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January 22, 2016 11:14
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dummy.coef() and print.dummy_coef() modified to deal with multivariate lm fits
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| # modified against R-Devel build 2016-01-22 r69971 | |
| # File src/library/stats/R/dummy.coef.R | |
| # Part of the R package, https://www.R-project.org | |
| # | |
| # Copyright (C) 1998 B. D. Ripley | |
| # Copyright (C) 1998-2015 The R Core Team | |
| # | |
| # This program is free software; you can redistribute it and/or modify | |
| # it under the terms of the GNU General Public License as published by | |
| # the Free Software Foundation; either version 2 of the License, or | |
| # (at your option) any later version. | |
| # | |
| # This program is distributed in the hope that it will be useful, | |
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| # GNU General Public License for more details. | |
| # | |
| # A copy of the GNU General Public License is available at | |
| # https://www.R-project.org/Licenses/ | |
| dummy.coef <- function(object, ...) UseMethod("dummy.coef") | |
| dummy.coef.lm <- function(object, use.na=FALSE, ...) | |
| { | |
| xl <- object$xlevels | |
| if(!length(xl)) # no factors in model | |
| return(as.list(coef(object))) | |
| Terms <- terms(object) | |
| tl <- attr(Terms, "term.labels") | |
| int <- attr(Terms, "intercept") | |
| facs <- attr(Terms, "factors")[-1, , drop=FALSE] | |
| Terms <- delete.response(Terms) | |
| vars <- all.vars(Terms) # e.g. drops I(.), ... | |
| nxl <- setNames(rep.int(1, length(vars)), vars) | |
| tmp <- lengths(xl) | |
| nxl[names(tmp)] <- tmp | |
| lterms <- apply(facs, 2L, function(x) prod(nxl[x > 0])) | |
| nl <- sum(lterms) | |
| args <- setNames(vector("list", length(vars)), vars) | |
| for(i in vars) | |
| args[[i]] <- if(nxl[[i]] == 1) rep.int(1, nl) | |
| else factor(rep.int(xl[[i]][1L], nl), levels = xl[[i]]) | |
| dummy <- do.call("data.frame", args) | |
| pos <- 0 | |
| rn <- rep.int(tl, lterms) | |
| rnn <- rep.int("", nl) | |
| for(j in tl) { | |
| i <- vars[facs[, j] > 0] | |
| ifac <- i[nxl[i] > 1] | |
| if(length(ifac) == 0L) { # quantitative factor | |
| rnn[pos+1] <- j | |
| } else if(length(ifac) == 1L) { # main effect | |
| dummy[ pos+1L:lterms[j], ifac ] <- xl[[ifac]] | |
| rnn[ pos+1L:lterms[j] ] <- as.character(xl[[ifac]]) | |
| } else { # interaction | |
| tmp <- expand.grid(xl[ifac]) | |
| dummy[ pos+1L:lterms[j], ifac ] <- tmp | |
| rnn[ pos+1L:lterms[j] ] <- | |
| apply(as.matrix(tmp), 1L, function(x) paste(x, collapse=":")) | |
| } | |
| pos <- pos + lterms[j] | |
| } | |
| ## some terms like poly(x,1) will give problems here, so allow | |
| ## NaNs and set to NA afterwards. | |
| mf <- model.frame(Terms, dummy, na.action=function(x)x, xlev=xl) | |
| mm <- model.matrix(Terms, mf, object$contrasts, xl) | |
| if(anyNA(mm)) { | |
| warning("some terms will have NAs due to the limits of the method") | |
| mm[is.na(mm)] <- NA | |
| } | |
| coef <- as.matrix(object$coefficients) | |
| if(!use.na) coef[is.na(coef)] <- 0 | |
| asgn <- attr(mm,"assign") | |
| res <- setNames(vector("list", length(tl)), tl) | |
| for(j in seq_along(tl)) { | |
| keep <- asgn == j | |
| ij <- rn == tl[j] | |
| dummyCoeffs <- t(mm[ij, keep, drop=FALSE] %*% coef[keep, ]) | |
| dimnames(dummyCoeffs) <- list(colnames(coef), rnn[ij]) | |
| res[[j]] <- dummyCoeffs | |
| } | |
| if(int > 0) { | |
| res <- c(list("(Intercept)" = coef[int]), res) | |
| } | |
| class(res) <- "dummy_coef" | |
| res | |
| } | |
| print.dummy_coef <- function(x, ..., title) | |
| { | |
| terms <- names(x) | |
| n <- length(x) | |
| xnrow <- vapply(x, function(y) nrow(as.matrix(y)), 1L) | |
| ansnrow <- sum(1L + xnrow) | |
| addcol <- max(xnrow)-1 | |
| nm <- addcol + max(vapply(x, function(y) ncol(as.matrix(y)), 1L)) | |
| ans <- matrix("", ansnrow , nm) | |
| rn <- rep.int("", ansnrow) | |
| lineBeg <- 0 | |
| lineEnd <- 0 | |
| for (j in seq_len(n)) { | |
| this <- as.matrix(x[[j]]) | |
| dnthis <- dimnames(this) | |
| rnthis <- if(is.null(dnthis[[1]])) rep.int("", nrow(this)) else dnthis[[1]] | |
| cnthis <- if(is.null(dnthis[[2]])) rep.int("", ncol(this)) else dnthis[[2]] | |
| dimnames(this) <- list(rnthis, cnthis) | |
| nr1 <- nrow(this) | |
| nc1 <- ncol(this) | |
| if(nc1 > 1L) { | |
| lineBeg <- lineEnd + 2 | |
| lineEnd <- lineBeg + nr1 - 1 | |
| ans[lineBeg-1, addcol + (1L:nc1)] <- colnames(this) | |
| ans[lineBeg:lineEnd, addcol + (1L:nc1)] <- format(this, ...) | |
| rn[lineBeg-1] <- paste0(terms[j], ": ") | |
| } else { | |
| lineBeg <- lineEnd + 1 | |
| lineEnd <- lineBeg + nr1 - 1 | |
| ans[lineBeg:lineEnd, addcol + 1L] <- format(this, ...) | |
| rn[lineBeg] <- paste0(terms[j], ": ") | |
| } | |
| if(addcol > 0) ans[lineBeg:lineEnd, addcol] <- rownames(this) | |
| } | |
| rownames(ans) <- rn | |
| colnames(ans) <- rep.int("", nm) | |
| cat(if(missing(title)) "Full coefficients are" else title, "\n") | |
| print(ans[1L:lineEnd, , drop=FALSE], quote=FALSE, right=TRUE) | |
| invisible(x) | |
| } |
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Line #83 is not quite correct, missing a
,but that was easy to fix. The bigger issue is that the other patch I had deals with NA coefficients nicely, and that's even a bit more complicated in the multivariate case. For now, I will omit the combined presence ofNA coefficients and multivariate response. No need, to post anything further... before I commit my version to the R source repository (soonish).