and keeping track of whether a term has
#' a plus or a minus sign.
#'
#' @return
#' \code{list_rhs.formula} returns an object of type [`term_list`].
#'
#' @examples
#' stopifnot(identical(list_rhs.formula(a~b),
#'           structure(alist(b), sign=1, env=list(globalenv()), class="term_list")))
#' stopifnot(identical(list_rhs.formula(~b),
#'           structure(alist(b), sign=1, env=list(globalenv()), class="term_list")))
#' stopifnot(identical(list_rhs.formula(~b+NULL),
#'           structure(alist(b, NULL),
#'                     sign=c(1,1), env=rep(list(globalenv()), 2), class="term_list")))
#' stopifnot(identical(list_rhs.formula(~-b+NULL),
#'           structure(alist(b, NULL),
#'                     sign=c(-1,1), env=rep(list(globalenv()), 2), class="term_list")))
#' stopifnot(identical(list_rhs.formula(~+b-NULL),
#'           structure(alist(b, NULL),
#'                     sign=c(1,-1), env=rep(list(globalenv()), 2), class="term_list")))
#' stopifnot(identical(list_rhs.formula(~+b-(NULL+c)),
#'           structure(alist(b, NULL, c),
#'                     sign=c(1,-1,-1), env=rep(list(globalenv()), 3), class="term_list")))
#'
#' @export
list_rhs.formula<-function(object){
  if (!is(object, "formula"))
    stop("Invalid formula of class ",sQuote(class(object)),".")
  
  o <- .recurse_summation(ult(object), sign=+1)
  structure(o, env = rep(list(environment(object)), length(o)))
}


#' @describeIn formula.utilities
#'
#' \code{eval_lhs.formula} extracts the LHS of a formula, evaluates it in the formula's environment, and returns the result.
#'
#' @return
#' \code{eval_lhs.formula} an object of whatever type the LHS evaluates to.
#' @examples
#' ## eval_lhs.formula
#' 
#' (result <- eval_lhs.formula((2+2)~1))
#'
#' stopifnot(identical(result,4))
#' @export
eval_lhs.formula <- function(object){
  if (!is(object, "formula"))
    stop("Invalid formula of class ",sQuote(class(object)),".")
  if(length(object)<3)
    stop("Formula given is one-sided.")

  eval(object[[2L]],envir=environment(object))
}

#' Make a copy of an environment with just the selected objects.
#'
#' @param object An [`environment`] or an object with
#'   [`environment()`] and `environment()<-` methods.
#' @param ... Additional arguments, passed on to lower-level methods.
#'
#' @param keep A character vector giving names of variables in the
#'   environment (including its ancestors) to copy over, defaulting to
#'   dropping all. Variables that cannot be resolved are silently
#'   ignored.
#'
#' @return An object of the same type as `object`, with updated environment.
#' @export
trim_env <- function(object, keep=NULL, ...){
  UseMethod("trim_env")
}

#' @describeIn trim_env A method for environment objects.
#' @export
trim_env.environment <- function(object, keep=NULL, ...){
  # NB: The parent should be baseenv(), not emptyenv(), because :: and
  # ::: are defined in baseenv(), so PKG:::NAME calls won't work.
  e <- new.env(parent=baseenv())
  for(vn in keep){
    try(assign(vn, get(vn, envir=object), envir=e), silent=TRUE)
  }
  e
}

#' @describeIn trim_env Default method, for objects such as [`formula`] and [`function`] that have [`environment()`] and `environment()<-` methods.
#' @export
trim_env.default <- function(object, keep=NULL, ...){
  environment(object) <- trim_env(environment(object), keep, ...)
  object
}

#' Replace an object's environment with a simple, static environment.
#'
#' @param object An object with the `environment()<-` method.
#'
#' @return An object of the same type as `object`, with updated environment.
#'
#' @examples
#' f <- y~x
#' environment(f) # GlobalEnv
#'
#' environment(empty_env(f)) # EmptyEnv
#'
#' \dontshow{
#' stopifnot(identical(environment(empty_env(f)), emptyenv()))
#' }
#' @export
empty_env <- function(object){
  environment(object) <- emptyenv()
  object
}

#' @rdname empty_env
#' @examples
#'
#' environment(base_env(f)) # base package environment
#'
#' \dontshow{
#' stopifnot(identical(environment(base_env(f)), baseenv()))
#' }
#' @export
base_env <- function(object){
  environment(object) <- baseenv()
  object
}