update packages and add valign
This commit is contained in:
@@ -16,4 +16,4 @@ File: dir, Node: Top This is the top of the INFO tree
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Emacs
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* ESS: (ess). Emacs Speaks Statistics (R/S/S+, SAS,
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BUGS/JAGS and Stata).
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BUGS/NIMBLE and Stata).
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@@ -58,18 +58,28 @@
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(cons "^[ \t]*\\(model\\|var\\)\\>"
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font-lock-keyword-face)
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(cons (concat "\\<d\\(bern\\|beta\\|bin\\|cat\\|chisq\\|"
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"dexp\\|dirch\\|exp\\|\\(gen[.]\\)?gamma\\|hyper\\|"
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"interval\\|lnorm\\|logis\\|mnorm\\|mt\\|multi\\|"
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"negbin\\|norm\\(mix\\)?\\|par\\|pois\\|sum\\|t\\|"
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"unif\\|weib\\|wish\\)[ \t\n]*(")
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(cons (concat "\\<d\\(bern\\|beta\\|bin\\|binom\\|"
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"cat\\|chisq\\|chisqr\\|CRP\\|"
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"dexp\\|dirch\\|dirich\\|"
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"exp\\|\\(gen[.]\\|inv\\)?gamma\\|hyper\\|"
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"interval\\|lkj_corr_cholesky\\|laplace\\|lnorm\\|logis\\|"
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"mnorm\\|mt\\|multi\\|multinom\\|mvt\\|"
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"negbin\\|nbinom\\|norm\\(mix\\)?\\|par\\|pois\\|sum\\|t\\|"
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"unif\\|weib\\|weibull\\|\\(inv\\)?wish\\|wishart\\)[ \t\n]*(")
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font-lock-constant-face)
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(cons (concat "\\<\\(abs\\|cos\\|C\\|dim\\|\\(i\\)?cloglog\\|equals\\|"
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"exp\\|for\\|inprod\\|interp[.]line\\|inverse\\|length\\|"
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"\\(i\\)?logit\\|logdet\\|logfact\\|loggam\\|max\\|mean\\|"
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"mexp\\|min\\|phi\\|pow\\|probit\\|prod\\|rank\\|round\\|"
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"sd\\|sin\\|sort\\|sqrt\\|step\\|sum\\|t\\|trunc\\|T\\)[ \t\n]*(")
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(cons (concat "\\<\\(abs\\|acos\\|acosh\\|asin\\|asinh\\|atan\\|atanh\\|"
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"asCol\\|asRow\\|backsolve\\|besselK\\|ceiling\\|chol\\|"
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"cos\\|C\\|dim\\|\\(i\\)?cloglog\\|cube\\|"
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"equals\\|exp\\|expm\\|expAv\\|expit\\|"
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"floor\\|for\\|forwardsolve\\|"
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"inprod\\|interp[.]lin\\(e\\)?\\|inverse\\|"
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"lgamma\\|length\\|lfactorial\\|"
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"log\\|log1p\\|\\(i\\)?logit\\|logdet\\|logfact\\|loggam\\|"
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"max\\|mean\\|mexp\\|min\\|pmax\\|pmin\\|"
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"phi\\|pow\\|\\(i\\)?probit\\|prod\\|rank\\|ranked\\|round\\|"
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"sd\\|sin\\|solve\\|sort\\|sqrt\\|step\\|sum\\|"
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"t\\|tan\\|trunc\\|T\\)[ \t\n]*(")
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font-lock-function-name-face)
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;; .bmd files
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@@ -29,14 +29,14 @@
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(require 'ess-utils)
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(defvar ess-bugs-command)
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(defvar ess-bugs-chains)
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(defvar ess-jags-command)
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(defvar ess-jags-chains)
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;;(defvar ess-jags-command)
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;;(defvar ess-jags-chains)
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(defvar ess-bugs-default-bins)
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(declare-function ess-bugs-na-bug "ess-bugs-d")
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(declare-function ess-jags-na-bug "ess-jags-d")
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;;(declare-function ess-jags-na-bug "ess-jags-d")
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(declare-function ess-bugs-na-bmd "ess-bugs-d")
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(declare-function ess-jags-na-jmd "ess-jags-d")
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;;(declare-function ess-jags-na-jmd "ess-jags-d")
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(defgroup ess-bugs nil
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"ESS: BUGS."
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@@ -140,8 +140,9 @@ Users whose default is not \\='sh, but are accessing a remote machine with
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(defvar ess-bugs-mode-map
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(let ((map (make-sparse-keymap)))
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(define-key map (quote [f2]) #'ess-revert-wisely)
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(define-key map "\C-c\C-c" #'ess-bugs-next-action)
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(define-key map "=" #'ess-bugs-hot-arrow)
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;;(define-key map "\C-c\C-c" #'ess-bugs-next-action)
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(define-key map "<" #'ess-bugs-hot-arrow) ;; NIMBLE needs equals character
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;; (define-key map "=" #'ess-bugs-hot-arrow)
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;; (define-key map "_" #'ess-bugs-hot-arrow)
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map)
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"ESS[BUGS]: Keymap for mode.")
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@@ -191,20 +192,20 @@ and `ess-bugs-file-dir'."
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(interactive)
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(insert " <- "))
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(defun ess-bugs-next-action ()
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"ESS[BUGS/JAGS]: Perform the appropriate next action."
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(interactive)
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(ess-bugs-file)
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;; (defun ess-bugs-next-action ()
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;; "ESS[BUGS/JAGS]: Perform the appropriate next action."
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;; (interactive)
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;; (ess-bugs-file)
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(cond ((equal ".bug" ess-bugs-file-suffix) (ess-bugs-na-bug))
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((equal ".jag" ess-bugs-file-suffix) (ess-jags-na-bug))
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((equal ".bmd" ess-bugs-file-suffix)
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(ess-save-and-set-local-variables)
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(ess-bugs-na-bmd ess-bugs-command ess-bugs-chains))
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((equal ".jmd" ess-bugs-file-suffix)
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(ess-save-and-set-local-variables)
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(ess-jags-na-jmd ess-jags-command ess-jags-chains)))
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)
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;; (cond ((equal ".bug" ess-bugs-file-suffix) (ess-bugs-na-bug))
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;; ((equal ".jag" ess-bugs-file-suffix) (ess-jags-na-bug))
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;; ((equal ".bmd" ess-bugs-file-suffix)
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;; (ess-save-and-set-local-variables)
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;; (ess-bugs-na-bmd ess-bugs-command ess-bugs-chains))
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;; ((equal ".jmd" ess-bugs-file-suffix)
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;; (ess-save-and-set-local-variables)
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;; (ess-jags-na-jmd ess-jags-command ess-jags-chains)))
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;; )
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(defun ess-bugs-sci-to-round-4-dp ()
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"ESS[BUGS]: round output from +/-0.000E+/-0 to 4 decimal places."
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@@ -1,6 +1,6 @@
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;;; ess-custom.el --- Customize variables for ESS -*- lexical-binding: t; -*-
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;; Copyright (C) 1997-2025 Free Software Foundation, Inc.
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;; Copyright (C) 1997-2026 Free Software Foundation, Inc.
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;; Author: Rodney Sparapani
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;; Maintainer: ESS-help <ess-help@r-project.org>
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@@ -1571,11 +1571,21 @@ by `ess-function-template'."
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:group 'ess
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:type 'regexp)
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(defcustom ess-r-outline-regexp
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"^[ \t]*#+ +.*\\(?:----\\|====\\|####\\)\\s-*$"
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"Regexp used to detect the beginning of R headings."
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(defcustom ess-r-outline-style 'none
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"Outline convention used by `ess-r-mode'.
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Choose between comment rulers like RStudio (\"### Section title ----\"),
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\"Org-like\" headings (\"### *** Section title\"), or no outline support.
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When using the RStudio outline style, `ess-indent-with-fancy-comments'
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is automatically set to nil locally in the buffer. When switching back,
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the original local binding is restored; if the variable was not
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buffer-local, the current global default applies. You can also use
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(setq ess-style \\='RStudio) to achieve the same effect globally."
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:group 'ess-R
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:type 'regexp)
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:type '(choice (const :tag "No outline support" none)
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(const :tag "RStudio comment rulers" RStudio)
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(const :tag "Org-Like (### *** headings)" Org-like))
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:safe #'symbolp)
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; ess-inf: variables for inferior-ess.
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@@ -1,10 +1,10 @@
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;; -*- no-byte-compile: t; lexical-binding: nil -*-
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(define-package "ess" "20251212.937"
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(define-package "ess" "20260322.1703"
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"Emacs Speaks Statistics."
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'((emacs "25.1"))
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:url "https://ess.r-project.org/"
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:commit "e39ca8fa7fce703aa2851e83987a412737d575f0"
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:revdesc "e39ca8fa7fce"
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:commit "4e112590d1c13cfe464ca7de77837f1b956e4a9f"
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:revdesc "4e112590d1c1"
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:authors '(("David Smith" . "dsmith@stats.adelaide.edu.au")
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("A.J. Rossini" . "blindglobe@gmail.com")
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("Richard M. Heiberger" . "rmh@temple.edu")
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@@ -1,6 +1,6 @@
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;;; ess-r-mode.el --- R customization -*- lexical-binding: t; -*-
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;; Copyright (C) 1997-2025 Free Software Foundation, Inc.
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;; Copyright (C) 1997-2026 Free Software Foundation, Inc.
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;; Author: A.J. Rossini
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;; Created: 12 Jun 1997
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;; Maintainer: ESS-core <ESS-core@r-project.org>
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@@ -299,14 +299,111 @@ When t, loading a file into a namespaced will output information
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about which objects are exported and which stay hidden in the
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namespace.")
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(defun ess-r-outline-level ()
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"R mode `outline-level` function."
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(defconst ess-r--outline-rstudio-regexp
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"^[ \t]*#+ +.*\\(?:----\\|====\\|####\\)\\s-*$"
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"R outline Regexp when `ess-r-outline-style' is `RStudio'.")
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(defconst ess-r--outline-org-like-regexp
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"^\\(?:> \\)?###\\s-+\\(\\*+\\)\\s-+.*$"
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"R outline regexp used when `ess-r-outline-style' is `Org-like'.")
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(defconst ess-r-outline-style-alist
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`((none
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(outline-regexp . "\\`a\\`")
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(outline-level . ,#'ess-r--outline-level-none))
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(RStudio
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(outline-regexp . ,ess-r--outline-rstudio-regexp)
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(outline-level . ,#'ess-r--outline-level-rstudio))
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(Org-like
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(outline-regexp . ,ess-r--outline-org-like-regexp)
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(outline-level . ,#'ess-r--outline-level-org-like)))
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"Mapping between outline styles and their regexp/level helpers.")
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(defun ess-r--outline-style-definition (&optional style)
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"Return the style definition for STYLE, defaulting to `ess-r-outline-style'."
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(let ((style (or style ess-r-outline-style)))
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(or (assq style ess-r-outline-style-alist)
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(error "Unknown ESS outline style: %s" style))))
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(defun ess-r--outline-style-value (key &optional style)
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"Return value for KEY in STYLE's definition."
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(cdr (assq key (cdr (ess-r--outline-style-definition style)))))
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(defun ess-r--outline-level-rstudio ()
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"Compute outline level for `RStudio` style headings."
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(save-excursion
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(beginning-of-line)
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(if (looking-at "^[ \t]*\\(#+\\)\\s-")
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(length (match-string 1))
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(length (match-string 1))
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1000)))
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(defun ess-r--outline-level-org-like ()
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"Compute outline level for `Org-like` style headings."
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(save-excursion
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(beginning-of-line)
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(if (looking-at "^\\(?:> \\)?###\\s-+\\(\\*+\\)\\s-+")
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(length (match-string 1))
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1000)))
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(defun ess-r--outline-level-none ()
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"Dummy outline level function for no outline support."
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1000)
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(defun ess-r-outline-level ()
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"R mode `outline-level` dispatcher for the current outline style."
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(funcall (ess-r--outline-style-value 'outline-level)))
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(defvar-local ess-r--saved-indent-with-fancy-comments nil
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"Saved state of `ess-indent-with-fancy-comments' before RStudio style.
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Stored as (VALUE . WAS-LOCAL) to restore both value and local binding.")
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(defun ess-r-set-outline-style (&optional style)
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"Apply STYLE (or `ess-r-outline-style') to the current buffer.
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When switching to RStudio style, `ess-indent-with-fancy-comments' is
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automatically set to nil locally. The previous value is saved and
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restored when switching to a different style."
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(interactive
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(list (intern (completing-read
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"Outline style"
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(mapcar (lambda (entry) (symbol-name (car entry)))
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ess-r-outline-style-alist)
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nil t nil nil
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(symbol-name (or ess-r-outline-style 'none))))))
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(let* ((style (or style ess-r-outline-style))
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(entry (ess-r--outline-style-definition style))
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(old-style ess-r-outline-style)
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(new-style (car entry)))
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;; Handle ess-indent-with-fancy-comments adjustment
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(cond
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;; Switching TO RStudio style
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((and (eq new-style 'RStudio)
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(not (eq old-style 'RStudio)))
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;; Save current value if not already saved
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(unless ess-r--saved-indent-with-fancy-comments
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(setq ess-r--saved-indent-with-fancy-comments
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(cons (if (local-variable-p 'ess-indent-with-fancy-comments)
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ess-indent-with-fancy-comments
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(default-value 'ess-indent-with-fancy-comments))
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(local-variable-p 'ess-indent-with-fancy-comments))))
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(setq-local ess-indent-with-fancy-comments nil))
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;; Switching FROM RStudio style to another
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((and (eq old-style 'RStudio)
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(not (eq new-style 'RStudio))
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ess-r--saved-indent-with-fancy-comments)
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;; Restore saved value and local state
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(let ((saved-value (car ess-r--saved-indent-with-fancy-comments))
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(saved-local (cdr ess-r--saved-indent-with-fancy-comments)))
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(if saved-local
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(setq-local ess-indent-with-fancy-comments saved-value)
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(when (local-variable-p 'ess-indent-with-fancy-comments)
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(kill-local-variable 'ess-indent-with-fancy-comments))))
|
||||
(setq ess-r--saved-indent-with-fancy-comments nil)))
|
||||
;; Apply outline style
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(setq-local ess-r-outline-style new-style)
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(setq-local outline-regexp (ess-r--outline-style-value 'outline-regexp style))
|
||||
(setq-local outline-level #'ess-r-outline-level)))
|
||||
|
||||
;; The syntax class for '\' is punctuation character to handle R 4.1
|
||||
;; lambdas. Inside strings it should be treated as an escape
|
||||
;; character which we ensure here.
|
||||
@@ -843,6 +940,8 @@ top level functions only."
|
||||
(setq-local electric-layout-rules '((?{ . after)))
|
||||
;; indentation
|
||||
(add-hook 'hack-local-variables-hook #'ess-set-style nil t)
|
||||
;; outline
|
||||
(add-hook 'hack-local-variables-hook #'ess-r-set-outline-style nil t)
|
||||
;; eldoc
|
||||
(ess--setup-eldoc #'ess-r-eldoc-function)
|
||||
;; auto-complete
|
||||
@@ -864,8 +963,7 @@ top level functions only."
|
||||
(when ess-imenu-use-S
|
||||
(imenu-add-to-menubar "Imenu-R"))
|
||||
;; outline
|
||||
(setq-local outline-level #'ess-r-outline-level)
|
||||
(setq-local outline-regexp ess-r-outline-regexp)
|
||||
(ess-r-set-outline-style)
|
||||
(setq-local beginning-of-defun-function #'ess-r-beginning-of-defun)
|
||||
(setq-local end-of-defun-function #'ess-r-end-of-defun)
|
||||
(ess-roxy-mode))
|
||||
|
||||
@@ -137,7 +137,7 @@ All Rd mode abbrevs start with a grave accent (`)."
|
||||
"dontshow" "donttest" "dots" "email" "emph" "enc" "env" "eqn" "figure" "file"
|
||||
"href"
|
||||
"ifelse" "if"
|
||||
"item" "kbd" "ldots" "linkS4class" "link" "method"
|
||||
"item" "kbd" "ldots" "linkS4class" "linkS4methods" "link" "method"
|
||||
"manual"
|
||||
"newcommand" "option" "out"
|
||||
"pkg" "sQuote" "renewcommand"
|
||||
|
||||
@@ -17,8 +17,8 @@
|
||||
;;
|
||||
;; Maintainer: ESS Core Team <ESS-core@r-project.org>
|
||||
;; Created: 7 Jan 1994
|
||||
;; Package-Version: 20251212.937
|
||||
;; Package-Revision: e39ca8fa7fce
|
||||
;; Package-Version: 20260322.1703
|
||||
;; Package-Revision: 4e112590d1c1
|
||||
;; URL: https://ess.r-project.org/
|
||||
;; Package-Requires: ((emacs "25.1"))
|
||||
;; ESSR-Version: 1.8
|
||||
|
||||
@@ -1,8 +1,8 @@
|
||||
This is ess.info, produced by makeinfo version 7.2 from ess.texi.
|
||||
This is ess.info, produced by makeinfo version 7.3 from ess.texi.
|
||||
|
||||
INFO-DIR-SECTION Emacs
|
||||
START-INFO-DIR-ENTRY
|
||||
* ESS: (ess). Emacs Speaks Statistics (R/S/S+, SAS, BUGS/JAGS and Stata).
|
||||
* ESS: (ess). Emacs Speaks Statistics (R/S/S+, SAS, BUGS/NIMBLE and Stata).
|
||||
END-INFO-DIR-ENTRY
|
||||
|
||||
ESS -- Emacs Speaks Statistics
|
||||
@@ -14,7 +14,7 @@ File: ess.info, Node: Top, Next: Introduction, Up: (dir)
|
||||
ESS: Emacs Speaks Statistics
|
||||
****************************
|
||||
|
||||
ESS version 25.01.0
|
||||
ESS version 26.01.0
|
||||
|
||||
by A.J. Rossini,
|
||||
R.M. Heiberger,
|
||||
@@ -30,7 +30,7 @@ ESS version 25.01.0
|
||||
|
||||
Emacs Speaks Statistics (ESS) provides an intelligent, consistent
|
||||
interface between the user and the software. ESS interfaces with
|
||||
R, SAS, S-PLUS, BUGS/JAGS and other statistical analysis packages
|
||||
R, SAS, S-PLUS, BUGS/NIMBLE and other statistical analysis packages
|
||||
on GNU/Linux, other Unix-like systems such as macOS, and Microsoft
|
||||
Windows. ESS is itself a package within the Emacs text editor and
|
||||
uses Emacs features to streamline the creation and use of
|
||||
@@ -66,7 +66,6 @@ the file COPYING in the same directory as this file for more details.
|
||||
* ESS for R:: Overview of ESS features for the S family
|
||||
* ESS for SAS::
|
||||
* ESS for BUGS::
|
||||
* ESS for JAGS::
|
||||
* Mailing lists/bug reports:: How to get assistance with ESS
|
||||
* Customization:: Customizing ESS
|
||||
* Indices::
|
||||
@@ -79,7 +78,7 @@ File: ess.info, Node: Introduction, Next: Installation, Prev: Top, Up: Top
|
||||
|
||||
ESS provides a generic interface, through Emacs, to statistical
|
||||
packages. It currently supports R (and the rest of the S family), SAS,
|
||||
BUGS/JAGS, Stata, and Julia with the level of support roughly in that
|
||||
BUGS/NIMBLE, Stata, and Julia with the level of support roughly in that
|
||||
order.
|
||||
|
||||
Throughout this manual, _Emacs_ refers to _GNU Emacs_ by the Free
|
||||
@@ -249,7 +248,14 @@ File: ess.info, Node: New features, Next: Credits, Prev: Features, Up: Intro
|
||||
1.2 New features in ESS
|
||||
=======================
|
||||
|
||||
Changes and New Features in 25.01.0:
|
||||
Changes and New Features in 26.01.0:
|
||||
• ESS[BUGS] is still relevant due to NIMBLE keeping the language
|
||||
alive. However, only syntax highlighting and key-presses will be
|
||||
supported moving forward. For example, the ‘<’ key now generates
|
||||
‘<-’ rather than the former ‘=’ since equals is a valid character
|
||||
in NIMBLE BUGS.
|
||||
|
||||
Changes and New Features in 25.01.0:
|
||||
|
||||
• polymode: In our transition from literate libraries (such as noweb
|
||||
documented below with respect to 19.04), we now recommend the
|
||||
@@ -3510,29 +3516,48 @@ File: ess.info, Node: Outline, Next: Toolbar, Prev: Imenu, Up: Extras
|
||||
R editing buffers integrate with ‘outline-minor-mode’. When you toggle
|
||||
the minor mode (for example via ‘M-x outline-minor-mode’ or by adding it
|
||||
to ‘ess-r-mode-hook’), ESS assigns ‘ess-r-outline-level’ to
|
||||
‘outline-level’ and installs ‘ess-r-outline-regexp’ so that comment
|
||||
headings drive folding. Lines that begin with one or more ‘#’, followed
|
||||
by text and a trailing marker of ‘----’, ‘====’, or ‘####’, are treated
|
||||
as outline headings. This matches the section markers convention
|
||||
adopted by RStudio.
|
||||
‘outline-level’ and configures ‘outline-regexp’ according to
|
||||
‘ess-r-outline-style’ so that comment headings drive folding. By
|
||||
default, outline support is disabled (‘none’), but you can enable it by
|
||||
setting ‘ess-r-outline-style’ to ‘RStudio’ or ‘Org-like’. With the
|
||||
‘RStudio’ style, lines that begin with one or more ‘#’, followed by text
|
||||
and a trailing marker of ‘----’, ‘====’, or ‘####’, are treated as
|
||||
outline headings. This matches the section markers convention adopted
|
||||
by RStudio.
|
||||
|
||||
# Setup ----
|
||||
## Data ----
|
||||
### Models ====
|
||||
#### Helpers ####
|
||||
|
||||
The number of leading ‘#’ characters sets the outline depth. Use
|
||||
standard Outline commands (such as ‘C-c C-t’) to cycle visibility once
|
||||
the minor mode is active. To enable Outlining automatically, add it to
|
||||
the R mode hook:
|
||||
The number of leading ‘#’ characters sets the outline depth. When
|
||||
using the RStudio outline style, ‘ess-indent-with-fancy-comments’ is
|
||||
automatically set to ‘nil’ locally in the buffer to prevent single-hash
|
||||
comments from being treated as right-margin comments with
|
||||
‘comment-column’ 40. When switching back to a different outline style,
|
||||
the original local binding is restored; if the variable was not
|
||||
buffer-local, the current global default applies.
|
||||
|
||||
Use standard Outline commands (such as ‘C-c C-t’) to cycle
|
||||
visibility once the minor mode is active. To enable Outlining
|
||||
automatically, add it to the R mode hook:
|
||||
|
||||
(add-hook 'ess-r-mode-hook #'outline-minor-mode)
|
||||
|
||||
-- User Option: ess-r-outline-regexp
|
||||
Regular expression used by ESS to recognise outline headings in R
|
||||
buffers. The default matches the RStudio-style sections shown
|
||||
above, but you can customise it if you prefer a different comment
|
||||
convention.
|
||||
-- User Option: ess-r-outline-style
|
||||
Select which outline convention ‘ess-r-mode’ should use. The
|
||||
default ‘none’ disables outline support to preserve backward
|
||||
compatibility. Set to ‘RStudio’ to recognise the comment rulers
|
||||
shown above, or choose ‘Org-like’ to match the ‘### * Section’
|
||||
pattern, inspired from org-mode:
|
||||
|
||||
### * Setup
|
||||
### ** Data
|
||||
### *** Models
|
||||
### **** Helpers
|
||||
|
||||
You can switch styles via ‘M-x ess-r-set-outline-style’ or by
|
||||
customizing this option.
|
||||
|
||||
|
||||
File: ess.info, Node: Toolbar, Next: Xref, Prev: Outline, Up: Extras
|
||||
@@ -3662,48 +3687,6 @@ polymode <https://github.com/polymode/poly-R/>,
|
||||
<https://polymode.github.io/>, or markdown-mode with edit-indirect
|
||||
<https://jblevins.org/projects/markdown-mode>.
|
||||
|
||||
ESS provides support for writing and processing Sweave
|
||||
(<https://leisch.userweb.mwn.de/Sweave/>), building up on Emacs'
|
||||
ess-noweb-mode for literate programming. When working on an Sweave
|
||||
document, the following key bindings are available:
|
||||
|
||||
-- Command: ess-swv-weave CHOOSE
|
||||
‘M-n s’ Run Sweave on the current .Rnw file. If CHOOSE is
|
||||
non-‘nil’, offer a menu of available weavers.
|
||||
|
||||
-- Command: ess-swv-latex
|
||||
‘M-n l’ Run LaTeX after Sweave'ing.
|
||||
|
||||
-- Command: ess-swv-PS
|
||||
‘M-n p’ Generate and display a postscript file after LaTeX'ing.
|
||||
|
||||
-- Command: ess-swv-PDF PDFLATEX-CMD
|
||||
‘M-n P’ Generate and display a PDF file after LaTeX'ing. Optional
|
||||
argument PDFLATEX-CMD is the command to use, which by default, is
|
||||
the command used to generate the PDF file is the first element of
|
||||
‘ess-swv-pdflatex-commands’.
|
||||
|
||||
-- User Option: ess-swv-pdflatex-commands
|
||||
Commands used by ‘ess-swv-PDF’ to run a version of pdflatex; the
|
||||
first entry is the default command.
|
||||
|
||||
Sweave'ing with ‘ess-swv-weave’ starts an inferior-ESS process, if
|
||||
one is not available. Other commands are available from the ‘Sweaving,
|
||||
Tangling, ...’ submenu of the Noweb menu.
|
||||
|
||||
AUCTeX (<https://www.gnu.org/software/auctex>) users may prefer to
|
||||
set the variable ‘ess-swv-plug-into-AUCTeX-p’ (available from the "ESS
|
||||
Sweave" customization group) to t. Alternatively, the same can be
|
||||
achieved by activating the entry "AUCTeX Interface" from the ‘Sweaving,
|
||||
Tangling, ...’ submenu, which toggles this variable on or off. When the
|
||||
interface is activated, new entries for Sweave'ing and LaTeX'ing
|
||||
thereafter are available from AUCTeX's "Command" menu. Sweave'ing can,
|
||||
thus, be done by ‘C-c C-c Sweave RET’ without an inferior-ESS process.
|
||||
Similarly, LaTeX'ing can be done by ‘C-c C-c LaTeXSweave RET’. In both
|
||||
cases, the process can be monitored with ‘C-c C-l’
|
||||
(‘TeX-recenter-output-buffer’). Open the viewer with ‘C-c C-v’
|
||||
(‘TeX-view’), as usual in AUCTeX.
|
||||
|
||||
|
||||
File: ess.info, Node: ESS for R, Next: ESS for SAS, Prev: Extras, Up: Top
|
||||
|
||||
@@ -4403,120 +4386,26 @@ File: ess.info, Node: ESS(SAS)--Windows, Prev: ESS(SAS)--Graphics, Up: ESS fo
|
||||
'submit-region' or paste them into SAS Display Manager.
|
||||
|
||||
|
||||
File: ess.info, Node: ESS for BUGS, Next: ESS for JAGS, Prev: ESS for SAS, Up: Top
|
||||
File: ess.info, Node: ESS for BUGS, Next: Mailing lists/bug reports, Prev: ESS for SAS, Up: Top
|
||||
|
||||
14 ESS for BUGS
|
||||
***************
|
||||
|
||||
ESS[BUGS] provides 5 features. First, BUGS syntax is described to allow
|
||||
for proper fontification of statements, distributions, functions,
|
||||
commands and comments in BUGS model files, command files and log files.
|
||||
Second, ESS creates templates for the command file from the model file
|
||||
so that a BUGS batch process can be defined by a single file. Third,
|
||||
ESS provides a BUGS batch script that allows ESS to set BUGS batch
|
||||
parameters. Fourth, key sequences are defined to create a command file
|
||||
and submit a BUGS batch process. Lastly, interactive submission of BUGS
|
||||
commands is also supported.
|
||||
ESS[BUGS] NIMBLE has re-vitalized the BUGS language. All previous
|
||||
instances of BUGS such as OpenBUGS and JAGS are now deprecated.
|
||||
Therefore, ESS suppors BUGS syntax to allow for proper fontification of
|
||||
statements, distributions, functions, commands and comments in
|
||||
BUGS/NIMBLE model files.
|
||||
|
||||
14.1 ESS[BUGS]-Model files
|
||||
==========================
|
||||
|
||||
Model files with the ‘.bug’ extension are edited in ESS[BUGS] mode.
|
||||
Three keys are bound for your use in ESS[BUGS], ‘F2’, ‘C-c C-c’ and ‘=’.
|
||||
‘F2’ performs the same action as it does in ESS[SAS], *Note
|
||||
ESS(SAS)--Function keys for batch processing::. ‘C-c C-c’ performs the
|
||||
function ‘ess-bugs-next-action’ which you will use a lot. Pressing it
|
||||
in an empty buffer for a model file will produce a template for you.
|
||||
‘=’ inserts the set operator, ‘<-’.
|
||||
|
||||
14.2 ESS[BUGS]-Command files
|
||||
============================
|
||||
|
||||
Files ending in ‘.bmd’ are used for BUGS command files. When you have
|
||||
finished editing your model file and press ‘C-c C-c’, a command file is
|
||||
created if one does not already exist. When you are finished editing
|
||||
your command file, pressing ‘C-c C-c’ again will submit your command
|
||||
file as a batch job.
|
||||
|
||||
14.3 ESS[BUGS]-Log files
|
||||
========================
|
||||
|
||||
The ‘.bog’ extension is used for BUGS log files. The command line
|
||||
generated by ESS creates the ‘.bog’ transcript file.
|
||||
|
||||
|
||||
File: ess.info, Node: ESS for JAGS, Next: Mailing lists/bug reports, Prev: ESS for BUGS, Up: Top
|
||||
File: ess.info, Node: Mailing lists/bug reports, Next: Customization, Prev: ESS for BUGS, Up: Top
|
||||
|
||||
15 ESS for JAGS
|
||||
***************
|
||||
|
||||
ESS[JAGS] provides 4 features. First, JAGS syntax is described to allow
|
||||
for proper fontification of statements, distributions, functions,
|
||||
commands and comments in JAGS model files, command files and log files.
|
||||
Second, ESS creates templates for the command file from the model file
|
||||
so that a JAGS batch process can be defined by a single file. Third,
|
||||
ESS provides a JAGS batch script that allows ESS to set JAGS batch
|
||||
parameters. Fourth, key sequences are defined to create a command file
|
||||
and submit a JAGS batch process.
|
||||
|
||||
15.1 ESS[JAGS]-Model files
|
||||
==========================
|
||||
|
||||
Files with the ‘.jag’ extension are edited in ESS[JAGS] mode. Three
|
||||
keys are bound for your use in ESS[JAGS], ‘F2’, ‘C-c C-c’ and ‘=’. ‘F2’
|
||||
performs the same action as it does in ESS[SAS], *Note
|
||||
ESS(SAS)--Function keys for batch processing::. ‘C-c C-c’ performs the
|
||||
function ‘ess-bugs-next-action’ which you will use a lot. Pressing it
|
||||
in an empty buffer for a model file will produce a template for you.
|
||||
‘=’ inserts the set operator, ‘<-’.
|
||||
|
||||
The first press of ‘C-c C-c’ will set up a template, including some
|
||||
necessary file-local variables in an empty buffer. These variables are
|
||||
‘ess-jags-chains’, ‘ess-jags-monitor’, ‘ess-jags-thin’,
|
||||
‘ess-jags-burnin’ and ‘ess-jags-update’; they appear in the ‘Local
|
||||
Variables’ section. When you are finished editing your model file,
|
||||
pressing ‘C-c C-c’ will perform the necessary actions to build your
|
||||
command file for you.
|
||||
|
||||
The ‘ess-jags-chains’ variable is the number of chains that you want
|
||||
to initialize and sample from; defaults to 1. The ‘ess-jags-monitor’
|
||||
variable is a list of variables that you want monitored: encase each
|
||||
variable in double quotes. When you press ‘C-c C-c’, the appropriate
|
||||
statements are created in the command file to monitor the list of
|
||||
variables. By default, no variables are explicitly monitored which
|
||||
means JAGS will implicitly monitor all "default" variables. The
|
||||
‘ess-jags-thin’ variable is the thinning parameter. By default, the
|
||||
thinning parameter is set to 1, i.e. no thinning. The
|
||||
‘ess-jags-burnin’ variable is the number of initial samples to discard.
|
||||
By default, the burnin parameter is set to 10000. The ‘ess-jags-update’
|
||||
variable is the number of post-burnin samples to keep. By default, the
|
||||
update parameter is set to 10000. Both ‘ess-jags-burnin’ and
|
||||
‘ess-jags-update’ are multiplied by ‘ess-jags-thin’ since JAGS does not
|
||||
do it automatically.
|
||||
|
||||
15.2 ESS[JAGS]-Command files
|
||||
============================
|
||||
|
||||
Files ending in ‘.jmd’ are for JAGS command files. For your ‘.jmd’
|
||||
file, there is only one variable, ‘ess-jags-command’, in the ‘Local
|
||||
Variables’ section. When you have finished editing your model file and
|
||||
press ‘C-c C-c’, a command file is created if one does not already
|
||||
exist. When you are finished editing your command file, pressing ‘C-c
|
||||
C-c’ again will submit your command file as a batch job. The
|
||||
‘ess-jags-command’ variable allows you to specify a different JAGS
|
||||
program to use to run your model; defaults to "jags".
|
||||
|
||||
15.3 ESS[JAGS]-Log files
|
||||
========================
|
||||
|
||||
The ‘.jog’ extension is used for JAGS log files. You may find ‘F2’
|
||||
useful to refresh the ‘.jog’ if the batch process over-writes or appends
|
||||
it.
|
||||
|
||||
|
||||
File: ess.info, Node: Mailing lists/bug reports, Next: Customization, Prev: ESS for JAGS, Up: Top
|
||||
|
||||
16 Bugs and Bug Reporting, Mailing Lists
|
||||
15 Bugs and Bug Reporting, Mailing Lists
|
||||
****************************************
|
||||
|
||||
* Menu:
|
||||
@@ -4529,7 +4418,7 @@ File: ess.info, Node: Mailing lists/bug reports, Next: Customization, Prev: E
|
||||
|
||||
File: ess.info, Node: Bugs, Next: Reporting Bugs, Up: Mailing lists/bug reports
|
||||
|
||||
16.1 Bugs
|
||||
15.1 Bugs
|
||||
=========
|
||||
|
||||
• Commands like ‘ess-display-help-on-object’ and list completion
|
||||
@@ -4569,7 +4458,7 @@ File: ess.info, Node: Bugs, Next: Reporting Bugs, Up: Mailing lists/bug repor
|
||||
|
||||
File: ess.info, Node: Reporting Bugs, Next: Mailing Lists, Prev: Bugs, Up: Mailing lists/bug reports
|
||||
|
||||
16.2 Reporting Bugs
|
||||
15.2 Reporting Bugs
|
||||
===================
|
||||
|
||||
Please post bug reports, suggestions etc. on our github issue tracker
|
||||
@@ -4594,7 +4483,7 @@ donations are also more than welcome.
|
||||
|
||||
File: ess.info, Node: Mailing Lists, Next: Help with Emacs, Prev: Reporting Bugs, Up: Mailing lists/bug reports
|
||||
|
||||
16.3 Mailing Lists
|
||||
15.3 Mailing Lists
|
||||
==================
|
||||
|
||||
There is a mailing list for discussions and announcements relating to
|
||||
@@ -4614,7 +4503,7 @@ this is a fairly low-volume mailing list.
|
||||
|
||||
File: ess.info, Node: Help with Emacs, Prev: Mailing Lists, Up: Mailing lists/bug reports
|
||||
|
||||
16.4 Help with Emacs
|
||||
15.4 Help with Emacs
|
||||
====================
|
||||
|
||||
Emacs is a complex editor with many abilities that we do not have space
|
||||
@@ -4726,9 +4615,6 @@ Key index
|
||||
* M-;: Indenting. (line 65)
|
||||
* M-?: Object names. (line 33)
|
||||
* M-C-q: Indenting. (line 49)
|
||||
* M-n l: Sweave and AUCTeX. (line 24)
|
||||
* M-n P: Sweave and AUCTeX. (line 30)
|
||||
* M-n s: Sweave and AUCTeX. (line 20)
|
||||
* M-RET: Resubmit. (line 10)
|
||||
* RET: Command-line editing. (line 10)
|
||||
* RET <1>: Resubmit. (line 18)
|
||||
@@ -4770,7 +4656,7 @@ Function and program index
|
||||
* dump(): Edit buffer. (line 35)
|
||||
* ess-change-directory: Package listing. (line 29)
|
||||
* ess-cleanup: Hot keys. (line 71)
|
||||
* ess-cleanup <1>: Help. (line 170)
|
||||
* ess-cleanup <1>: Help. (line 169)
|
||||
* ess-complete-object-name: Object names. (line 32)
|
||||
* ess-describe-help-mode: Help. (line 21)
|
||||
* ess-display-help-on-object: Hot keys. (line 65)
|
||||
@@ -4810,7 +4696,7 @@ Function and program index
|
||||
* ess-parse-errors: Hot keys. (line 54)
|
||||
* ess-parse-errors <1>: Error Checking. (line 9)
|
||||
* ess-quit: Hot keys. (line 70)
|
||||
* ess-quit <1>: Help. (line 170)
|
||||
* ess-quit <1>: Help. (line 169)
|
||||
* ess-R-complete-object-name: roxygen2. (line 80)
|
||||
* ess-r-outline-level: Outline. (line 6)
|
||||
* ess-r-package-list-available-packages: Package listing. (line 12)
|
||||
@@ -4843,10 +4729,6 @@ Function and program index
|
||||
* ess-submit-bug-report: Reporting Bugs. (line 6)
|
||||
* ess-switch-to-end-of-ESS: Help. (line 117)
|
||||
* ess-switch-to-inferior-or-script-buffer: Other. (line 12)
|
||||
* ess-swv-latex: Sweave and AUCTeX. (line 23)
|
||||
* ess-swv-PDF: Sweave and AUCTeX. (line 29)
|
||||
* ess-swv-PS: Sweave and AUCTeX. (line 26)
|
||||
* ess-swv-weave: Sweave and AUCTeX. (line 19)
|
||||
* ess-tracebug: ESS tracebug. (line 6)
|
||||
* ess-transcript-clean-region: Clean. (line 10)
|
||||
* ess-transcript-copy-command: Resubmit. (line 13)
|
||||
@@ -4913,14 +4795,13 @@ Variable index
|
||||
* ess-r-flymake-linters: ESS Flymake. (line 16)
|
||||
* ess-r-flymake-lintr-cache: ESS Flymake. (line 23)
|
||||
* ess-R-font-lock-keywords: Highlighting. (line 19)
|
||||
* ess-r-outline-regexp: Outline. (line 6)
|
||||
* ess-r-outline-regexp <1>: Outline. (line 27)
|
||||
* ess-r-outline-style: Outline. (line 6)
|
||||
* ess-r-outline-style <1>: Outline. (line 37)
|
||||
* ess-search-list: Source Directories. (line 62)
|
||||
* ess-source-directory: Source Directories. (line 22)
|
||||
* ess-style: Styles. (line 21)
|
||||
* ess-style-alist: Styles. (line 28)
|
||||
* ess-switch-to-end-of-proc-buffer: Other. (line 21)
|
||||
* ess-swv-pdflatex-commands: Sweave and AUCTeX. (line 35)
|
||||
* ess-use-eldoc: ESS ElDoc. (line 13)
|
||||
* ess-use-flymake: ESS Flymake. (line 12)
|
||||
* iESS program arguments: Customizing startup. (line 48)
|
||||
@@ -5091,111 +4972,110 @@ Concept Index
|
||||
|
||||
|
||||
Tag Table:
|
||||
Node: Top268
|
||||
Node: Introduction2906
|
||||
Node: Features5692
|
||||
Node: Current Features6518
|
||||
Node: New features10065
|
||||
Node: Credits37885
|
||||
Node: Manual41544
|
||||
Node: Installation44254
|
||||
Node: Installing from a third-party repository45191
|
||||
Node: Installing from source46138
|
||||
Node: Activating and Loading ESS47762
|
||||
Node: Check Installation48844
|
||||
Node: Interactive ESS49068
|
||||
Node: Starting up49913
|
||||
Node: Multiple ESS processes50673
|
||||
Node: ESS processes on Remote Computers51786
|
||||
Node: Customizing startup56013
|
||||
Node: Controlling buffer display58995
|
||||
Node: Entering commands61632
|
||||
Node: Command-line editing62794
|
||||
Node: Transcript64059
|
||||
Node: Last command65856
|
||||
Node: Process buffer motion67314
|
||||
Node: Transcript resubmit68857
|
||||
Node: Saving transcripts70854
|
||||
Node: Command History72688
|
||||
Node: Saving History76189
|
||||
Node: History expansion76970
|
||||
Node: Hot keys80361
|
||||
Node: Statistical Process running in ESS?84531
|
||||
Node: Emacsclient85878
|
||||
Node: Other86698
|
||||
Node: Evaluating code87741
|
||||
Node: Transcript Mode91673
|
||||
Node: Resubmit92846
|
||||
Node: Clean93921
|
||||
Node: Editing objects94921
|
||||
Node: Edit buffer96039
|
||||
Node: Loading98129
|
||||
Node: Error Checking99184
|
||||
Node: Indenting100257
|
||||
Node: Styles103409
|
||||
Node: Other edit buffer commands105911
|
||||
Node: Source Files107623
|
||||
Node: Source Directories112339
|
||||
Node: Help115548
|
||||
Node: Completion120250
|
||||
Node: Object names120465
|
||||
Node: Function arguments123179
|
||||
Node: Minibuffer completion124158
|
||||
Node: Company124656
|
||||
Node: Icicles125055
|
||||
Node: Developing with ESS126431
|
||||
Node: ESS tracebug126877
|
||||
Node: Getting started with tracebug129934
|
||||
Node: Editing documentation132220
|
||||
Node: R documentation files132772
|
||||
Node: roxygen2136587
|
||||
Node: Namespaced Evaluation141110
|
||||
Node: Extras143124
|
||||
Node: ESS ElDoc144216
|
||||
Node: ESS Flymake145796
|
||||
Node: Handy commands146926
|
||||
Node: Highlighting148203
|
||||
Node: Parens149254
|
||||
Node: Graphics149730
|
||||
Node: printer150401
|
||||
Node: X11151173
|
||||
Node: winjava151512
|
||||
Node: Imenu151924
|
||||
Node: Outline152779
|
||||
Node: Toolbar154091
|
||||
Node: Xref154501
|
||||
Node: Rdired154831
|
||||
Node: Package listing155910
|
||||
Node: Org157358
|
||||
Node: Sweave and AUCTeX158312
|
||||
Node: ESS for R160944
|
||||
Node: ESS(R)--Editing files161244
|
||||
Node: iESS(R)--Inferior ESS processes161749
|
||||
Node: Philosophies for using ESS(R)164468
|
||||
Node: Example ESS usage165395
|
||||
Node: ESS for SAS166799
|
||||
Node: ESS(SAS)--Design philosophy167526
|
||||
Node: ESS(SAS)--Editing files168463
|
||||
Node: ESS(SAS)--TAB key170407
|
||||
Node: ESS(SAS)--Batch SAS processes171821
|
||||
Node: ESS(SAS)--Function keys for batch processing177041
|
||||
Node: iESS(SAS)--Interactive SAS processes186948
|
||||
Node: iESS(SAS)--Common problems190890
|
||||
Node: ESS(SAS)--Graphics192504
|
||||
Node: ESS(SAS)--Windows193303
|
||||
Node: ESS for BUGS193887
|
||||
Node: ESS for JAGS195699
|
||||
Node: Mailing lists/bug reports199195
|
||||
Node: Bugs199459
|
||||
Node: Reporting Bugs201135
|
||||
Node: Mailing Lists202054
|
||||
Node: Help with Emacs202792
|
||||
Node: Customization203328
|
||||
Node: Indices204106
|
||||
Node: Key index204281
|
||||
Node: Function and program index209413
|
||||
Node: Variable index218979
|
||||
Node: Concept index222686
|
||||
Node: Top270
|
||||
Node: Introduction2893
|
||||
Node: Features5681
|
||||
Node: Current Features6507
|
||||
Node: New features10054
|
||||
Node: Credits38231
|
||||
Node: Manual41890
|
||||
Node: Installation44600
|
||||
Node: Installing from a third-party repository45537
|
||||
Node: Installing from source46484
|
||||
Node: Activating and Loading ESS48108
|
||||
Node: Check Installation49190
|
||||
Node: Interactive ESS49414
|
||||
Node: Starting up50259
|
||||
Node: Multiple ESS processes51019
|
||||
Node: ESS processes on Remote Computers52132
|
||||
Node: Customizing startup56359
|
||||
Node: Controlling buffer display59341
|
||||
Node: Entering commands61978
|
||||
Node: Command-line editing63140
|
||||
Node: Transcript64405
|
||||
Node: Last command66202
|
||||
Node: Process buffer motion67660
|
||||
Node: Transcript resubmit69203
|
||||
Node: Saving transcripts71200
|
||||
Node: Command History73034
|
||||
Node: Saving History76535
|
||||
Node: History expansion77316
|
||||
Node: Hot keys80707
|
||||
Node: Statistical Process running in ESS?84877
|
||||
Node: Emacsclient86224
|
||||
Node: Other87044
|
||||
Node: Evaluating code88087
|
||||
Node: Transcript Mode92019
|
||||
Node: Resubmit93192
|
||||
Node: Clean94267
|
||||
Node: Editing objects95267
|
||||
Node: Edit buffer96385
|
||||
Node: Loading98475
|
||||
Node: Error Checking99530
|
||||
Node: Indenting100603
|
||||
Node: Styles103755
|
||||
Node: Other edit buffer commands106257
|
||||
Node: Source Files107969
|
||||
Node: Source Directories112685
|
||||
Node: Help115894
|
||||
Node: Completion120596
|
||||
Node: Object names120811
|
||||
Node: Function arguments123525
|
||||
Node: Minibuffer completion124504
|
||||
Node: Company125002
|
||||
Node: Icicles125401
|
||||
Node: Developing with ESS126777
|
||||
Node: ESS tracebug127223
|
||||
Node: Getting started with tracebug130280
|
||||
Node: Editing documentation132566
|
||||
Node: R documentation files133118
|
||||
Node: roxygen2136933
|
||||
Node: Namespaced Evaluation141456
|
||||
Node: Extras143470
|
||||
Node: ESS ElDoc144562
|
||||
Node: ESS Flymake146142
|
||||
Node: Handy commands147272
|
||||
Node: Highlighting148549
|
||||
Node: Parens149600
|
||||
Node: Graphics150076
|
||||
Node: printer150747
|
||||
Node: X11151519
|
||||
Node: winjava151858
|
||||
Node: Imenu152270
|
||||
Node: Outline153125
|
||||
Node: Toolbar155358
|
||||
Node: Xref155768
|
||||
Node: Rdired156098
|
||||
Node: Package listing157177
|
||||
Node: Org158625
|
||||
Node: Sweave and AUCTeX159579
|
||||
Node: ESS for R160176
|
||||
Node: ESS(R)--Editing files160476
|
||||
Node: iESS(R)--Inferior ESS processes160981
|
||||
Node: Philosophies for using ESS(R)163700
|
||||
Node: Example ESS usage164627
|
||||
Node: ESS for SAS166031
|
||||
Node: ESS(SAS)--Design philosophy166758
|
||||
Node: ESS(SAS)--Editing files167695
|
||||
Node: ESS(SAS)--TAB key169639
|
||||
Node: ESS(SAS)--Batch SAS processes171053
|
||||
Node: ESS(SAS)--Function keys for batch processing176273
|
||||
Node: iESS(SAS)--Interactive SAS processes186180
|
||||
Node: iESS(SAS)--Common problems190122
|
||||
Node: ESS(SAS)--Graphics191736
|
||||
Node: ESS(SAS)--Windows192535
|
||||
Node: ESS for BUGS193119
|
||||
Node: Mailing lists/bug reports193675
|
||||
Node: Bugs193939
|
||||
Node: Reporting Bugs195615
|
||||
Node: Mailing Lists196534
|
||||
Node: Help with Emacs197272
|
||||
Node: Customization197808
|
||||
Node: Indices198586
|
||||
Node: Key index198761
|
||||
Node: Function and program index203674
|
||||
Node: Variable index212948
|
||||
Node: Concept index216582
|
||||
|
||||
End Tag Table
|
||||
|
||||
|
||||
Reference in New Issue
Block a user