From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rainer M Krug Subject: Re: Bug: can not evaluate any code blocks after enabling additional languages [8.3.4 (release_8.3.4-639-gd5a603 @ /Users/rainerkrug/.emacs.d/elpa/25.0/org-20151005/)] Date: Thu, 10 Mar 2016 21:55:40 +0100 Message-ID: References: <87r3fio5gw.fsf@nicolasgoaziou.fr> <8737rywehj.fsf@kyleam.com> Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:41398) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ae7ct-0007ry-Q0 for emacs-orgmode@gnu.org; Thu, 10 Mar 2016 15:56:19 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ae7ch-00080F-So for emacs-orgmode@gnu.org; Thu, 10 Mar 2016 15:56:07 -0500 Received: from mail-wm0-f43.google.com ([74.125.82.43]:37475) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ae7ch-0007zr-81 for emacs-orgmode@gnu.org; Thu, 10 Mar 2016 15:55:55 -0500 Received: by mail-wm0-f43.google.com with SMTP id p65so3529055wmp.0 for ; Thu, 10 Mar 2016 12:55:54 -0800 (PST) In-Reply-To: <8737rywehj.fsf@kyleam.com> (Kyle Meyer's message of "Thu, 10 Mar 2016 10:15:52 -0500") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Kyle Meyer Cc: emacs-orgmode@gnu.org --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Kyle Meyer writes: > Rainer M Krug writes: > >> Nicolas Goaziou writes: >> >>> Hello, >>> >>> Rainer M Krug writes: >>> >>>> Debugger entered--Lisp error: (void-function org-babel-get-header) >>> >>> This looks like a mixed installation. This function was removed in >>> development version and code base doesn't use it anymore. >> >> I don't think so - I use org from git uncompiled and, as you can see int >> the init.el, initialize it (require 'org) before calling (package-initia= lize). >> >> For some unknown reasons, the function >> org-babel-execute-src-block(nil) (in the org-git directory) calls >> org-babel-execute:sh in the installation directory of emacs. >> >> So wy is this the case? I see that the file ob.sh.el seems to be renamed >> in ob-shell.el - is this the case? Do I have to change the language sh >> to shell? > > This has been reported on the list a few times. See > http://thread.gmane.org/gmane.emacs.orgmode/102877/focus=3D102882. OK - thanks. This is solved now. But now I am stuck with the following, where again, org-element-cache-reset is in the emacs packed org-mode, while orgmode() is in the git version, and the changed org-set-local() causes an error. Any suggestions? ,---- | Debugger entered--Lisp error: (void-function org-set-local) | org-set-local(org-element--cache [cl-struct-avl-tree- [nil nil nil 0] o= rg-element--cache-compare]) | org-element-cache-reset() | (let ((delay-mode-hooks t)) (outline-mode) (setq major-mode (quote org-= mode)) (setq mode-name "Org") (progn (if (get (quote outline-mode) (quote m= ode-class)) (put (quote org-mode) (quote mode-class) (get (quote outline-mo= de) (quote mode-class)))) (if (keymap-parent org-mode-map) nil (set-keymap-= parent org-mode-map (current-local-map))) (let ((parent (char-table-parent = org-mode-syntax-table))) (if (and parent (not (eq parent (standard-syntax-t= able)))) nil (set-char-table-parent org-mode-syntax-table (syntax-table))))= (if (or (abbrev-table-get org-mode-abbrev-table :parents) (eq org-mode-abb= rev-table local-abbrev-table)) nil (abbrev-table-put org-mode-abbrev-table = :parents (list local-abbrev-table)))) (use-local-map org-mode-map) (set-syn= tax-table org-mode-syntax-table) (setq local-abbrev-table org-mode-abbrev-t= able) (if (featurep (quote xemacs)) (if (boundp (quote outline-mode-menu-he= ading)) (progn (easy-menu-remove outline-mode-menu-heading) (easy-menu-remo= ve outline-mode-menu-show) (easy-menu-remove outline-mode-menu-hide))) (def= ine-key org-mode-map [menu-bar headings] (quote undefined)) (define-key org= -mode-map [menu-bar hide] (quote undefined)) (define-key org-mode-map [menu= -bar show] (quote undefined))) (org-load-modules-maybe) (if (featurep (quot= e xemacs)) (progn (easy-menu-add org-org-menu) (easy-menu-add org-tbl-menu)= )) (org-install-agenda-files-menu) (if org-descriptive-links (progn (add-to= -invisibility-spec (quote (org-link))))) (add-to-invisibility-spec (quote (= org-cwidth))) (add-to-invisibility-spec (quote (org-hide-block . t))) (if (= featurep (quote xemacs)) (progn (set (make-local-variable (quote line-move-= ignore-invisible)) t))) (set (make-local-variable (quote outline-regexp)) o= rg-outline-regexp) (set (make-local-variable (quote outline-level)) (quote = org-outline-level)) (setq bidi-paragraph-direction (quote left-to-right)) (= if (and org-ellipsis (fboundp (quote set-display-table-slot)) (boundp (quot= e buffer-display-table)) (fboundp (quote make-glyph-code))) (progn (if org-= display-table nil (setq org-display-table (make-display-table))) (set-displ= ay-table-slot org-display-table 4 (vconcat (mapcar (function (lambda ... ..= .)) (if (stringp org-ellipsis) org-ellipsis "...")))) (setq buffer-display-= table org-display-table))) (org-set-regexps-and-options) (org-set-font-lock= -defaults) (if (and org-tag-faces (not org-tags-special-faces-re)) (progn (= org-set-tag-faces (quote org-tag-faces) org-tag-faces))) (set (make-local-v= ariable (quote calc-embedded-open-mode)) "# ") (modify-syntax-entry 64 "w")= (modify-syntax-entry 34 "\"") (modify-syntax-entry 92 "_") (modify-syntax-= entry 126 "_") (set (make-local-variable (quote font-lock-unfontify-region-= function)) (quote org-unfontify-region)) (set (make-local-variable (quote o= rg-table-may-need-update)) t) (org-add-hook (quote before-change-functions)= (quote org-before-change-function) nil (quote local)) (org-add-hook (quote= kill-buffer-hook) (quote org-check-running-clock) nil (quote local)) (org-= macro-initialize-templates) (org-update-radio-target-regexp) (set (make-loc= al-variable (quote indent-line-function)) (quote org-indent-line)) (set (ma= ke-local-variable (quote indent-region-function)) (quote org-indent-region)= ) (org-setup-filling) (org-setup-comments-handling) (org-element-cache-rese= t) (set (make-local-variable (quote beginning-of-defun-function)) (quote or= g-backward-element)) (set (make-local-variable (quote end-of-defun-function= )) (function (lambda nil (if (not (org-at-heading-p)) (org-forward-element)= (org-forward-element) (forward-char -1))))) (set (make-local-variable (quo= te next-error-function)) (quote org-occur-next-match)) (if org-enforce-todo= -dependencies (add-hook (quote org-blocker-hook) (quote org-block-todo-from= -children-or-siblings-or-parent)) (remove-hook (quote org-blocker-hook) (qu= ote org-block-todo-from-children-or-siblings-or-parent))) (if org-enforce-t= odo-checkbox-dependencies (add-hook (quote org-blocker-hook) (quote org-blo= ck-todo-from-checkboxes)) (remove-hook (quote org-blocker-hook) (quote org-= block-todo-from-checkboxes))) (set (make-local-variable (quote align-mode-r= ules-list)) (quote ((org-in-buffer-settings (regexp . "^[ ]*#\\+[A-Z_]+:\\= (\\s-*\\)\\S-+") (modes quote (org-mode)))))) (set (make-local-variable (qu= ote imenu-create-index-function)) (quote org-imenu-get-tree)) (set (make-lo= cal-variable (quote outline-isearch-open-invisible-function)) (function (la= mbda (&rest _) (org-show-context (quote isearch))))) (set (make-local-varia= ble (quote pcomplete-command-completion-function)) (quote org-pcomplete-ini= tial)) (set (make-local-variable (quote pcomplete-command-name-function)) (= quote org-command-at-point)) ...) | (progn (make-local-variable (quote delay-mode-hooks)) (let ((delay-mode= -hooks t)) (outline-mode) (setq major-mode (quote org-mode)) (setq mode-nam= e "Org") (progn (if (get (quote outline-mode) (quote mode-class)) (put (quo= te org-mode) (quote mode-class) (get (quote outline-mode) (quote mode-class= )))) (if (keymap-parent org-mode-map) nil (set-keymap-parent org-mode-map (= current-local-map))) (let ((parent (char-table-parent org-mode-syntax-table= ))) (if (and parent (not (eq parent ...))) nil (set-char-table-parent org-m= ode-syntax-table (syntax-table)))) (if (or (abbrev-table-get org-mode-abbre= v-table :parents) (eq org-mode-abbrev-table local-abbrev-table)) nil (abbre= v-table-put org-mode-abbrev-table :parents (list local-abbrev-table)))) (us= e-local-map org-mode-map) (set-syntax-table org-mode-syntax-table) (setq lo= cal-abbrev-table org-mode-abbrev-table) (if (featurep (quote xemacs)) (if (= boundp (quote outline-mode-menu-heading)) (progn (easy-menu-remove outline-= mode-menu-heading) (easy-menu-remove outline-mode-menu-show) (easy-menu-rem= ove outline-mode-menu-hide))) (define-key org-mode-map [menu-bar headings] = (quote undefined)) (define-key org-mode-map [menu-bar hide] (quote undefine= d)) (define-key org-mode-map [menu-bar show] (quote undefined))) (org-load-= modules-maybe) (if (featurep (quote xemacs)) (progn (easy-menu-add org-org-= menu) (easy-menu-add org-tbl-menu))) (org-install-agenda-files-menu) (if or= g-descriptive-links (progn (add-to-invisibility-spec (quote (org-link))))) = (add-to-invisibility-spec (quote (org-cwidth))) (add-to-invisibility-spec (= quote (org-hide-block . t))) (if (featurep (quote xemacs)) (progn (set (mak= e-local-variable (quote line-move-ignore-invisible)) t))) (set (make-local-= variable (quote outline-regexp)) org-outline-regexp) (set (make-local-varia= ble (quote outline-level)) (quote org-outline-level)) (setq bidi-paragraph-= direction (quote left-to-right)) (if (and org-ellipsis (fboundp (quote set-= display-table-slot)) (boundp (quote buffer-display-table)) (fboundp (quote = make-glyph-code))) (progn (if org-display-table nil (setq org-display-table= (make-display-table))) (set-display-table-slot org-display-table 4 (vconca= t (mapcar (function ...) (if ... org-ellipsis "...")))) (setq buffer-displa= y-table org-display-table))) (org-set-regexps-and-options) (org-set-font-lo= ck-defaults) (if (and org-tag-faces (not org-tags-special-faces-re)) (progn= (org-set-tag-faces (quote org-tag-faces) org-tag-faces))) (set (make-local= -variable (quote calc-embedded-open-mode)) "# ") (modify-syntax-entry 64 "w= ") (modify-syntax-entry 34 "\"") (modify-syntax-entry 92 "_") (modify-synta= x-entry 126 "_") (set (make-local-variable (quote font-lock-unfontify-regio= n-function)) (quote org-unfontify-region)) (set (make-local-variable (quote= org-table-may-need-update)) t) (org-add-hook (quote before-change-function= s) (quote org-before-change-function) nil (quote local)) (org-add-hook (quo= te kill-buffer-hook) (quote org-check-running-clock) nil (quote local)) (or= g-macro-initialize-templates) (org-update-radio-target-regexp) (set (make-l= ocal-variable (quote indent-line-function)) (quote org-indent-line)) (set (= make-local-variable (quote indent-region-function)) (quote org-indent-regio= n)) (org-setup-filling) (org-setup-comments-handling) (org-element-cache-re= set) (set (make-local-variable (quote beginning-of-defun-function)) (quote = org-backward-element)) (set (make-local-variable (quote end-of-defun-functi= on)) (function (lambda nil (if (not (org-at-heading-p)) (org-forward-elemen= t) (org-forward-element) (forward-char -1))))) (set (make-local-variable (q= uote next-error-function)) (quote org-occur-next-match)) (if org-enforce-to= do-dependencies (add-hook (quote org-blocker-hook) (quote org-block-todo-fr= om-children-or-siblings-or-parent)) (remove-hook (quote org-blocker-hook) (= quote org-block-todo-from-children-or-siblings-or-parent))) (if org-enforce= -todo-checkbox-dependencies (add-hook (quote org-blocker-hook) (quote org-b= lock-todo-from-checkboxes)) (remove-hook (quote org-blocker-hook) (quote or= g-block-todo-from-checkboxes))) (set (make-local-variable (quote align-mode= -rules-list)) (quote ((org-in-buffer-settings (regexp . "^[ ]*#\\+[A-Z_]+:= \\(\\s-*\\)\\S-+") (modes quote (org-mode)))))) (set (make-local-variable (= quote imenu-create-index-function)) (quote org-imenu-get-tree)) (set (make-= local-variable (quote outline-isearch-open-invisible-function)) (function (= lambda (&rest _) (org-show-context (quote isearch))))) (set (make-local-var= iable (quote pcomplete-command-completion-function)) (quote org-pcomplete-i= nitial)) (set (make-local-variable (quote pcomplete-command-name-function))= (quote org-command-at-point)) ...)) | org-mode() | (let ((org-mode-hook nil) (org-inhibit-startup t)) (org-mode)) | (let ((inhibit-modification-hooks t)) (let ((org-mode-hook nil) (org-in= hibit-startup t)) (org-mode)) (set (make-local-variable (quote org-table-ma= y-need-update)) (quote t)) (set (make-local-variable (quote org-latex-and-r= elated-regexp)) (quote "")) (set (make-local-variable (quote org-todo-line-= tags-regexp)) (quote "^\\(\\*+\\)\\(?: +\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\\|= DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)\\)?\\(?: +\\(.*?\\)\\)??\\(?:= [ ]+\\(:[[:alnum:]:_@#%]+:\\)\\)?[ ]*$")) (set (make-local-variable (quot= e org-complex-heading-regexp-format)) (quote "^\\(\\*+\\)\\(?: +\\(C\\(?:AN= CELED\\|HECK\\|ODE\\)\\|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)\\)?\\= (?: +\\(\\[#.\\]\\)\\)?\\(?: +\\(?:\\[[0-9%%/]+\\] *\\)*\\(%s\\)\\(?: *\\[[= 0-9%%/]+\\]\\)*\\)\\(?:[ ]+\\(:[[:alnum:]_@#%%:]+:\\)\\)?[ ]*$")) (set (m= ake-local-variable (quote org-complex-heading-regexp)) (quote "^\\(\\*+\\)\= \(?: +\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\\|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\= )\\|WAIT\\)\\)?\\(?: +\\(\\[#.\\]\\)\\)?\\(?: +\\(.*?\\)\\)??\\(?:[ ]+\\(:= [[:alnum:]_@#%:]+:\\)\\)?[ ]*$")) (set (make-local-variable (quote org-tod= o-line-regexp)) (quote "^\\(\\*+\\)\\(?: +\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\= \|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)\\)?\\(?: +\\(.*?\\)\\)?[ ]= *$")) (set (make-local-variable (quote org-not-done-heading-regexp)) (quote= "^\\(\\*+\\)\\(?: +\\(C\\(?:HECK\\|ODE\\)\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\= |WAIT\\)\\)\\(?: +\\(.*?\\)\\)?[ ]*$")) (set (make-local-variable (quote o= rg-not-done-regexp)) (quote "\\(C\\(?:HECK\\|ODE\\)\\|EXECUTE\\|T\\(?:EXT\\= |ODO\\)\\|WAIT\\)")) (set (make-local-variable (quote org-todo-regexp)) (qu= ote "\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\\|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)= \\|WAIT\\)")) (set (make-local-variable (quote org-not-done-keywords)) (quo= te ("TODO" "WAIT" "CHECK" "EXECUTE" "CODE" "TEXT"))) (set (make-local-varia= ble (quote org-todo-log-states)) (quote nil)) (set (make-local-variable (qu= ote org-todo-sets)) (quote (("TODO" "WAIT" "CHECK" "EXECUTE" "CODE" "TEXT" = "DONE" "CANCELED")))) (set (make-local-variable (quote org-todo-heads)) (qu= ote ("TODO"))) (set (make-local-variable (quote org-done-keywords)) (quote = ("DONE" "CANCELED"))) (set (make-local-variable (quote org-todo-keywords-1)= ) (quote ("TODO" "WAIT" "CHECK" "EXECUTE" "CODE" "TEXT" "DONE" "CANCELED"))= ) (set (make-local-variable (quote org-todo-key-trigger)) (quote (116 119 9= 9 101 111 121 100 120))) (set (make-local-variable (quote org-todo-key-alis= t)) (quote ((:startgroup) ("TODO" . 116) ("WAIT" . 119) ("CHECK" . 99) ("EX= ECUTE" . 101) ("CODE" . 111) ("TEXT" . 121) ("DONE" . 100) ("CANCELED" . 12= 0) (:endgroup)))) (set (make-local-variable (quote org-todo-kwd-alist)) (qu= ote (("TODO" sequence "TODO" "DONE" "CANCELED") ("WAIT" sequence "TODO" "DO= NE" "CANCELED") ("CHECK" sequence "TODO" "DONE" "CANCELED") ("EXECUTE" sequ= ence "TODO" "DONE" "CANCELED") ("CODE" sequence "TODO" "DONE" "CANCELED") (= "TEXT" sequence "TODO" "DONE" "CANCELED") ("DONE" sequence "TODO" "DONE" "C= ANCELED") ("CANCELED" sequence "TODO" "DONE" "CANCELED")))) (set (make-loca= l-variable (quote org-hide-block-startup)) (quote t)) (set (make-local-vari= able (quote org-use-sub-superscripts)) (quote t)) (set (make-local-variable= (quote org-table-formula-constants-local)) (quote nil)) (set (make-local-v= ariable (quote org-file-properties)) (quote (("header-args:R" . ":session t= est :comments link") ("header-args" . ":tangle-mode (identity #o444) :tangl= e no :mkdirp yes :exports both :padline no :eval never-export :noweb yes"))= )) (set (make-local-variable (quote org-tag-alist)) (quote nil)) (set (make= -local-variable (quote org-tag-groups-alist)) (quote nil)) (set (make-local= -variable (quote org-file-tags)) (quote nil)) (set (make-local-variable (qu= ote buffer-file-name)) (quote "/Users/rainerkrug/Documents/Projects/ASM_Opt= imization/asmOptim.org")) (set (make-local-variable (quote default-director= y)) (quote "/Users/rainerkrug/Documents/Projects/ASM_Optimization/")) (set = (make-local-variable (quote buffer-file-coding-system)) (quote utf-8-unix))= (insert "#+TITLE: Optimizing management actions for invasive alien plants = under different budgetary scenarios\n#+AUTHOR: Rainer M. Krug, N=C3=BAria R= oura-Pascual & David M. Richardson\n#+EMAIL: Rainer@krugs.de\n#+DESCRIPTION= :\n#+KEYWORDS:\n\n:CONFIG:\n#+OPTIONS: ':nil *:t -:t ::t <:t H:3 \\n:nil ^:= t arch:headline\n#+OPTIONS: author:t c:nil creator:comment d:(not \"LOGBOOK= \") date:t\n#+OPTIONS: e:t email:nil f:t inline:t num:t p:nil pri:nil prop:= nil\n#+OPTIONS: stat:t tags:t tasks:t tex:t timestamp:t toc:t todo:t |:t\n#= +LANGUAGE: en\n#+SELECT_TAGS: export\n#+EXCLUDE_TAGS: noexport\n#+CREATOR: = Emacs 24.4.1 (Org mode 8.3beta)\n#+OPTIONS: H:6\n#+OPTIONS: toc:6\n#+STARTU= P: hideblocks\n#+TODO: TODO(t) WAIT(w) CHECK(c) EXECUTE(e) CODE(o) TEXT(y) = | DONE(d) CANCELED(x)\n:END:\n:LATEXHEADER:\n#+LaTeX_CLASS_OPTIONS: [a4pape= r,usenames,dvipsnames,table]\n\n#+LATEX_HEADER: \\lstset{%\n#+LATEX_HEADER:= basicstyle=3D\\ttfamily\\footnotesize, % the font that is used f= or the code\n#+LATEX_HEADER: tabsize=3D4, % sets = default tabsize to 4 spaces\n#+LATEX_HEADER: numbers=3Dleft, = % where to put the line numbers\n#+LATEX_HEADER: numberstyle= =3D\\tiny, % line number font size\n#+LATEX_HEADER: stepn= umber=3D0, % step between two line numbers\n#+LATEX_HEAD= ER: breaklines=3Dtrue, %!! don't break long lines of co= de\n#+LATEX_HEADER: showtabs=3Dfalse, % show tabs with= in strings adding particular underscores\n#+LATEX_HEADER: showspaces=3D= false, % show spaces adding particular underscores\n#+LATEX_= HEADER: showstringspaces=3Dfalse, % underline spaces within st= rings\n#+LATEX_HEADER: keywordstyle=3D\\color{blue},\n#+LATEX_HEADER: = identifierstyle=3D\\color{black},\n#+LATEX_HEADER: stringstyle=3D\\c= olor{ForestGreen},\n#+LATEX_HEADER: commentstyle=3D\\color{red},\n#+LAT= EX_HEADER: backgroundcolor=3D\\color{light-gray}, % sets the backgrou= nd color\n#+LATEX_HEADER: columns=3Dfullflexible, \n#+LATEX_HEADER: = basewidth=3D{0.5em,0.4em}, \n#+LATEX_HEADER: captionpos=3Db, = % sets the caption position to `bottom'\n#+LATEX_HEADER: ext= endedchars=3Dfalse %!?? 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Krug\nMaintainer: Rainer M Krug \nDepends= : ASMOptimPackage (>=3D 0.2.0)\n#+end_src\n\n\n* TODO Setup .Rprofile file = :noexport:\nThis file will only be u= sed when R is not started with --vanilla!!!!\n#+begin_src R :tangle ./.Rpro= file\n.libPaths(normalizePath(\"library\"))\nlibrary(devtools)\n# load_all(= \"./package/asm\")\n#+end_src\n\n* Code Snippets for Analysis and Results = :noexport:\n:PROPERTIES:\n:header-args+: :tangle n= o\n:header-args+: :eval never\n:END:\n** initR\nLoad lEnergyBalance and Win= dProfilePaper packages\n#+NAME: initR\n#+begin_src R\n\n## \nlibrar= y(devtools)\n## install_bitbucket(repo=3D\"rkrug/WindProfiles\", ref=3D\"v_= 0.7.0\", auth_user=3D\"rkrug\", password=3D\"\")\nload_all(\"./package/ASMO= ptimPaper/ASMOptimPaper.org/\")\n## gInit()\n## \n\n#+end_src\n\n*= * getMapsetTypes\nThis is a template to be remembered and to be used as a b= ase for getting the results types from a simulation.\n\n#+NAME: getMapsetTy= pes\n#+begin_src R \n getMapNames(\n site =3D \"CapePeninsula= \",\n strategy =3D \"Consensus\",\n budget =3D \"CapePenins= ula_1_0\",\n run =3D 5,\n type =3D \"raster\",\n = pattern =3D \"*\",\n fullMapNames =3D FALSE\n ) %>%\n = strsplit(split=3D\"_\") %>%\n subset(sapply(., FUN=3D\"length\") = =3D=3D 2) %>%\n sapply(FUN=3D\"[[\", 2) %>%\n unique()\n\n#+e= nd_src\n* emails = :noexport:\n[[notmuch:id:002301d10bf4$ed38e670$c7aab350$@gmail.com][Email f= rom N=C3=BAria Roura-Pascual: RE: Missing piece ...]]\n\n* Data preparation= :noexport:\n** Split compl= ete data into different types\n:PROPERTIES:\n:heade-args: :eval never-expor= t\n:END:\n- csv ::\n#+begin_src sh :session data :results none\nmkdir ./inp= utdata/csv/ \nrsync -avz --include=3D\"*/\" --include=3D\"*.csv\" --exclud= e=3D\"*\" /Volumes/Seagate_1TB/HomeExternal/Documents/ASM_Optimization ./in= putdata/csv/ \nfind . -type f -name \"*.asc\" -exec gzip -v {} \\;\nrsync = -avz --include=3D\"*/\" --include=3D\"*.csv\" --exclude=3D\"*\" rainerkrug@= pogoplug:~/clusterResults/clusterResults/simASM/RandomClearingPaper/results= /simASMRightFire ./inputdata/csv/\n#+end_src\n\n- png ::\n#+begin_src sh :s= ession data :results none\nmkdir ./inputdata/png// \nrsync -avz --include= =3D\"*/\" --include=3D\"*.png\" --exclude=3D\"*\" /Volumes/Seagate_1TB/Home= External/Documents/ASM_Optimization ./inputdata/png/ \nrsync -avz --includ= e=3D\"*/\" --include=3D\"*.png\" --exclude=3D\"*\" /Volumes/Home\\ on\\ Pog= oplug/clusterResults/clusterResults/simASM/RandomClearingPaper/results/simA= SMRightFire/ ./inputdata/csv/\nrsync -avz --include=3D\"*/\" --include=3D\"= *.png\" --exclude=3D\"*\" rainerkrug@pogoplug:~/clusterResults/clusterResul= ts/simASM/RandomClearingPaper/results/simASMRightFire ./inputdata/png/\n#+e= nd_src\n\n** Merge directory structure into\n./inputdata/csv/ASM_Otimizatio= n/Simulations/SITE/simASM/STRATEGY/BUDGET/FIRE/RUN\n\n* Bash scripts for da= ta preparation and handling :noexport:\n** tar2grass - e= xtract grass/simulation directories and create single grass location\n:PROP= ERTIES:\n:header-args:sh: :tangle ./tar2grass\n:header-args:sh: :comments n= o\n:header-args:sh+: :tangle-mode (identity #o755)\n:END:\nThis script extr= acts the =3Dgrass/simulation=3D directory from a tar.gz\nfile of the simula= tion and moves it into the folder =3D./simASM=3D folder\nand renames it to = the name of the =3Dtar.gz=3D without the =3D.tar.gz=3D.\n\nAfter adding the= \n#+begin_src sh \nTAR=3D\"$1\"\necho $TAR ...\ntar -xvzf $TAR --include= =3D'*/grass/simulation/*'\nmkdir -p simASM\ncd tmp\ncd $(ls)\nSIM=3D$(ls)\n= cd $(ls)\ncd grass\nmv simulation $SIM\nmv $SIM ./../../../../simASM/\ncd .= /../../../../\nrm -rf ./tmp\n#+end_src\n\n** make the squashfs\n:PROPERTIES= :\n:header-args:sh: :tangle ./addPERMANENT\n:header-args:sh: :comments no\n= :header-args:sh+: :tangle-mode (identity #o755)\n:END:\nCopies =3DPERMANENT= =3D from =3D./inputdata/PERMANENT=3D into the location and\nadds the link t= o a mapset =3D./../grassAnalysis=3D which can be used for\nwrite access out= side the mapset, i.e. the complete mapset can be\nconverted into a SquashFS= and be mounted afterwards.\n\n#+begin_src sh \ncp -R ./inputdata/PERMANENT= ./simASM/\nln ln -s ./../../grassAnalysis ./simASM/grassAnalysis\n#+end_sr= c\n\n#+begin_src sh :tangle no\nmksquashfs ./simASM ./simASM.squashfs -pro= cessors 6\n#+end_src\n\n** COMMENT tar2sqfs - Prepare .tar.gz files and co= nvert to SquashFS\n:PROPERTIES:\n:header-args:sh: :tangle ./tar2sqfs\n:head= er-args:sh+: :comments no\n:header-args:sh+: :tangle-mode (identity #o755)\= n:END:\nThis script converts is converting tar.gz fines in tto .squashfs fi= les\nin the current directory. It should be run in the ./input directory.\n= \n*** Extract .tar.gz simulation but exclude certain redundant files\n#+beg= in_src sh\nTAR=3D\"$1\"\ntar -xvzf $TAR --exclude=3D'*/output/*' --exclude= =3D'input.tar.gz' --exclude=3D'output.tar.gz'\n#+end_src\n\n*** Climb in di= rrectory into single unique directory\n#+begin_src sh \ncd tmp\ncd `ls`\n#+= end_src\n\n*** Replace link to =3DPERMANENT=3D with link to existing =3DPER= MANENT=3D \n#+begin_src sh \nfind . -type \"link\" -name \"PERMANENT\" -exe= c ln -fhs ./../../PERMANENT {} \\;\n#+end_src\n\n*** Create squashfs in bas= e folder and delete original folder\n#+begin_src sh \nNAME=3D$(ls)\nmksquas= hfs $NAME ./../../$NAME.squashfs -b 1048576 -comp xz -Xdict-size 100%\ncd .= /../../\nrm -rf ./tmp\n#+end_src\n\n\n\n** COMMENT oneGrass\n:PROPERTIES:\n= :header-args:sh: :tangle ./oneGRASS\n:header-args:sh+: :comments no\n:heade= r-args:sh+: :tangle-mode (identity #o755)\n:END:\n#+begin_src sh \nDEST=3D.= /DEST$$\nGRASS=3D./GRASS$$/simASM\n\nfunction finish {\n rm -rf \"$DEST\= "\n rm -rf \"$GRASS\"\n}\ntrap finish EXIT\n\nmkdir -p \"$GRASS\"\n\nech= o Copying ./inputdata/PERMANENT to $GRASS ...\ncp -R ./inputdata/PERMANENT = $GRASS/\nfor F in ./inputdata/simASM.*.squashfs; do \n BN=3D$(basename $= F)\n DN=3D$(dirname $F)\n DIR=3D\"${BN%.*}\"\n echo \"<<<<<\"\n = echo Extracting grass/simulation from $F to ./$DEST/grass/simulation\n = unsquashfs -dest $DEST \"$F\" -e grass/simulation/*\n echo Moving \"./$D= EST/grass/simulation\" to \"$GRASS/simASM/grass/$DIR\"\n mv \"./$DEST/gr= ass/simulation\" \"$GRASS\"\n mv \"$GRASS/simulation\" \"$GRASS/$DIR\"\n= echo Deleting \"$DEST\"\n rm -rf \"$DEST\"\n echo \">>>>>\"\ndone= \necho Create link $GRASS/analysis out of the squashfs for editable mapse= t\nln -s \"./../../grassAnalysis\" \"$GRASS/analysis\"\necho Making SquashF= S ./input/simASM.grass.squashfs from $GRASS/simASM ...\nmksquashfs \"$GRASS= \" ./input/simASM.grass.squashfs -b 1048576 -comp xz -Xdict-size 100%\necho= Done\n#+end_src\n\n** COMMENT mountSimASM - mount simASM.grass.squashfs to= ./inputdata/simASM\n:PROPERTIES:\n:header-args:sh: :tangle ./mountSimASM\n= :header-args:sh+: :comments no\n:header-args:sh+: :tangle-mode (identity #o= 755)\n:END:\n#+begin_src sh \nDIR=3D./inputdata/simASM\nSFS=3D./inputdata/s= imASM.grass.squashfs\nFN=3D./umountSimASM\necho \"#!/bin/sh\" > $FN\necho \= "umount $DIR\" >> $FN\necho \"rm $DIR/NOT_MOUNTED\" >> $FN\necho \"rmdir $D= IR\" >> $FN\necho \"rm $FN\" >> $FN\nchmod +x $FN\nmkdir -p \"$DIR\"\ntouch= \"$DIR/NOT_MOUNTED\"\nsquashfuse \"$SFS\" \"$DIR\"\n#+end_src\n\n\n** COMM= ENT mountSims - mount all ./input/simASM.*.squashfs \n:PROPERTIES:\n:header= -args:sh: :tangle ./mountsimASM\n:header-args:sh+: :comments no\n:header-ar= gs:sh+: :tangle-mode (identity #o755)\n:END:\n#+begin_src sh \nFN=3D./umoun= tsimASM\necho \"#!/bin/sh\" > $FN\nchmod +x umountsimASM\nfor F in ./inputd= ata/simASM.*.squashfs; do \n BN=3D$(basename $F)\n DN=3D$(dirname $F)= \n DIR=3D$DN/\"${BN%.*}\"\n echo ###\n echo Mounting $F to $D\n = mkdir -p \"$DIR\"\n squashfuse \"$F\" \"$DIR\" \n echo \"umount $DIR= ; rmdir $DIR\" >> $FN\ndone \necho \"rm ./umountsimASM\" >> $FN\n#+end_src= \n\n\n\n* Introduction = :noexport:\nInvasive alien plants pose a significant threat to the environm= ent and society. They are known to cause significant changes in species, co= mmunities and ecosystems citep:Vila2011 and to be responsible for major eco= nomic losses citep:Pimentel2005. Economic expenses are in the form of losse= s to provisioning services, but more importantly in the form of management = costs, including eradication, control, and monitoring citep:Vila2010. This = is particularly certain for strongly dominating plant species, since eradic= ation is not always an option and the maintenance and effectiveness of cont= rol measures are largely uncertain. Economics are known to play an importan= t role in clearing operations citep:Higgins1997a,Marais2004a.\n \n[[comment= :Needs to be reworded.][For example, cite:Odom2005 showed that investment i= n managing the Scotch broom (/Cytisus scoparius/) is economically justified= and that higher budgets yield higher value for the society. citep:Cacho200= 8 used a decision model based on economic analysis to identify the most app= ropriate management goal (eradication, containment or no management). Both = studies coincide in indicating that the major factor determining the manage= ment goal is the available budget, with higher budgets resulting in more er= adication oriented goals.]]\n\nBesides the overreaching importance of budge= t, the effectivity of management actions is also constrained by the charact= eristics of species} and the environment citep:Cacho2008,Krug2010_rmk and t= he strategy adopted for clearing invasive alien plants ([[comment:Ref neede= d][REF]]). Investment needs to be adjusted to the particularities of each s= tudy site and maintained over time to maximize the efficiency of clearing p= rograms citep:Krug2010_rmk. The maintenance of management measures over tim= e is, however, not exempt of nuances. [[comment:TAlk about the problems as= sociated with clearing the same site over time][TALK ABOUTTHE PROBLEMS ASSO= CIATED WITH CLEARING THE SAME SITE OVER TIME]] The selection of the optimal= clearing strategy, based on the characteristics of the environment and the= allocation of resources over time, is thus crucial to provide practical gu= idelines for use in fiscal and policy decisions of IAP management. \n\nThis= study builds on our previous work that examined the impact of different bu= dget scenarios on the effectivity of clearing actions on a selected priorit= ization strategy citep:Krug2010_rmk, but instead of focusing on a single pr= ioritization strategy we also examine the effect of several prioritization = strategies. In particular, we aim to identify the optimal combination of el= ements =E2=80=93budget and clearing strategy=E2=80=93 that ensures the effe= ctive management of IAPs at regional scales, while taking into account the = particularities of invasive species and the hosting environment.\n\nIn this= study, we use the three sites in the South Africa=E2=80=99s Cape Floristic= Region as a case study (Agulhas Plains, Cape Peninsula, Outeniqua, see ref= :map-All), an area subject to extensive control operations to reduce the ex= pansion of woody IAPs that threaten the persistence of its high biological = diversity. \n\n** #### clearpage #### = :ignoreheading:\n{{{clearpage}}}\n\n\n* Methods\n\n** Study sites\nThe sim= ulations for this study are based on three study sites within South Africa= =E2=80=99s Cape Floristic Region: Agulhas Plain, Cape Peninsula and Outeniq= ua (see Fig. ref:map-All and Table ref:tab-All for details). All three site= s contain large areas that are formally protected. Whereas the Cape Peninsu= la and Outeniqua regions have large areas of natural or seminatural vegetat= ion, the Agulhas Plains consists of a mosaic of agricultural landscapes and= conservation areas. All sites are invaded by IAPs, albeit by different spe= cies and to different degrees (see ref:tab-All for details). The most impor= tant IAP groups in the study sites and in the CFR overall are major woody p= lants, particularly species of /Acacia/, /Hakea/ and /Pinus/ citep:Richards= on1986_rmka,Richardson1992_rmk,Richardson1994_rmk,Wilgen1994_rmk,Richardson= 2008_rmk [[comment:Further References needed?]]). \n\nDifferent usage and m= anagement pattern as well as topography of the three sites result in differ= ent fire patterns, e.g. with respect to the average area burned per year an= d the average number of fires per year (see supplemental material from cite= :Krug2010_rmk for details).\n\n#+CAPTION: Study label:map-All sites in Sout= h Africa's Cape Floristic Region\n[[file:map-All.png]]\n\n#+ATTR_LATEX: :ca= ption \\caption{Details \\label{tab-All} the study sites used in this study= . $\\bpc$ is the budget per year per cell, $\\bpci$ is the budget per year = per invaded cell (1ha =3D 1cell).} \\todo[inline]{Units in headers only or = in table itself?}\n| | Area | Area invaded | Budget= | 2007/2008 | |\n| | in ha | = in ha | Overall in R | $\\bpc$ in R/ha | $\\bpci$ in R/ha |\n= |----------------+---------+--------------------+--------------+-----------= -----+------------------|\n| Agulhas Plains | 215,982 | 142,672 ( 66.1 % ) = | 3,691,728 | 17.09 | 25.88 |\n| Cape Peninsula | 49= ,179 | 19,226 ( 39.1 % ) | 6,675,539 | 135.74 | 347.= 21 |\n| Outeniqua | 57,697 | 57,454 ( 99.6 % ) | 1,937,220 | = 33.58 | 33.72 |\n| | | = | | | |\n|--------------= --+---------+--------------------+--------------+----------------+---------= ---------|\n\n\n\n** Model description\nTo model the spread of species unde= r different management strategies, we used the spatio-temporal explicit sim= ulation model {{{sc(SpreadSim)}}} ( [[comment:This needs to be added][The s= ource code is available at]] [[comment:Merge all different into one - the = only difference should be the prioritisation file!]]). In this section, we = present a short overview of the model, a detailed description can be found = in cite:Krug2010_rmk. \n\nThe purpose of the model is to simulate the sprea= d of three IAPs groups, namely /Acacia/, /Hakea/ and /Pinus/ citep:Krug2010= _rmk, by incorporating spatial population dynamics (seed production, seed d= ispersal, germination and establishment), fire dynamics and the clearing of= IAPs based on a certain prioritization strategy, the costs of clearing act= ions and the budget available per year. The aim is to assess the effectiven= ess of different clearing strategies and budget scenarios over time. \n\nTh= e model {{{sc(SpreadSim)}}} was written in R citep:R2008_rmk, (with additio= nal packages by cite:Pebesma2005_rmk,Petzoldt2007_rmk,Bivand2009_rmk,James2= 009_rmk,Keitt2009_rmk,Lewin-Koh2009_rmk,Urbanek_rmk) and uses GRASS citep:G= RASS2007 for the storage of the spatial results and spatial calculations. I= t can be separated into five different modules, namely {{{sc(clearing)}}}, = {{{sc(fire)}}}, {{{sc(seedProduction)}}}, {{{sc(seedDispersal)}}} and {{{sc= (germEst)}}}, which are executed consecutively (see Figure ref:fig-Model fo= r the flowchart of the model). Each module contains parameter controlling t= he stochastic spread and management of IAPs of the genera /Acacia/, /Hakea/= and /Pinus/ citep:Krug2010_rmk. \n\nDue to the stochastic nature of the m= odel, each *simulation* (defined by the =3Dsite=3D, prioritization =3Dstrat= egy=3D and =3Dbudget=3D) was repeated five times. For further analysis, we = defined a *simulation set* as different =3Dbudget=3D scenarios for the same= =3Dsite=3D and clearing =3Dstrategy=3D.\n\nThe input data for the simulati= ons was provided by the relevant nature conservation agencies and Working f= or Water (see cite:Roura-Pascual2009_rmkb,Roura-Pascual2009_rmkc for detail= s [[comment:REF for topography and natural vegetation data needed? I don't= think so, as referred to the papers)]]. \n\nSimulations were done on a ras= ter with a resolution of $100m \\times 100m$ cells and with a time step of = one year. \n\n#+ATTR_LATEX: :caption \\caption{\\label{fig-Model} from \\p= rotect\\cite{Krug2010_rmk}} \\todo[inline]{If we need this here, I will red= o it - just let me know.}\n{{{if-latex-else([[file:fig-Model.pdf]], [[file:= fig-Model.png]])}}}\n\n\n** Prioritization =3Dstrategy=3D\n\nThe prioritiza= tion =3Dstrategy=3D assigns each individual cell a priority value for clear= ing of the IAPs out of these cells. Subsequently, cells are cleared in desc= ending order of their priority until the budget is spend (see cite:Krug2010= _rmk). \n\nThe strategies are based on weights and consider the following f= actors:\n\n- Area burnt recently\n- Density of IAPs\n- Spread based on topo= graphy\n- Area at fire risk\n- Age of IAPs\n- Identity of IAPs\n- Last clea= ring operation\n\nFor a detailed description of these factors and how they = were derived, see citep:Roura-Pascual2009_rmkb,Roura-Pascual2009_rmkc. \n\n= The prioritization strategies evaluated in this study are (Fig. ref:fig-Str= ategies):\n\n- =3Dconsensus=3D :: this strategy was developed through a par= ticipatory process with managers and researchers experts on various aspects= of IAPs citep:Roura-Pascual2009_rmkb. This resulted in priority was given = to areas burnt recently and the density of the IAPs was reduced citep:Roura= -Pascual2009_rmkc. The following =3Dstrategies=3D are based on the =3Dconse= nsus strategy=3D and were modified based on certain aims.\n- =3Dmaintain fo= llow-ups=3D :: (aka =3Dpast=3D) aims at prioritizing areas based on previou= s clearing operations, i.e. giving higher priority to areas which have been= cleared already or in follow-ups. It relies on accurate information of fir= e and clearing history of the site citep:Roura-Pascual2009_rmkc;\n- =3Dkeep= clean=3D :: (aka =3Dpresent=3D) is a strategy where management operations = do not rely on fire opportunities to clear invaded stands and the potential= of a stand to be a major source of invasion is minimized. It relies on acc= urate information of the present, i.e. present density of the IAPs and spre= ad potential based on topography citep:Roura-Pascual2009_rmkc;\n- =3Dwater = production=3D :: (aka =3Dfuture=3D)is orientated towards increasing water p= roduction in the future, with higher priority given to riparian areas in lo= wer parts of the catchment invaded by dense stands of /Acacia/ species. It = uses mainly static information, i.e. spread based on topography citep:Roura= -Pascual2009_rmkc;\n- =3Drandom=3D :: is a null-strategy which does not req= uire any knowledge about the past and randomly assigns priorities citep:Kru= g2010_rmk.\n\nA visualization of these prioritization strategies can be see= n in Fig. ref:fig-Strategies.\n\n#+ATTR_LATEX: :caption \\caption{\\label{f= ig-Strategies} from \\protect\\cite{Roura-Pascual2009_rmkc}} \\todo[inline]= {This figure needs to be redone and further info added}\n{{{if-latex-else([= [file:fig-Strategies.pdf]], [[file:fig-Strategies.png]])}}}\n\n** Budget\nT= he budget as well as the costs used in this study are based on the actual b= udget for the three areas of the financial year 2007/2008. They are specifi= ed in South African Rand (R) as $\\boldmath\\bpc$ (IAP clearing budget per = year per cell) and $\\boldmath\\bpci$ (IAP clearing budget per year per in= vaded cell).\n\nThe actual budgets were multiplied with a factor ranging fr= om 0.1 to 6.0 to obtain 14 to 15 different budget scenarios for each simula= tion set defined by a =3Dsite=3D and a =3Dstrategy=3D (see Figure ref:fig-B= udgets and Table ref:tab-Budgets in the Appendix for values from cite:Krug2= 010_rmk).\n\nThe budgets and the factors used for the three sites are[[comm= ent:We could leave the factors out here but I think it is a useful addition= . All information also also in the table in the Appendix]]:\n\n| = budget | Agulhas | CapePeninsula | Outeniqua |\n| = factor | | | |\n|---------------------= -----+-----------+---------------+-----------|\n| $\\bpc$ $\\frac{R}{cell}= $ | 17.09 | 135.05 | 33.58 |\n| $\\bpci$ | = 25.88 | 347.21 | 33.72 |\n|--------------------------+------= -----+---------------+-----------|\n| 0.1 | C M K W - = | C M K W R | C M K W R |\n| 0.2 | | - -= - - R | - - - - R |\n| 0.3 | | - - - - = R | - - - - R |\n| 0.4 | | - - - - R = | - - - - R |\n| 0.5 | - - - - R | C M K W R | C = M K W R |\n| 0.6 | | - - - - R | - - - -= R |\n| 0.7 | | C M K W R | - - - - R |\= n| 0.8 | | - - - - R | - - - - R |\n| = 0.9 | | - - - - R | - - - - R |\n| = 1. | - - - - R | C M K W R | - - - - R |\n| = 1.1 | | | |\n| = 1.2 | - - - - R | | |\n| 1= .3 | | - - - - R | C M K W R |\n| 1.4 | = | | |\n| 1.5 | - - -= - R | C M K W R | C M K W R |\n| 1.6 | = | | |\n| 1.7 | - - - - R | - -= - - R | |\n| 1.8 | | = | |\n| 1.9 | | = | |\n| 2. | - - - - R | - - - - R | C = M K W R |\n| 2.2 | - - - - R | | = |\n| 2.5 | C M K W R | | |\= n| 3. | - - - - R | | |\n| = 3.5 | - - - - R | | |\n| = 4. | - - - - R | | |\n| = 4.5 | - - - - R | | |\n| = 5. | C M K W R | | |\n| 5= .5 | C M K W R | | |\n| 6. | = C M K W R | | |\n\n\n- Agulhas Plains :: $\\bpc =3D= $ 17.09 R/cell, $\\bpci =3D$ 25.88 R/cell\n - Consensus, Maintain Follow U= ps, Keep clean, Water production :: 0.1; 2.5; 5.0; 5.5; 6.0\n - Random :: = 0.5; 1.0; 1.2; 1.5; 1.7; 2.0; 2.2; 2.5; 3.0; 3.5; 4.0; 4.5; 5.0; 5.5; 6.0; = 6.5; 7.0\n- CapePeninsula :: $\\bpc =3D$ 135.047 R/cell, $\\bpci =3D$ 347.2= 1R/cell\n - Consensus, Maintain Follow Ups, Keep clean, Water production := : 0.1; 0.5; 0.7; 1.0; 1.5\n - Random :: 0.1; 0.2; 0.3; 0.4; 0.5; 0.6; 0.7;= 0.8; 0.9; 1.0; 1.3; 1.5; 1.7; 2.0\n- Outeniqua :: $\\bpc =3D$ 33.58R/cell,= $\\bpci =3D$ 33.72R/cell\n - Consensus, Maintain Follow Ups, Keep clean, = Water production :: 0.1; 0.5; 1.3; 1.5; 2.0\n - Random :: 0.1; 0.2; 0.3; 0= .4; 0.5; 0.6; 0.7; 0.8; 0.9; 1.0; 1.3; 1.5; 1.7; 2.0\n\n#+CAPTION: Differen= t label:fig-Budgets budgets of the different sites in comparison. Colours i= ndicate different sites, pattern indicate if the budget is \"per all cells\= " or \"per invaded cells\"\n{{{if-latex-else([[file:fig-Budgets.pdf]], [[fi= le:fig-Budgets.png]])}}}\n\n** TODO Analysis\nThe analysis follows the anal= ysis done in cite:Krug2010_rmk and uses very similar measures and indicator= s to assess the efficiency of the different strategies. We therefore calcul= ated for each individual =3Dsimulation=3D run (i.e. five per =3Dsimulation= =3D)\n\n# - $\\cua$ :: number of cells covered by IAPs per year, where *cov= ered* is defined as $dc \\leq 1$ i.e. *rare* or less\n- $\\cov$ :: as the p= roportion of the cells covered by aliens in year $t$\n (i.e. all cells = for which the density class of aliens is higher\n than *rare*). $\\cov = =3D 0$ indicates no alien infestation and $\\cov\n =3D 1$ indicates com= plete cover of IAPs. (From cite:Krug2010_rmk) \n# - $\\ac$ :: number of cel= ls cleared of IAPs in year $t$\n\nTo assess the effectiveness of the =3Dsim= ulation=3D run, we defined a\n- management goal :: as to be having 95% of t= he area (cells) alien free (density class of aliens smaller or equal *rare*= ), i.e. $\\cov \\leq 0.95$\nwhere each individual simulation run is regarde= d as successful after reaching the *management goal*.\n\nIf the *management= goal* was reached, we calculated for each =3Dsimulation=3D run\n- $\\tmg$ = :: as the time when we reached the management goal\n- $\\bmg$ :: as the cum= ulative budget needed to achieve the management goal\n\nFor each =3Dsimulat= ion=3D (i.e. over the five simulation runs) we then calculated\n+ $\\pmg$ := : proportions of all the runs (here five simulation runs) in one =3Dsimulat= ion=3D which reached the *management goal*\n\nTo accumulate over each =3Dsi= mulation set=3D, i.e. one =3Dsite=3D and one =3Dstrategy=3D and multiple = =3Dbudget=3Ds, we calculated\n- $\\bc$ :: the *critical budget* is the lowe= st budget at which more than 50% of all simulations resulted in achieving t= he *management goal* of 95% alien free within the time-frame of 30 years,\n= - $\\bci$ :: as $\\bc$ but the using $\\bpci$ instead of $\\bpc$\n\n# Final= ly, we calculated for each set of =3Dsite=3D and =3Dstrategy=3D a\n# - budg= et index :: $\\bm{\\idb} =3D \\frac{\\bpc}{\\bc}$\n# - time index :: $\\bm{= \\idt} =3D \\frac{\\tmg(\\bc)-1}{\\mathit{mean}\\left(\\tmg(\\bc)-1\\right)= }$ [[comment:I have to confess I am not sure what I did here!]]\n\n# The va= riables used to evaluate the efficiency of the clearing operations under di= fferent prioritization strategies and budgetary scenarios were: area covere= d by IAPs per year, IAP clearing budget per year, and area cleared of IAPs = per year. The proportion of the site covered by aliens in year t, i.e. all = cells for which the density class of aliens is higher than =E2=80=98=E2=80= =98rare=E2=80=99=E2=80=99, is called cov(t). cov(t) =3D 0 indicates no alie= n infestation and cov(t) =3D 1 indicates complete cover of IAPs.\n\n# We se= t our =E2=80=98=E2=80=98management goal=E2=80=99=E2=80=99 arbitrarily at cl= earing 95% (and for some scenarios 90%) of the area of IAPs. This =E2=80=98= =E2=80=98management goal=E2=80=99=E2=80=99 represents the threshold cover, = below which the management is considered as being successful. An eradicatio= n of all IAPs would be ideal, but would require much higher resources.\n \n= # If during the simulation the cover of IAPs was reduced below the =E2=80= =98=E2=80=98management goal=E2=80=99=E2=80=99, we determined the year in wh= ich it occurred (tnf95) and the cumulative costs per cell up to tnf95 (BPC = 95). Note that BPC 95 <=3D bPC=C2=B7tnf95 as the whole budget might not be = spent. The lowest budget at which more than 50% of all simulations resulted= in a reduction of the alien cover to less than 5% within the time-frame of= 30 years, was called the =E2=80=98=E2=80=98critical budget=E2=80=99=E2=80= =99 (bPC relating to bPC and bPCINV relating to bPCINV). Each budget scenar= io was simulated five times.\n\n# In addition, we calculated a budget index= and a time index for each species separately. The budget index was calcula= ted by dividing the actual budget bPC by the critical budget ^ bPC. Consequ= ently, the budget index was one for the critical budget. The time index was= calculated as follow:\n\n# ??ADD FORMULA??\n\n# By subtracting one from tn= f95 we achieved that the lowest value of the index is zero, while 1 represe= nts the average tnf95=C3=B0 ^ bPC=C3=9E.\n\n** #### clearpage #### = :ignoreheading:\n{{{clearpage}}}\n\n\n\n\n# = LocalWords: IAPs\n\n* TODO [2/6] Make Analysis and Graphs = :noexport:\n:PROPERTIES:\n:COOKIE_DATA: todo recursive\n:heade= r-args+: :eval no-export\n:END:\n** DONE Budget graph fig-budgets\n\n\n#+NA= ME: tabBudgets\n| budget | Agulhas | | CapePeninsula | = | Outeniqua | |\n| factor | R/Cell | R/Cell_inv | R/Ce= ll | R/Cell_inv | R/Cell | R/Cell_inv |\n|--------+---------+-----------= -+---------------+------------+-----------+------------|\n| 0.1 | 1.70= 9 | 2.588 | 13.504 | 34.721 | 3.358 | 3.372 |\n| = 0.2 | | | 27.008 | 69.442 | 6.716 | = 6.744 |\n| 0.3 | | | 40.512 | 104.163 | = 10.074 | 10.116 |\n| 0.4 | | | 54.016 | = 138.884 | 13.432 | 13.488 |\n| 0.5 | | | = 67.52 | 173.605 | 16.79 | 16.86 |\n| 0.6 | | = | 81.024 | 208.326 | 20.148 | 20.232 |\n| 0.7= | | | 94.528 | 243.047 | 23.506 | 23.6= 04 |\n| 0.8 | | | 108.032 | 277.768 | 26.= 864 | 26.976 |\n| 0.9 | | | 121.536 | 31= 2.489 | 30.222 | 30.348 |\n| 1. | 17.09 | 25.88 | = 135.04 | 347.21 | 33.58 | 33.72 |\n| 1.1 | | = | | | | |\n| 1.2 | 2= 0.508 | 31.056 | | | | |\= n| 1.3 | | | 175.552 | 451.373 | 43.654 |= 43.836 |\n| 1.4 | | | | = | | |\n| 1.5 | 25.635 | 38.82 | 202.5= 6 | 520.815 | 50.37 | 50.58 |\n| 1.6 | | = | | | | |\n| 1.7 | 29.053= | 43.996 | 229.568 | 590.257 | 57.086 | 57.324 |\n| = 1.8 | | | | | | = |\n| 1.9 | | | | | = | |\n| 2. | 34.18 | 51.76 | 270.08 | = 694.42 | 67.16 | 67.44 |\n| 2.2 | 37.598 | 56.936 | = | | | |\n| 2.5 | 42.725 | = 64.7 | | | | |\n| 3. = | 51.27 | 77.64 | | | | = |\n| 3.5 | 59.815 | 90.58 | | | = | |\n| 4. | 68.36 | 103.52 | | = | | |\n| 4.5 | 76.905 | 116.46 | = | | | |\n| 5. | 85.45 | 12= 9.4 | | | | |\n| 5.5 | 93= .995 | 142.34 | | | | |\n= | 6. | 102.54 | 155.28 | | | | = |\n\n\n#+NAME: fig-Budgets\n#+begin_src R :var BUDGET=3DtabBudge= ts :exports results :file-ext pdf :results graphics :width 7 :height 7\n<<= initR>>\nlibrary(magrittr)\nx <- BUDGET\nx <- BUDGET %>%\n extract(-(1:2= ),) %>%\n set_names(\n c(\n \"f\",\n \"Agul= has\", \"Agulhas_I\",\n \"CapePeninsula\", \"CapePeninsula_I\",\= n \"Outeniqua\", \"Outeniqua_I\"\n )\n )\n\n##\nfor (i= in 1:length(x)) {\n x[[i]] <- as.numeric(x[[i]])\n}\n\n##\nx %<>%\n = extract(-1) %>%\n unlist %>%\n extract(!is.na(.)) %>%\n sort(decr= easing =3D TRUE)\n\n##\nAG_I <- x %>%\n names %>%\n grep(\"Agulhas_I\= ", .)\nAG <- x %>%\n names %>%\n grep(\"Agulhas[1-9]\", .)\n##\nCP_I = <- x %>%\n names %>%\n grep(\"CapePeninsula_I\", .)\nCP <- x %>%\n = names %>%\n grep(\"CapePeninsula[1-9]\", .)\n##\nOU_I <- x %>%\n nam= es %>%\n grep(\"Outeniqua_I\", .)\nOU <- x %>%\n names %>%\n grep(= \"Outeniqua[1-9]\", .)\n\n##\ncols <- rep(\"black\", length(x))\ncols[c(AG,= AG_I)] <- \"green\"\ncols[c(CP, CP_I)] <- \"red\"\ncols[c(OU, OU_I)] <- \"= blue\"\n\n##\ndens <- rep(-1, length(x))\ndens[c(AG_I, CP_I, OU_I)] <- 30\n= \n##\npar(\n mar =3D c(4.1, 0.3, 0.1, 0.8)\n)\nbarplot(\n x,\n xla= b =3D \"Budget per cell\",\n xlim =3D c(0, 700),\n names.arg =3D \"\"= ,\n horiz =3D TRUE,\n col =3D cols,\n density =3D dens\n)\nsiteNam= es <- c(\"Agulhas Plains\", \"Cape Peninsula\", \"Outeniqua\")\nlegend(\n = x =3D \"topright\",\n legend =3D c( siteNames, \"\", \"per all cells\= ", \"per invaded cells\"),\n fill =3D c(\"green\", \"red\", \"blue\",= NA, \"black\", \"black\"),\n border =3D c(\"black\", \"black\", \"blac= k\", NA, \"black\", \"black\"),\n density =3D c(-1, -1, -1, NA, -1, 30)\= n)\n#+end_src\n\n#+RESULTS: fig-Budgets\n[[file:fig-Budgets.pdf]]\n\n\n** D= ONE Calculate dc\n#+begin_src R :results output :tangle ./package/ASMOptimP= aper/inst/scripts/analysis.calculate.dc.R :eval never \n<>\ndc <- ge= tDc( new =3D TRUE, cores =3D 6 )\n#+end_src\n\n#+RESULTS:\n#+begin_example\= nLoading ASMOptimPaper\nLoading required package: sp\nLoading required pack= age: raster\nLoading required package: rgrass7\nLoading required package: X= ML\nGRASS GIS interface loaded with GRASS version: (GRASS not running)\nLoa= ding required package: magrittr\n\nAttaching package: =E2=80=98magrittr=E2= =80=99\n\nThe following object is masked from =E2=80=98package:raster=E2=80= =99:\n\n extract\n\nLoading required package: parallel\ngisdbase ./in= putdata \nlocation simASM \nmapset grassAnalysis \nrows 210 = \ncolumns 790 \nnorth 6263000 \nsouth 6242000 \nwest = 574000 \neast 653000 \nnsres 100 \newres 100 \nprojecti= on +proj=3Dutm +south +zone=3D34 +a=3D6378137 +rf=3D298.257223563 +no_defs= \n+towgs84=3D0.000,0.000,0.000 +to_meter=3D1.0\n#+end_example\n\n** TODO Ex= amples of some simulations :noexport:\n#+begin= _src R \nua <- getUaWide(site =3D \"Agulhas\", strategy=3D\"Consensus\", sp= ecies =3D \"all\")\n\ndcs <- split(\n dc, dc$run\n)\nmatplot(x =3D dc$ye= ar, dc[as.character(1:7)])\nua <- rowSums(dc[as.character(1:7)])\n\nplot(ua= )\n\nua <- getUa(site =3D \"Agulhas\", budget=3D\"None\", species =3D \"all= \", proportion=3DTRUE)\nplot(ua$cl)\nb\n#+end_src\n** CHECK Figures --- =3D= simulation sets=3D by site\n:PROPERTIES:\n:header-args+: :epilogue rm(ST, S= I)\n:END:\n\n:CODESNIPPETS:\n#+NAME: plotScenarios\n#+begin_src R :eval nev= er\n<>\npar(\n mfcol =3D c(length(STRATEGIES)-1, 1),\n mar = =3D c(1.2, 4.1, 1.1, 0.1),\n cex =3D 0.7\n)\nfor (i in 1:(length(STRAT= EGIES)-1)) {\n if (i =3D=3D length(STRATEGIES)-1) {\n par(\n = mar =3D c(4.2, 4.1, 1.1, 0.1)\n ) \n }\n plotS= cenario( site =3D SI, strategy =3D STRATEGIES[i])\n}\n#+end_src\n:END:\n\n#= +NAME: fig-ScenAgulhas\n#+HEADER: :var SI=3D\"Agulhas\"\n#+begin_src R :exp= orts results :file-ext pdf :results graphics :width 7 :height 7\n<>\n#+end_src\n\n#+RESULTS: fig-ScenAgulhas\n[[file:fig-ScenAgulhas.pd= f]]\n\n\n#+NAME: fig-ScenCapePeninsula\n#+HEADER: :var SI=3D\"CapePeninsula= \"\n#+begin_src R :exports results :file-ext pdf :results graphics :width 7= :height 7\n<>\n#+end_src\n\n#+RESULTS: fig-ScenCapePeninsul= a\n[[file:fig-ScenCapePeninsula.pdf]]\n\n\n#+NAME: fig-ScenOuteniqua\n#+HEA= DER: :var SI=3D\"Outeniqua\"\n#+begin_src R :exports results :file-ext pdf = :results graphics :width 7 :height 7\n<>\n#+end_src\n\n\n#+R= ESULTS: fig-ScenOuteniqua\n[[file:fig-ScenOuteniqua.pdf]]\n\n{{{clearpage}}= }\n\n** CHECK Figures --- Proportion reaching Management Goal\n#+NAME: fig-= CritBudProp\n#+begin_src R :exports results :file-ext pdf :results graphics= :width 7 :height 7\n<>\npar(\n mfcol =3D c(length(SITES), 1),\n = mar =3D c(1.2, 4.1, 1.1, 0.1),\n cex =3D 0.7\n)\nfor (i in 1:leng= th(SITES)) {\n if (i =3D=3D length(SITES)) {\n par(\n = mar =3D c(4.2, 4.1, 1.1, 0.1)\n ) \n }\n plotCritBud(= \n site =3D SITES[i],\n ylab =3D \"Prop Man. Goal\",\n = dx =3D 0.6,\n xlim =3D c(0, 150)\n )\n}\n#+end_src\n\n#+RESULTS= : fig-CritBudProp\n[[file:fig-CritBudProp.pdf]]\n\n** CHECK Plot of Critica= l Budgets[[ comment:Here is something not right and needs to be checked. It= could be the functions?]] :noexport:\n#+NAME: fig-BcOverview\n#+begin_src = R :exports results :file-ext pdf :results graphics :width 7 :height 4.5\n<<= initR>>\ncb <- getCriticalBudget(species =3D \"all\")\n\n\nplot(\n bc$bu= dgetPerCell ~ bc$tmg.mean,\n xlab =3D \"mean time until management goal = is achieved at critical budget\",\n ylab =3D \"critical budget ber cell\= ",\n cex =3D 1,\n col =3D as.factor(bc$strategy),\n pch =3D as.int= eger(as.factor(bc$site))\n)\n\nsite <- unique(bc$site)\nstrategy <- unique(= bc$strategy)\nlegend(\n \"bottomright\",\n legend =3D c(\n sit= e,\n \"\",\n strategy\n ),\n pch =3D c(\n as.int= eger(as.factor(site)),\n 1,\n rep(15, length(strategy))\n = ),\n col =3D c(\n rep(\"black\", length(site)),\n \"white\= ",\n as.factor(strategy)\n )\n)\n\npar(op)\n#+end_src\n\n#+RESULT= S: fig-BcOverview\n[[file:fig-BcOverview.pdf]]\n\n* Results\n** =3Dsimulati= on sets=3D by Site\n\n#+CAPTION: Proportion label:fig-ScenAgulhas of cells = under aliens for the different strategies at *Agulhas Plains*. Horizontal l= ine at y =3D 0.05 indicates the management target.\n{{{if-latex-else([[file= :fig-ScenAgulhas.pdf]], [[file:fig-ScenAgulhas.png]])}}}\n\n#+CAPTION: Prop= ortion label:fig-ScenCapePeninsula of cells under aliens for the different = strategies at *Cape Peninsula*. Horizontal line at y =3D 0.05 indicates the= management target.\n{{{if-latex-else([[file:fig-ScenCapePeninsula.pdf]], [= [file:fig-ScenCapePeninsula.png]])}}}\n\n#+CAPTION: Proportion label:fig-Sc= enOuteniqua of cells under aliens for the different strategies at *Outeniqu= a*. Horizontal line at y =3D 0.05 indicates the management target.\n{{{if-l= atex-else([[file:fig-ScenOuteniqua.pdf]], [[file:fig-ScenOuteniqua.png]])}}= }\n\n*** #### clearpage #### :ignorehea= ding:\n{{{clearpage}}}\n\n** Proportion reaching Management Goal\n#+CAPTION= : label:fig-CritBudProp Proportion of five simulation runs which reached t= he Management Goal. Colors depict different sites. Horizontal line at y =3D= 0.05 indicates the critical budget $\\bc$\n{{{if-latex-else([[file:fig-Cri= tBudProp.pdf]], [[file:fig-CritBudProp.pdf]])}}}\n\n*** #### clearpage ####= :ignoreheading:\n{{{clearpage}}}\n\n* = Discussion\n- Based on Figure ref:fig-CritBudProp, it is clear that the cho= ice of\n strategy is heavily site dependent. E.g. for Cape Peninsula, it\n= really doesn't matter what strategy is used - just go in and clear\n wha= t you see. While in the case of Agulhas Plains and Outeniqua, there are\n = considerable differences with for Agulhas Plains =3DFuture=3D and =3DRandom= =3D\n being the worst, this is not true for Outeniqua, where =3DFuture=3D = and\n =3DConsensus=3D is the worst.\n\n- No clear pattern which one is bet= ter - heavily site dependent\n\n- Random is not necessarily the worst - som= etimes better than wrong choice\n\n- ???\n\n* Acknowledgements\n* Reference= s\nbibliographystyle:plainnat\n# <>\nbibliography:asmOpt= im.bib\n\n \n* Appendix\n\\appendix\n* Simulations\nSimulations are differe= ntiated by their =3Dsite=3D, =3Dstrategy=3D and\n=3Dbudget=3D (see Table re= f:tab-simulations for the different\ncombinations).\n\n#+CAPTION: Parameter= label:tab-simulations sets used forthe different simulations.\n| =3Dsite= =3D | =3Dstrategy=3D | =3Dbudget=3D |\n|---------------+----------= --+------------|\n| | Consensus | depends |\n| Agulhas = | Future | on |\n| CapePeninsula | Past | =3Dsite=3D = |\n| Outeniqua | Present | and |\n| | Rando= m | =3Dstrategy=3D |\n| | | |\n|---= ------------+------------+------------|\n\n* Budget\n#+CAPTION: label:tab-B= udgets Different budget factors and their actual values per cell.\n| budget= | Agulhas | | CapePeninsula | | Outeniqua | = |\n| factor | R/Cell | R/Cell_inv | R/Cell | R/Cell_inv | R/C= ell | R/Cell_inv |\n|--------+---------+------------+---------------+------= ------+-----------+------------|\n| 0.1 | 1.709 | 2.588 | = 13.504 | 34.721 | 3.358 | 3.372 |\n| 0.2 | | = | 27.008 | 69.442 | 6.716 | 6.744 |\n| 0.3 | = | | 40.512 | 104.163 | 10.074 | 10.116 |\= n| 0.4 | | | 54.016 | 138.884 | 13.432 |= 13.488 |\n| 0.5 | | | 67.52 | 173.605= | 16.79 | 16.86 |\n| 0.6 | | | 81.02= 4 | 208.326 | 20.148 | 20.232 |\n| 0.7 | | = | 94.528 | 243.047 | 23.506 | 23.604 |\n| 0.8 | = | | 108.032 | 277.768 | 26.864 | 26.976 |\n| = 0.9 | | | 121.536 | 312.489 | 30.222 | = 30.348 |\n| 1. | 17.09 | 25.88 | 135.04 | 347.21 | = 33.58 | 33.72 |\n| 1.1 | | | | = | | |\n| 1.2 | 20.508 | 31.056 | = | | | |\n| 1.3 | | = | 175.552 | 451.373 | 43.654 | 43.836 |\n| 1.4 = | | | | | | = |\n| 1.5 | 25.635 | 38.82 | 202.56 | 520.815 | 50.= 37 | 50.58 |\n| 1.6 | | | | = | | |\n| 1.7 | 29.053 | 43.996 | 22= 9.568 | 590.257 | 57.086 | 57.324 |\n| 1.8 | | = | | | | |\n| 1.9 | = | | | | | |\n= | 2. | 34.18 | 51.76 | 270.08 | 694.42 | 67.16 | = 67.44 |\n| 2.2 | 37.598 | 56.936 | | = | | |\n| 2.5 | 42.725 | 64.7 | = | | | |\n| 3. | 51.27 | 77.64 |= | | | |\n| 3.5 | 59.815 = | 90.58 | | | | |\n| = 4. | 68.36 | 103.52 | | | | = |\n| 4.5 | 76.905 | 116.46 | | | = | |\n| 5. | 85.45 | 129.4 | | = | | |\n| 5.5 | 93.995 | 142.34 | = | | | |\n| 6. | 102.54 | = 155.28 | | | | |\n\n\n* Figu= res and tables for pandoc\n\n{{{pandoc(\\\\section*{List of Figures})}}}\n\= n\n{{{pandoc(FiguresHere\\\\par)}}}\n\n{{{pandoc(\\\\section*{List of Table= s})}}}\n\n\n{{{pandoc(TablesHere\\\\par)}}}\n\n\n* Some initial plots of hi= stograms :noexport:\n\n#+begin_src R \n<>\n\nsim <- getDir(\n type =3D \"csv\",\n site =3D \"CapePeninsul= a\",\n strategy =3D \"Consensus\",\n budget =3D \"CapePeninsula_1_0= \",\n run =3D 1)\n\nh <- read.csv(file.path(sim, \"all_dc_hist.csv\"))\n= #+end_src\n\n#+RESULTS:\n\n* Results from Simulations = :noexport:\n** Directory structure = :noexport:\n*** Example\n#+begin_example\n./inputdata= /csv/ASM_Optimization/\n=E2=94=94=E2=94=80=E2=94=80 Simulations\n =E2=94= =9C=E2=94=80=E2=94=80 Agulhas\n =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80= =E2=94=80 simASM\n =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80= Consensus\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C= =E2=94=80=E2=94=80 Agulhas_0_1\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2= =A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 Agulhas\n = =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 = =E2=94=9C=E2=94=80=E2=94=80 47835.1\n =E2=94=82=C2=A0=C2=A0 =E2=94= =82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80 47835= .2\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2= =A0 =E2=94=9C=E2=94=80=E2=94=80 47835.3\n =E2=94=82=C2=A0=C2=A0 = =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80= 47835.4\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2= =A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 47835.5\n =E2=94=82=C2=A0=C2= =A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80 Agulhas_2_5\n = =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2= =94=94=E2=94=80=E2=94=80 ...\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0= =C2=A0 =E2=94=9C=E2=94=80=E2=94=80 Agulhas_5_0\n =E2=94=82=C2=A0=C2=A0 = =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 = ...\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80= =E2=94=80 Agulhas_5_5\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 = =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 ...\n =E2=94=82=C2=A0= =C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 Agulhas_6_0 \n= =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80= =E2=94=80 ...\n =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80 Fu= ture\n =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80 Past ...\n = =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 Present ...\n = =E2=94=9C=E2=94=80=E2=94=80 CapePeninsula ...\n =E2=94=9C=E2=94=80=E2=94= =80 Outeniqua ...\n =E2=94=94=E2=94=80=E2=94=80 log\n#+end_example\n\n./= inputdata/*csv*/SITE/simASM/STRATEGY/BUDGET/FIRE/RUN\n\n*** R functions\nse= e package ASMOptimPaper for the functions used in the analysis. \n\n** GRAS= S simASM input data\n*** Mapset name structure\nThe [[file:inputdata/simASM= /][GRASS location]] contains the following mapsets:\n- [[file:inputdata/sim= ASM/PERMANENT/][PERMANENT]] mapset - read-only :: which contains the South = Africa wide data used in the simulations\n- [[file:inputdata/simASM/grassAn= alysis/][grassAnalysis]] - read-write :: which can be used for analysis\n- = [[file:inputdata/simASM/simASM.Outeniqua.Random.Outeniqua_2_0.Outeniqua.417= 19.5/][simulations]] :: about 530 mapsets whose names are build as follow:\= n\n {{{if-latex-else(simASM.\\\\texttt{SITE}.\\\\texttt{STRATEGY}.\\\\t= exttt{BUDGET}.\\\\texttt{FIREREGIME}.\\\\texttt{JOBID}.\\\\texttt{ARRAYID},= simASM . =3DSITE=3D . =3DSTRATEGY=3D . =3DBUDGET=3D . =3DFIREREGIME=3D . = =3DJOBID=3D . =3DARRAYID=3D)}}}\n #+CAPTION: Simulations conducted and = combination of different parameter values. =3Df=3D is the factor which, mul= tiplied with the yearly original budget of year 2006 [[comment:Check!]] bec= omes the initial budget of the simulation. The factor f is written with und= erscore ({{{us}}}) instead of the decimal point (e.g. 1.5 becomes 1{{{us}}}= 1).\n | =3DSITE=3D | =3DSTRATEGY=3D | =3DBUDGET=3D = | =3DFIREREGIME=3D | =3DJOBID=3D | =3DARRAYID=3D |\n |---------------+= ------------+------------------------+--------------+---------+-----------|= \n | | Consensus | | = | | 1 |\n | Agulhas | Future | =3DSITE=3D {{= {us}}}f | | | 2 |\n | CapePeninsula = | Past | | =3DSITE=3D | number | = 3 |\n | Outeniqua | Present | none | = | | 4 |\n | | Random | = | | | 5 |\n |--------------= -+------------+------------------------+--------------+---------+----------= -|\n\n*** Map name structure in the =3Dsimulation=3D mapsets\nUsing =3DsimA= SM.CapePeninsula.Random.CapePeninsula_1_0.CapePeninsula.xxx.5=3D as an exap= mle.\n**** Static data\n#+begin_src R :colnames yes :exports results\n<>\nx <- getMapNames(\n site =3D \"CapePeninsula\",\n strategy = =3D \"Random\",\n budget =3D \"CapePeninsula_1_0\",\n run =3D = 5,\n type =3D \"raster\",\n pattern =3D \"*\",\n fullMapNames= =3D FALSE\n) %>%\n strsplit(split=3D\"_\") %>%\n subset(sapply(., FU= N=3D\"length\") =3D=3D 1) %>%\n sapply(FUN=3D\"[[\", 1) %>%\n unique(= )\nx <- c(x, \"SPECIES\\{{{us}}}suitability\")\ndata.frame(\"names\" =3D x)= \n#+end_src\n\n#+RESULTS:\n| names |\n|------= -------------------------------|\n| MASK |\n= | NBALs |\n| TPI = |\n| ignitionRisk |\n| region = |\n| vegetationID |\n| vegetationStatus = |\n| SPECIES{{{us}}}suitability |\n\n**** Dynamic, i.e. o= ver time changing, raster maps\nThe maps have the following naming structur= e:\n\n# =3DSPECIES=3D {{{us}}} =3DTYPE=3D {{{us}}} =3DYEAR=3D\n\n\\texttt{S= PECIES}{{{us}}}\\texttt{TYPE}{{{us}}}\\texttt{YEAR}\n\n\nBlocks of combinat= ions are separated by ------ and all combinations are available for all =3D= YEAR=3D\n\n#+begin_src R :colnames yes :exports results\n<>\nx <- ge= tMapNames(\n site =3D \"CapePeninsula\",\n strategy =3D \"Random\= ",\n budget =3D \"CapePeninsula_1_0\",\n run =3D 5,\n type = =3D \"raster\",\n pattern =3D \"*\",\n fullMapNames =3D FALSE\n)= %>%\n strsplit(split=3D\"_\") %>%\n subset(sapply(., FUN=3D\"length\= ") =3D=3D 3) %>%\n data.frame(stringsAsFactors =3D FALSE) %>%\n t() %= >%\n data.frame(stringsAsFactors =3D FALSE)\n##\nrownames(x) <- NULL\n\n= ##\nSP <- x$X1 %in% c(\"ACyclops\", \"HSericea\", \"PPinaster\")\nALL <- x$= X1 %in% \"all\"\nOTHER <- !SP & !ALL\n\n##\nxsp <- x[SP,] %>%\n lapply(u= nique)\nyears <- sort(xsp[[3]])\nmn <- max(sapply (xsp[-3], length))\nxsp <= - lapply(\n xsp[-3],\n function(y) {\n y <- c(sort(y), rep(\"\= ", mn - length(y)))\n }\n)\n\n##\nxall <- x[ALL,] %>%\n lapply(unique= )\nmn <- max(sapply (xall[-3], length))\nxall <- lapply(\n xall[-3],\n = function(y) {\n y <- c(sort(y), rep(\"\", mn - length(y)))\n }\= n)\n\n##\nxother <- x[OTHER,] %>%\n lapply(unique)\nmn <- max(sapply (xo= ther[-3], length))\nxother <- lapply(\n xother[-3],\n function(y) {\n= y <- c(sort(y), rep(\"\", mn - length(y)))\n }\n)\n\n##\n\nx <- = list(\n SPECIES =3D c( xsp$X1, \"------------\", xall$X1, \"------------= \", xother$X1),\n TYPE =3D c( xsp$X2, \"--------------------\", xall$= X2, \"--------------------\", xother$X2)\n)\nx$YEAR <- c(years, rep(\"\", l= ength(x$SPECIES)-length(years)))\ndata.frame(x)\n#+end_src\n\n#+CAPTION: Na= mes label:tab-MapNames of the rastermaps in the simulations. They have the = structure \\texttt{SPECIES}{{{us}}}\\texttt{TYPE}{{{us}}}\\texttt{YEAR}\n#+= RESULTS:\n| SPECIES | TYPE | YEAR |\n|--------------+-= ---------------------+------|\n| ACyclops | age | 2006= |\n| HSericea | ageClass | 2007 |\n| PPinaster | ageCla= ssFire | 2008 |\n| | clearingCost | 2009 |\n| = | dc | 2010 |\n| | dcEstablishe= d | 2011 |\n| | dcFire | 2012 |\n| = | dcSeedlings | 2013 |\n| | disturbances = | 2014 |\n| | fuelModel | 2015 |\n| = | individuals | 2016 |\n| | noEstablished | 2= 017 |\n| | noSeedlings | 2018 |\n| | per= sonDay | 2019 |\n| | pGerm | 2020 |\= n| | seedsDisperse | 2021 |\n| | seedsPlan= t | 2022 |\n| | seedsProduced | 2023 |\n| = | seedsSoil | 2024 |\n| ------------ | ---------------= ----- | 2025 |\n| all | cleared | 2026 |\n| = | clearingCosts | 2027 |\n| | dc = | 2028 |\n| | fuelModel | 2029 |\n| | = personDay | 2030 |\n| | prioStand | 2031= |\n| ------------ | -------------------- | 2032 |\n| clearing | 1h = | 2033 |\n| fire | count | 2034 |\n| = ignition | fuelModel | 2035 |\n| moisture | last = | 2036 |\n| NatVeg | live | 2037 |\n| = | Points | |\n| | stage = | |\n| | | |\n\n* Tool Funct= ions :noexport:\n#+begin_= src sh :results output \nmogrify -format png -density 300 -quality 100 ./fi= g-*.pdf \n#+end_src\n\n#+RESULTS:\n#+begin_example\n12\n3\n1\n17541\n0\n3\n= 0\n3\n17541\n(3 0 obj\\350\\262}\\303\\327\\330\\312\\334\\330-\\336\\017m8= \\223\\337p\\)i\\302\\257\\304h\\267\\376-\\267\\024-\\370\\225\\030,\\365\= \370\\226\\237\\203&\\374R\\2642\\222\\215\\276\\301\\302=3D\\013`\\303\\22= 5h\\355\\t\\351\\316o\\370=3Dh\">\\032c\\321\\241\\205\\177\\374\\364\\377\= \000\\t\\235\\273\\207endstream\\331\\177\\305\\315\\262\\365\\317\\255\\36= 0\\272\\320\\312z\\267|\\376\\033\\355\\367\\347Vx]h\\305\\257\\313\\327\\2= 56\\356q~n\\205\\327\\205V~\\372\\272\\234\\341\\272l\\317BR\\303u\\331\\37= 21\\226\\247p]\\276v\\353FZL+\\274.\\264\\342\\327\\3457\\337}e\\222\\370\\= 365\\337\\265W}}\\367o\\257:\\327\\260\\242\\177\\231\\\\\\353\\004t\\355Y\= \310\\237@\\362\\273\\357_\\277\\250\\003...)\n65535\n21250\n12\n4\n1\n1762= 4\n0\n4\n0\n4\n17624\n(4 0 obje /Pages /Kids [ 7 0 R ] /Count 1 /MediaBox [= 0 0 504 324] >>=3Dh\">\\032c\\321\\241\\205\\177\\374\\364\\377\\000\\t\\23= 5\\273\\207endstream\\331\\177\\305\\315\\262\\365\\317\\255\\360\\272\\320= \\312z\\267|\\376\\033\\355\\367\\347Vx]h\\305\\257\\313\\327\\256\\356q~n\= \205\\327\\205V~\\372\\272\\234\\341\\272l\\317BR\\303u\\331\\3721\\226\\24= 7p]\\276v\\353FZL+\\274.\\264\\342\\327\\3457\\337}e\\222\\370\\365\\337\\2= 65W}}\\367o\\257:\\327\\260\\242\\177\\231\\\\\\353\\004t\\355Y\\310\\237@\= \362\\273\\357_\\277\\250\\003...)\n65535\n21250\n12\n5\n1\n17747\n0\n5\n0\= n5\n17747\n(5 0 objpace << /sRGB 5 0 R >> >>/Count 1 /MediaBox [0 0 504 324= ] >>=3Dh\">\\032c\\321\\241\\205\\177\\374\\364\\377\\000\\t\\235\\273\\207= endstream\\331\\177\\305\\315\\262\\365\\317\\255\\360\\272\\320\\312z\\267= |\\376\\033\\355\\367\\347Vx]h\\305\\257\\313\\327\\256\\356q~n\\205\\327\\= 205V~\\372\\272\\234\\341\\272l\\317BR\\303u\\331\\3721\\226\\247p]\\276v\\= 353FZL+\\274.\\264\\342\\327\\3457\\337}e\\222\\370\\365\\337\\265W}}\\367o= \\257:\\327\\260\\242\\177\\231\\\\\\353\\004t\\355Y\\310\\237@\\362\\273\\= 357_\\277\\250\\003...)\n65535\n21250\n12\n6\n1\n17780\n0\n6\n0\n6\n17780\n= (6 0 objsed 6 0 R]RGB 5 0 R >> >>/Count 1 /MediaBox [0 0 504 324] >>=3Dh\">= \\032c\\321\\241\\205\\177\\374\\364\\377\\000\\t\\235\\273\\207endstream\\= 331\\177\\305\\315\\262\\365\\317\\255\\360\\272\\320\\312z\\267|\\376\\033= \\355\\367\\347Vx]h\\305\\257\\313\\327\\256\\356q~n\\205\\327\\205V~\\372\= \272\\234\\341\\272l\\317BR\\303u\\331\\3721\\226\\247p]\\276v\\353FZL+\\27= 4.\\264\\342\\327\\3457\\337}e\\222\\370\\365\\337\\265W}}\\367o\\257:\\327= \\260\\242\\177\\231\\\\\\353\\004t\\355Y\\310\\237@\\362\\273\\357_\\277\\= 250\\003...)\n65535\n21250\n#+end_example\n\n\n\n* File Local Variables = :noexport:\n\n# Local Variables:\n= # 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":tangle-mode (identity #= o444) :tangle no :mkdirp yes :exports both :padline no :eval never-export := noweb yes")))) (set (make-local-variable (quote org-tag-alist)) (quote nil)= ) (set (make-local-variable (quote org-tag-groups-alist)) (quote nil)) (set= (make-local-variable (quote org-file-tags)) (quote nil)) (set (make-local-= variable (quote buffer-file-name)) (quote "/Users/rainerkrug/Documents/Proj= ects/ASM_Optimization/asmOptim.org")) (set (make-local-variable (quote defa= ult-directory)) (quote "/Users/rainerkrug/Documents/Projects/ASM_Optimizati= on/")) (set (make-local-variable (quote buffer-file-coding-system)) (quote = utf-8-unix)) (insert "#+TITLE: Optimizing management actions for invasive a= lien plants under different budgetary scenarios\n#+AUTHOR: Rainer M. Krug, = N=C3=BAria Roura-Pascual & David M. Richardson\n#+EMAIL: Rainer@krugs.de\n#= +DESCRIPTION:\n#+KEYWORDS:\n\n:CONFIG:\n#+OPTIONS: ':nil *:t -:t ::t <:t H:= 3 \\n:nil ^:t arch:headline\n#+OPTIONS: author:t c:nil creator:comment d:(n= ot \"LOGBOOK\") date:t\n#+OPTIONS: e:t email:nil f:t inline:t num:t p:nil p= ri:nil prop:nil\n#+OPTIONS: stat:t tags:t tasks:t tex:t timestamp:t toc:t t= odo:t |:t\n#+LANGUAGE: en\n#+SELECT_TAGS: export\n#+EXCLUDE_TAGS: noexport\= n#+CREATOR: Emacs 24.4.1 (Org mode 8.3beta)\n#+OPTIONS: H:6\n#+OPTIONS: toc= :6\n#+STARTUP: hideblocks\n#+TODO: TODO(t) WAIT(w) CHECK(c) EXECUTE(e) CODE= (o) TEXT(y) | DONE(d) CANCELED(x)\n:END:\n:LATEXHEADER:\n#+LaTeX_CLASS_OPTI= ONS: [a4paper,usenames,dvipsnames,table]\n\n#+LATEX_HEADER: \\lstset{%\n#+L= ATEX_HEADER: basicstyle=3D\\ttfamily\\footnotesize, % the font th= at is used for the code\n#+LATEX_HEADER: tabsize=3D4, = % sets default tabsize to 4 spaces\n#+LATEX_HEADER: numbers=3Dleft= , % where to put the line numbers\n#+LATEX_HEADER: n= umberstyle=3D\\tiny, % line number font size\n#+LATEX_HEADER:= stepnumber=3D0, % step between two line numbers\n#+= LATEX_HEADER: breaklines=3Dtrue, %!! don't break long l= ines of code\n#+LATEX_HEADER: showtabs=3Dfalse, % show= tabs within strings adding particular underscores\n#+LATEX_HEADER: sho= wspaces=3Dfalse, % show spaces adding particular underscores= \n#+LATEX_HEADER: showstringspaces=3Dfalse, % underline spaces= within strings\n#+LATEX_HEADER: keywordstyle=3D\\color{blue},\n#+LATEX= _HEADER: identifierstyle=3D\\color{black},\n#+LATEX_HEADER: strings= tyle=3D\\color{ForestGreen},\n#+LATEX_HEADER: commentstyle=3D\\color{re= d},\n#+LATEX_HEADER: backgroundcolor=3D\\color{light-gray}, % sets th= e background color\n#+LATEX_HEADER: columns=3Dfullflexible, \n#+LATEX_= HEADER: basewidth=3D{0.5em,0.4em}, \n#+LATEX_HEADER: captionpos=3Db= , % sets the caption position to `bottom'\n#+LATEX_HEADE= R: extendedchars=3Dfalse %!?? 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Krug\nMaintainer: Rainer M Krug \nDepends: ASMOptimPackage (>=3D 0.2.0)\n#+end_src\n\n\n* TODO Setup .Rpro= file file :noexport:\nThis file will= only be used when R is not started with --vanilla!!!!\n#+begin_src R :tang= le ./.Rprofile\n.libPaths(normalizePath(\"library\"))\nlibrary(devtools)\n#= load_all(\"./package/asm\")\n#+end_src\n\n* Code Snippets for Analysis and= Results :noexport:\n:PROPERTIES:\n:header-args+:= :tangle no\n:header-args+: :eval never\n:END:\n** initR\nLoad lEnergyBalan= ce and WindProfilePaper packages\n#+NAME: initR\n#+begin_src R\n\n## \nlibrary(devtools)\n## install_bitbucket(repo=3D\"rkrug/WindProfiles\", = ref=3D\"v_0.7.0\", auth_user=3D\"rkrug\", password=3D\"\")\nload_all(\"./pa= ckage/ASMOptimPaper/ASMOptimPaper.org/\")\n## gInit()\n## \n\n#+en= d_src\n\n** getMapsetTypes\nThis is a template to be remembered and to be u= sed as a base for getting the results types from a simulation.\n\n#+NAME: g= etMapsetTypes\n#+begin_src R \n getMapNames(\n site =3D \"Cap= ePeninsula\",\n strategy =3D \"Consensus\",\n budget =3D \"= CapePeninsula_1_0\",\n run =3D 5,\n type =3D \"raste= r\",\n pattern =3D \"*\",\n fullMapNames =3D FALSE\n ) %>= %\n strsplit(split=3D\"_\") %>%\n subset(sapply(., FUN=3D\"le= ngth\") =3D=3D 2) %>%\n sapply(FUN=3D\"[[\", 2) %>%\n unique(= )\n\n#+end_src\n* emails = :noexport:\n[[notmuch:id:002301d10bf4$ed38e670$c7aab350$@gmail.com]= [Email from N=C3=BAria Roura-Pascual: RE: Missing piece ...]]\n\n* Data pre= paration :noexport:\n** Spl= it complete data into different types\n:PROPERTIES:\n:heade-args: :eval nev= er-export\n:END:\n- csv ::\n#+begin_src sh :session data :results none\nmkd= ir ./inputdata/csv/ \nrsync -avz --include=3D\"*/\" --include=3D\"*.csv\" = --exclude=3D\"*\" /Volumes/Seagate_1TB/HomeExternal/Documents/ASM_Optimizat= ion ./inputdata/csv/ \nfind . -type f -name \"*.asc\" -exec gzip -v {} \\;= \nrsync -avz --include=3D\"*/\" --include=3D\"*.csv\" --exclude=3D\"*\" rai= nerkrug@pogoplug:~/clusterResults/clusterResults/simASM/RandomClearingPaper= /results/simASMRightFire ./inputdata/csv/\n#+end_src\n\n- png ::\n#+begin_s= rc sh :session data :results none\nmkdir ./inputdata/png// \nrsync -avz --= include=3D\"*/\" --include=3D\"*.png\" --exclude=3D\"*\" /Volumes/Seagate_1= TB/HomeExternal/Documents/ASM_Optimization ./inputdata/png/ \nrsync -avz -= -include=3D\"*/\" --include=3D\"*.png\" --exclude=3D\"*\" /Volumes/Home\\ o= n\\ Pogoplug/clusterResults/clusterResults/simASM/RandomClearingPaper/resul= ts/simASMRightFire/ ./inputdata/csv/\nrsync -avz --include=3D\"*/\" --inclu= de=3D\"*.png\" --exclude=3D\"*\" rainerkrug@pogoplug:~/clusterResults/clust= erResults/simASM/RandomClearingPaper/results/simASMRightFire ./inputdata/pn= g/\n#+end_src\n\n** Merge directory structure into\n./inputdata/csv/ASM_Oti= mization/Simulations/SITE/simASM/STRATEGY/BUDGET/FIRE/RUN\n\n* Bash scripts= for data preparation and handling :noexport:\n** tar2gra= ss - extract grass/simulation directories and create single grass location= \n:PROPERTIES:\n:header-args:sh: :tangle ./tar2grass\n:header-args:sh: :com= ments no\n:header-args:sh+: :tangle-mode (identity #o755)\n:END:\nThis scri= pt extracts the =3Dgrass/simulation=3D directory from a tar.gz\nfile of the= simulation and moves it into the folder =3D./simASM=3D folder\nand renames= it to the name of the =3Dtar.gz=3D without the =3D.tar.gz=3D.\n\nAfter add= ing the \n#+begin_src sh \nTAR=3D\"$1\"\necho $TAR ...\ntar -xvzf $TAR --i= nclude=3D'*/grass/simulation/*'\nmkdir -p simASM\ncd tmp\ncd $(ls)\nSIM=3D$= (ls)\ncd $(ls)\ncd grass\nmv simulation $SIM\nmv $SIM ./../../../../simASM/= \ncd ./../../../../\nrm -rf ./tmp\n#+end_src\n\n** make the squashfs\n:PROP= ERTIES:\n:header-args:sh: :tangle ./addPERMANENT\n:header-args:sh: :comment= s no\n:header-args:sh+: :tangle-mode (identity #o755)\n:END:\nCopies =3DPER= MANENT=3D from =3D./inputdata/PERMANENT=3D into the location and\nadds the = link to a mapset =3D./../grassAnalysis=3D which can be used for\nwrite acce= ss outside the mapset, i.e. the complete mapset can be\nconverted into a Sq= uashFS and be mounted afterwards.\n\n#+begin_src sh \ncp -R ./inputdata/PER= MANENT ./simASM/\nln ln -s ./../../grassAnalysis ./simASM/grassAnalysis\n#+= end_src\n\n#+begin_src sh :tangle no\nmksquashfs ./simASM ./simASM.squashf= s -processors 6\n#+end_src\n\n** COMMENT tar2sqfs - Prepare .tar.gz files = and convert to SquashFS\n:PROPERTIES:\n:header-args:sh: :tangle ./tar2sqfs\= n:header-args:sh+: :comments no\n:header-args:sh+: :tangle-mode (identity #= o755)\n:END:\nThis script converts is converting tar.gz fines in tto .squas= hfs files\nin the current directory. It should be run in the ./input direct= ory.\n\n*** Extract .tar.gz simulation but exclude certain redundant files\= n#+begin_src sh\nTAR=3D\"$1\"\ntar -xvzf $TAR --exclude=3D'*/output/*' --e= xclude=3D'input.tar.gz' --exclude=3D'output.tar.gz'\n#+end_src\n\n*** Climb= in dirrectory into single unique directory\n#+begin_src sh \ncd tmp\ncd `l= s`\n#+end_src\n\n*** Replace link to =3DPERMANENT=3D with link to existing = =3DPERMANENT=3D \n#+begin_src sh \nfind . -type \"link\" -name \"PERMANENT\= " -exec ln -fhs ./../../PERMANENT {} \\;\n#+end_src\n\n*** Create squashfs = in base folder and delete original folder\n#+begin_src sh \nNAME=3D$(ls)\nm= ksquashfs $NAME ./../../$NAME.squashfs -b 1048576 -comp xz -Xdict-size 100%= \ncd ./../../\nrm -rf ./tmp\n#+end_src\n\n\n\n** COMMENT oneGrass\n:PROPERT= IES:\n:header-args:sh: :tangle ./oneGRASS\n:header-args:sh+: :comments no\n= :header-args:sh+: :tangle-mode (identity #o755)\n:END:\n#+begin_src sh \nDE= ST=3D./DEST$$\nGRASS=3D./GRASS$$/simASM\n\nfunction finish {\n rm -rf \"= $DEST\"\n rm -rf \"$GRASS\"\n}\ntrap finish EXIT\n\nmkdir -p \"$GRASS\"\= n\necho Copying ./inputdata/PERMANENT to $GRASS ...\ncp -R ./inputdata/PERM= ANENT $GRASS/\nfor F in ./inputdata/simASM.*.squashfs; do \n BN=3D$(base= name $F)\n DN=3D$(dirname $F)\n DIR=3D\"${BN%.*}\"\n echo \"<<<<<\= "\n echo Extracting grass/simulation from $F to ./$DEST/grass/simulation= \n unsquashfs -dest $DEST \"$F\" -e grass/simulation/*\n echo Moving = \"./$DEST/grass/simulation\" to \"$GRASS/simASM/grass/$DIR\"\n mv \"./$D= EST/grass/simulation\" \"$GRASS\"\n mv \"$GRASS/simulation\" \"$GRASS/$D= IR\"\n echo Deleting \"$DEST\"\n rm -rf \"$DEST\"\n echo \">>>>>\"= \ndone \necho Create link $GRASS/analysis out of the squashfs for editable= mapset\nln -s \"./../../grassAnalysis\" \"$GRASS/analysis\"\necho Making S= quashFS ./input/simASM.grass.squashfs from $GRASS/simASM ...\nmksquashfs \"= $GRASS\" ./input/simASM.grass.squashfs -b 1048576 -comp xz -Xdict-size 100%= \necho Done\n#+end_src\n\n** COMMENT mountSimASM - mount simASM.grass.squas= hfs to ./inputdata/simASM\n:PROPERTIES:\n:header-args:sh: :tangle ./mountSi= mASM\n:header-args:sh+: :comments no\n:header-args:sh+: :tangle-mode (ident= ity #o755)\n:END:\n#+begin_src sh \nDIR=3D./inputdata/simASM\nSFS=3D./input= data/simASM.grass.squashfs\nFN=3D./umountSimASM\necho \"#!/bin/sh\" > $FN\n= echo \"umount $DIR\" >> $FN\necho \"rm $DIR/NOT_MOUNTED\" >> $FN\necho \"rm= dir $DIR\" >> $FN\necho \"rm $FN\" >> $FN\nchmod +x $FN\nmkdir -p \"$DIR\"\= ntouch \"$DIR/NOT_MOUNTED\"\nsquashfuse \"$SFS\" \"$DIR\"\n#+end_src\n\n\n*= * COMMENT mountSims - mount all ./input/simASM.*.squashfs \n:PROPERTIES:\n:= header-args:sh: :tangle ./mountsimASM\n:header-args:sh+: :comments no\n:hea= der-args:sh+: :tangle-mode (identity #o755)\n:END:\n#+begin_src sh \nFN=3D.= /umountsimASM\necho \"#!/bin/sh\" > $FN\nchmod +x umountsimASM\nfor F in ./= inputdata/simASM.*.squashfs; do \n BN=3D$(basename $F)\n DN=3D$(dirna= me $F)\n DIR=3D$DN/\"${BN%.*}\"\n echo ###\n echo Mounting $F to $= D\n mkdir -p \"$DIR\"\n squashfuse \"$F\" \"$DIR\" \n echo \"umoun= t $DIR; rmdir $DIR\" >> $FN\ndone \necho \"rm ./umountsimASM\" >> $FN\n#+e= nd_src\n\n\n\n* Introduction = :noexport:\nInvasive alien plants pose a significant threat to the en= vironment and society. They are known to cause significant changes in speci= es, communities and ecosystems citep:Vila2011 and to be responsible for maj= or economic losses citep:Pimentel2005. Economic expenses are in the form of= losses to provisioning services, but more importantly in the form of manag= ement costs, including eradication, control, and monitoring citep:Vila2010.= This is particularly certain for strongly dominating plant species, since = eradication is not always an option and the maintenance and effectiveness o= f control measures are largely uncertain. Economics are known to play an im= portant role in clearing operations citep:Higgins1997a,Marais2004a.\n \n[[c= omment:Needs to be reworded.][For example, cite:Odom2005 showed that invest= ment in managing the Scotch broom (/Cytisus scoparius/) is economically jus= tified and that higher budgets yield higher value for the society. citep:Ca= cho2008 used a decision model based on economic analysis to identify the mo= st appropriate management goal (eradication, containment or no management).= Both studies coincide in indicating that the major factor determining the = management goal is the available budget, with higher budgets resulting in m= ore eradication oriented goals.]]\n\nBesides the overreaching importance of= budget, the effectivity of management actions is also constrained by the c= haracteristics of species} and the environment citep:Cacho2008,Krug2010_rmk= and the strategy adopted for clearing invasive alien plants ([[comment:Ref= needed][REF]]). Investment needs to be adjusted to the particularities of = each study site and maintained over time to maximize the efficiency of clea= ring programs citep:Krug2010_rmk. The maintenance of management measures ov= er time is, however, not exempt of nuances. [[comment:TAlk about the probl= ems associated with clearing the same site over time][TALK ABOUTTHE PROBLEM= S ASSOCIATED WITH CLEARING THE SAME SITE OVER TIME]] The selection of the o= ptimal clearing strategy, based on the characteristics of the environment a= nd the allocation of resources over time, is thus crucial to provide practi= cal guidelines for use in fiscal and policy decisions of IAP management. \n= \nThis study builds on our previous work that examined the impact of differ= ent budget scenarios on the effectivity of clearing actions on a selected p= rioritization strategy citep:Krug2010_rmk, but instead of focusing on a sin= gle prioritization strategy we also examine the effect of several prioritiz= ation strategies. In particular, we aim to identify the optimal combination= of elements =E2=80=93budget and clearing strategy=E2=80=93 that ensures th= e effective management of IAPs at regional scales, while taking into accoun= t the particularities of invasive species and the hosting environment.\n\nI= n this study, we use the three sites in the South Africa=E2=80=99s Cape Flo= ristic Region as a case study (Agulhas Plains, Cape Peninsula, Outeniqua, s= ee ref:map-All), an area subject to extensive control operations to reduce = the expansion of woody IAPs that threaten the persistence of its high biolo= gical diversity. \n\n** #### clearpage #### = :ignoreheading:\n{{{clearpage}}}\n\n\n* Methods\n\n** Study sites\nT= he simulations for this study are based on three study sites within South A= frica=E2=80=99s Cape Floristic Region: Agulhas Plain, Cape Peninsula and Ou= teniqua (see Fig. ref:map-All and Table ref:tab-All for details). All three= sites contain large areas that are formally protected. Whereas the Cape Pe= ninsula and Outeniqua regions have large areas of natural or seminatural ve= getation, the Agulhas Plains consists of a mosaic of agricultural landscape= s and conservation areas. All sites are invaded by IAPs, albeit by differen= t species and to different degrees (see ref:tab-All for details). The most = important IAP groups in the study sites and in the CFR overall are major wo= ody plants, particularly species of /Acacia/, /Hakea/ and /Pinus/ citep:Ric= hardson1986_rmka,Richardson1992_rmk,Richardson1994_rmk,Wilgen1994_rmk,Richa= rdson2008_rmk [[comment:Further References needed?]]). \n\nDifferent usage = and management pattern as well as topography of the three sites result in d= ifferent fire patterns, e.g. with respect to the average area burned per ye= ar and the average number of fires per year (see supplemental material from= cite:Krug2010_rmk for details).\n\n#+CAPTION: Study label:map-All sites in= South Africa's Cape Floristic Region\n[[file:map-All.png]]\n\n#+ATTR_LATEX= : :caption \\caption{Details \\label{tab-All} the study sites used in this = study. $\\bpc$ is the budget per year per cell, $\\bpci$ is the budget per = year per invaded cell (1ha =3D 1cell).} \\todo[inline]{Units in headers onl= y or in table itself?}\n| | Area | Area invaded | B= udget | 2007/2008 | |\n| | in ha= | in ha | Overall in R | $\\bpc$ in R/ha | $\\bpci$ in R/h= a |\n|----------------+---------+--------------------+--------------+------= ----------+------------------|\n| Agulhas Plains | 215,982 | 142,672 ( 66.1= % ) | 3,691,728 | 17.09 | 25.88 |\n| Cape Peninsula= | 49,179 | 19,226 ( 39.1 % ) | 6,675,539 | 135.74 | = 347.21 |\n| Outeniqua | 57,697 | 57,454 ( 99.6 % ) | 1,937,220 |= 33.58 | 33.72 |\n| | | = | | | |\n|---------= -------+---------+--------------------+--------------+----------------+----= --------------|\n\n\n\n** Model description\nTo model the spread of species= under different management strategies, we used the spatio-temporal explici= t simulation model {{{sc(SpreadSim)}}} ( [[comment:This needs to be added][= The source code is available at]] [[comment:Merge all different into one -= the only difference should be the prioritisation file!]]). In this section= , we present a short overview of the model, a detailed description can be f= ound in cite:Krug2010_rmk. \n\nThe purpose of the model is to simulate the = spread of three IAPs groups, namely /Acacia/, /Hakea/ and /Pinus/ citep:Kru= g2010_rmk, by incorporating spatial population dynamics (seed production, s= eed dispersal, germination and establishment), fire dynamics and the cleari= ng of IAPs based on a certain prioritization strategy, the costs of clearin= g actions and the budget available per year. The aim is to assess the effec= tiveness of different clearing strategies and budget scenarios over time. \= n\nThe model {{{sc(SpreadSim)}}} was written in R citep:R2008_rmk, (with ad= ditional packages by cite:Pebesma2005_rmk,Petzoldt2007_rmk,Bivand2009_rmk,J= ames2009_rmk,Keitt2009_rmk,Lewin-Koh2009_rmk,Urbanek_rmk) and uses GRASS ci= tep:GRASS2007 for the storage of the spatial results and spatial calculatio= ns. It can be separated into five different modules, namely {{{sc(clearing)= }}}, {{{sc(fire)}}}, {{{sc(seedProduction)}}}, {{{sc(seedDispersal)}}} and = {{{sc(germEst)}}}, which are executed consecutively (see Figure ref:fig-Mod= el for the flowchart of the model). Each module contains parameter controll= ing the stochastic spread and management of IAPs of the genera /Acacia/, /H= akea/ and /Pinus/ citep:Krug2010_rmk. \n\nDue to the stochastic nature of = the model, each *simulation* (defined by the =3Dsite=3D, prioritization =3D= strategy=3D and =3Dbudget=3D) was repeated five times. For further analysis= , we defined a *simulation set* as different =3Dbudget=3D scenarios for the= same =3Dsite=3D and clearing =3Dstrategy=3D.\n\nThe input data for the sim= ulations was provided by the relevant nature conservation agencies and Work= ing for Water (see cite:Roura-Pascual2009_rmkb,Roura-Pascual2009_rmkc for d= etails [[comment:REF for topography and natural vegetation data needed? I = don't think so, as referred to the papers)]]. \n\nSimulations were done on = a raster with a resolution of $100m \\times 100m$ cells and with a time ste= p of one year. \n\n#+ATTR_LATEX: :caption \\caption{\\label{fig-Model} fro= m \\protect\\cite{Krug2010_rmk}} \\todo[inline]{If we need this here, I wil= l redo it - just let me know.}\n{{{if-latex-else([[file:fig-Model.pdf]], [[= file:fig-Model.png]])}}}\n\n\n** Prioritization =3Dstrategy=3D\n\nThe prior= itization =3Dstrategy=3D assigns each individual cell a priority value for = clearing of the IAPs out of these cells. Subsequently, cells are cleared in= descending order of their priority until the budget is spend (see cite:Kru= g2010_rmk). \n\nThe strategies are based on weights and consider the follow= ing factors:\n\n- Area burnt recently\n- Density of IAPs\n- Spread based on= topography\n- Area at fire risk\n- Age of IAPs\n- Identity of IAPs\n- Last= clearing operation\n\nFor a detailed description of these factors and how = they were derived, see citep:Roura-Pascual2009_rmkb,Roura-Pascual2009_rmkc.= \n\nThe prioritization strategies evaluated in this study are (Fig. ref:fi= g-Strategies):\n\n- =3Dconsensus=3D :: this strategy was developed through = a participatory process with managers and researchers experts on various as= pects of IAPs citep:Roura-Pascual2009_rmkb. This resulted in priority was g= iven to areas burnt recently and the density of the IAPs was reduced citep:= Roura-Pascual2009_rmkc. The following =3Dstrategies=3D are based on the =3D= consensus strategy=3D and were modified based on certain aims.\n- =3Dmainta= in follow-ups=3D :: (aka =3Dpast=3D) aims at prioritizing areas based on pr= evious clearing operations, i.e. giving higher priority to areas which have= been cleared already or in follow-ups. It relies on accurate information o= f fire and clearing history of the site citep:Roura-Pascual2009_rmkc;\n- = =3Dkeep clean=3D :: (aka =3Dpresent=3D) is a strategy where management oper= ations do not rely on fire opportunities to clear invaded stands and the po= tential of a stand to be a major source of invasion is minimized. It relies= on accurate information of the present, i.e. present density of the IAPs a= nd spread potential based on topography citep:Roura-Pascual2009_rmkc;\n- = =3Dwater production=3D :: (aka =3Dfuture=3D)is orientated towards increasin= g water production in the future, with higher priority given to riparian ar= eas in lower parts of the catchment invaded by dense stands of /Acacia/ spe= cies. It uses mainly static information, i.e. spread based on topography ci= tep:Roura-Pascual2009_rmkc;\n- =3Drandom=3D :: is a null-strategy which doe= s not require any knowledge about the past and randomly assigns priorities = citep:Krug2010_rmk.\n\nA visualization of these prioritization strategies c= an be seen in Fig. ref:fig-Strategies.\n\n#+ATTR_LATEX: :caption \\caption{= \\label{fig-Strategies} from \\protect\\cite{Roura-Pascual2009_rmkc}} \\tod= o[inline]{This figure needs to be redone and further info added}\n{{{if-lat= ex-else([[file:fig-Strategies.pdf]], [[file:fig-Strategies.png]])}}}\n\n** = Budget\nThe budget as well as the costs used in this study are based on the= actual budget for the three areas of the financial year 2007/2008. They ar= e specified in South African Rand (R) as $\\boldmath\\bpc$ (IAP clearing bu= dget per year per cell) and $\\boldmath\\bpci$ (IAP clearing budget per ye= ar per invaded cell).\n\nThe actual budgets were multiplied with a factor r= anging from 0.1 to 6.0 to obtain 14 to 15 different budget scenarios for ea= ch simulation set defined by a =3Dsite=3D and a =3Dstrategy=3D (see Figure = ref:fig-Budgets and Table ref:tab-Budgets in the Appendix for values from c= ite:Krug2010_rmk).\n\nThe budgets and the factors used for the three sites = are[[comment:We could leave the factors out here but I think it is a useful= addition. All information also also in the table in the Appendix]]:\n\n| = budget | Agulhas | CapePeninsula | Outeniqua |\n| = factor | | | |\n|------------= --------------+-----------+---------------+-----------|\n| $\\bpc$ $\\frac= {R}{cell}$ | 17.09 | 135.05 | 33.58 |\n| $\= \bpci$ | 25.88 | 347.21 | 33.72 |\n|------------------------= --+-----------+---------------+-----------|\n| 0.1 | C= M K W - | C M K W R | C M K W R |\n| 0.2 | = | - - - - R | - - - - R |\n| 0.3 | |= - - - - R | - - - - R |\n| 0.4 | | - - = - - R | - - - - R |\n| 0.5 | - - - - R | C M K W R= | C M K W R |\n| 0.6 | | - - - - R = | - - - - R |\n| 0.7 | | C M K W R | - -= - - R |\n| 0.8 | | - - - - R | - - - - = R |\n| 0.9 | | - - - - R | - - - - R |\n= | 1. | - - - - R | C M K W R | - - - - R |\n| = 1.1 | | | |\n| = 1.2 | - - - - R | | |\n| = 1.3 | | - - - - R | C M K W R |\n| = 1.4 | | | |\n| 1.= 5 | - - - - R | C M K W R | C M K W R |\n| 1.6 | = | | |\n| 1.7 | - - - = - R | - - - - R | |\n| 1.8 | |= | |\n| 1.9 | | = | |\n| 2. | - - - - R | - - - - R= | C M K W R |\n| 2.2 | - - - - R | = | |\n| 2.5 | C M K W R | | = |\n| 3. | - - - - R | | = |\n| 3.5 | - - - - R | | |\n= | 4. | - - - - R | | |\n| = 4.5 | - - - - R | | |\n| = 5. | C M K W R | | |\n| = 5.5 | C M K W R | | |\n| = 6. | C M K W R | | |\n\n\n- Agulhas Plains :: $= \\bpc =3D$ 17.09 R/cell, $\\bpci =3D$ 25.88 R/cell\n - Consensus, Maintain= Follow Ups, Keep clean, Water production :: 0.1; 2.5; 5.0; 5.5; 6.0\n - R= andom :: 0.5; 1.0; 1.2; 1.5; 1.7; 2.0; 2.2; 2.5; 3.0; 3.5; 4.0; 4.5; 5.0; 5= .5; 6.0; 6.5; 7.0\n- CapePeninsula :: $\\bpc =3D$ 135.047 R/cell, $\\bpci = =3D$ 347.21R/cell\n - Consensus, Maintain Follow Ups, Keep clean, Water pr= oduction :: 0.1; 0.5; 0.7; 1.0; 1.5\n - Random :: 0.1; 0.2; 0.3; 0.4; 0.5;= 0.6; 0.7; 0.8; 0.9; 1.0; 1.3; 1.5; 1.7; 2.0\n- Outeniqua :: $\\bpc =3D$ 33= .58R/cell, $\\bpci =3D$ 33.72R/cell\n - Consensus, Maintain Follow Ups, Ke= ep clean, Water production :: 0.1; 0.5; 1.3; 1.5; 2.0\n - Random :: 0.1; 0= .2; 0.3; 0.4; 0.5; 0.6; 0.7; 0.8; 0.9; 1.0; 1.3; 1.5; 1.7; 2.0\n\n#+CAPTION= : Different label:fig-Budgets budgets of the different sites in comparison.= Colours indicate different sites, pattern indicate if the budget is \"per = all cells\" or \"per invaded cells\"\n{{{if-latex-else([[file:fig-Budgets.p= df]], [[file:fig-Budgets.png]])}}}\n\n** TODO Analysis\nThe analysis follow= s the analysis done in cite:Krug2010_rmk and uses very similar measures and= indicators to assess the efficiency of the different strategies. We theref= ore calculated for each individual =3Dsimulation=3D run (i.e. five per =3Ds= imulation=3D)\n\n# - $\\cua$ :: number of cells covered by IAPs per year, w= here *covered* is defined as $dc \\leq 1$ i.e. *rare* or less\n- $\\cov$ ::= as the proportion of the cells covered by aliens in year $t$\n (i.e. a= ll cells for which the density class of aliens is higher\n than *rare*)= . $\\cov =3D 0$ indicates no alien infestation and $\\cov\n =3D 1$ indi= cates complete cover of IAPs. (From cite:Krug2010_rmk) \n# - $\\ac$ :: numb= er of cells cleared of IAPs in year $t$\n\nTo assess the effectiveness of t= he =3Dsimulation=3D run, we defined a\n- management goal :: as to be having= 95% of the area (cells) alien free (density class of aliens smaller or equ= al *rare*), i.e. $\\cov \\leq 0.95$\nwhere each individual simulation run i= s regarded as successful after reaching the *management goal*.\n\nIf the *m= anagement goal* was reached, we calculated for each =3Dsimulation=3D run\n-= $\\tmg$ :: as the time when we reached the management goal\n- $\\bmg$ :: a= s the cumulative budget needed to achieve the management goal\n\nFor each = =3Dsimulation=3D (i.e. over the five simulation runs) we then calculated\n+= $\\pmg$ :: proportions of all the runs (here five simulation runs) in one = =3Dsimulation=3D which reached the *management goal*\n\nTo accumulate over = each =3Dsimulation set=3D, i.e. one =3Dsite=3D and one =3Dstrategy=3D and m= ultiple =3Dbudget=3Ds, we calculated\n- $\\bc$ :: the *critical budget* is = the lowest budget at which more than 50% of all simulations resulted in ach= ieving the *management goal* of 95% alien free within the time-frame of 30 = years,\n- $\\bci$ :: as $\\bc$ but the using $\\bpci$ instead of $\\bpc$\n\= n# Finally, we calculated for each set of =3Dsite=3D and =3Dstrategy=3D a\n= # - budget index :: $\\bm{\\idb} =3D \\frac{\\bpc}{\\bc}$\n# - time index := : $\\bm{\\idt} =3D \\frac{\\tmg(\\bc)-1}{\\mathit{mean}\\left(\\tmg(\\bc)-1= \\right)}$ [[comment:I have to confess I am not sure what I did here!]]\n\n= # The variables used to evaluate the efficiency of the clearing operations = under different prioritization strategies and budgetary scenarios were: are= a covered by IAPs per year, IAP clearing budget per year, and area cleared = of IAPs per year. The proportion of the site covered by aliens in year t, i= .e. all cells for which the density class of aliens is higher than =E2=80= =98=E2=80=98rare=E2=80=99=E2=80=99, is called cov(t). cov(t) =3D 0 indicate= s no alien infestation and cov(t) =3D 1 indicates complete cover of IAPs.\n= \n# We set our =E2=80=98=E2=80=98management goal=E2=80=99=E2=80=99 arbitrar= ily at clearing 95% (and for some scenarios 90%) of the area of IAPs. This = =E2=80=98=E2=80=98management goal=E2=80=99=E2=80=99 represents the threshol= d cover, below which the management is considered as being successful. An e= radication of all IAPs would be ideal, but would require much higher resour= ces.\n \n# If during the simulation the cover of IAPs was reduced below the= =E2=80=98=E2=80=98management goal=E2=80=99=E2=80=99, we determined the yea= r in which it occurred (tnf95) and the cumulative costs per cell up to tnf9= 5 (BPC 95). Note that BPC 95 <=3D bPC=C2=B7tnf95 as the whole budget might = not be spent. The lowest budget at which more than 50% of all simulations r= esulted in a reduction of the alien cover to less than 5% within the time-f= rame of 30 years, was called the =E2=80=98=E2=80=98critical budget=E2=80=99= =E2=80=99 (bPC relating to bPC and bPCINV relating to bPCINV). Each budget = scenario was simulated five times.\n\n# In addition, we calculated a budget= index and a time index for each species separately. The budget index was c= alculated by dividing the actual budget bPC by the critical budget ^ bPC. C= onsequently, the budget index was one for the critical budget. The time ind= ex was calculated as follow:\n\n# ??ADD FORMULA??\n\n# By subtracting one f= rom tnf95 we achieved that the lowest value of the index is zero, while 1 r= epresents the average tnf95=C3=B0 ^ bPC=C3=9E.\n\n** #### clearpage #### = :ignoreheading:\n{{{clearpage}}}\n\n\n\= n\n# LocalWords: IAPs\n\n* TODO [2/6] Make Analysis and Graphs = :noexport:\n:PROPERTIES:\n:COOKIE_DATA: todo recursive\n= :header-args+: :eval no-export\n:END:\n** DONE Budget graph fig-budgets\n\n= \n#+NAME: tabBudgets\n| budget | Agulhas | | CapePeninsula | = | Outeniqua | |\n| factor | R/Cell | R/Cell_inv | = R/Cell | R/Cell_inv | R/Cell | R/Cell_inv |\n|--------+---------+-----= -------+---------------+------------+-----------+------------|\n| 0.1 | = 1.709 | 2.588 | 13.504 | 34.721 | 3.358 | 3.372 = |\n| 0.2 | | | 27.008 | 69.442 | 6.716= | 6.744 |\n| 0.3 | | | 40.512 | 104.1= 63 | 10.074 | 10.116 |\n| 0.4 | | | 54.= 016 | 138.884 | 13.432 | 13.488 |\n| 0.5 | | = | 67.52 | 173.605 | 16.79 | 16.86 |\n| 0.6 | = | | 81.024 | 208.326 | 20.148 | 20.232 |\n| = 0.7 | | | 94.528 | 243.047 | 23.506 | = 23.604 |\n| 0.8 | | | 108.032 | 277.768 | = 26.864 | 26.976 |\n| 0.9 | | | 121.536 |= 312.489 | 30.222 | 30.348 |\n| 1. | 17.09 | 25.88 | = 135.04 | 347.21 | 33.58 | 33.72 |\n| 1.1 | | = | | | | |\n| 1.= 2 | 20.508 | 31.056 | | | | = |\n| 1.3 | | | 175.552 | 451.373 | 43= .654 | 43.836 |\n| 1.4 | | | | = | | |\n| 1.5 | 25.635 | 38.82 | = 202.56 | 520.815 | 50.37 | 50.58 |\n| 1.6 | | = | | | | |\n| 1.7 | = 29.053 | 43.996 | 229.568 | 590.257 | 57.086 | 57.324 |= \n| 1.8 | | | | | = | |\n| 1.9 | | | | = | | |\n| 2. | 34.18 | 51.76 | 270.= 08 | 694.42 | 67.16 | 67.44 |\n| 2.2 | 37.598 | 56.936= | | | | |\n| 2.5 | 42.72= 5 | 64.7 | | | | |\n| = 3. | 51.27 | 77.64 | | | | = |\n| 3.5 | 59.815 | 90.58 | | | = | |\n| 4. | 68.36 | 103.52 | | = | | |\n| 4.5 | 76.905 | 116.46 | = | | | |\n| 5. | 85.45 | = 129.4 | | | | |\n| 5.5= | 93.995 | 142.34 | | | | = |\n| 6. | 102.54 | 155.28 | | | = | |\n\n\n#+NAME: fig-Budgets\n#+begin_src R :var BUDGET=3Dta= bBudgets :exports results :file-ext pdf :results graphics :width 7 :height= 7\n<>\nlibrary(magrittr)\nx <- BUDGET\nx <- BUDGET %>%\n extract= (-(1:2),) %>%\n set_names(\n c(\n \"f\",\n = \"Agulhas\", \"Agulhas_I\",\n \"CapePeninsula\", \"CapePeninsula= _I\",\n \"Outeniqua\", \"Outeniqua_I\"\n )\n )\n\n##\n= for (i in 1:length(x)) {\n x[[i]] <- as.numeric(x[[i]])\n}\n\n##\nx %<>= %\n extract(-1) %>%\n unlist %>%\n extract(!is.na(.)) %>%\n sor= t(decreasing =3D TRUE)\n\n##\nAG_I <- x %>%\n names %>%\n grep(\"Agul= has_I\", .)\nAG <- x %>%\n names %>%\n grep(\"Agulhas[1-9]\", .)\n##\= nCP_I <- x %>%\n names %>%\n grep(\"CapePeninsula_I\", .)\nCP <- x %>= %\n names %>%\n grep(\"CapePeninsula[1-9]\", .)\n##\nOU_I <- x %>%\n = names %>%\n grep(\"Outeniqua_I\", .)\nOU <- x %>%\n names %>%\n = grep(\"Outeniqua[1-9]\", .)\n\n##\ncols <- rep(\"black\", length(x))\ncols= [c(AG, AG_I)] <- \"green\"\ncols[c(CP, CP_I)] <- \"red\"\ncols[c(OU, OU_I)]= <- \"blue\"\n\n##\ndens <- rep(-1, length(x))\ndens[c(AG_I, CP_I, OU_I)] <= - 30\n\n##\npar(\n mar =3D c(4.1, 0.3, 0.1, 0.8)\n)\nbarplot(\n x,\n = xlab =3D \"Budget per cell\",\n xlim =3D c(0, 700),\n names.arg = =3D \"\",\n horiz =3D TRUE,\n col =3D cols,\n density =3D dens\n)\= nsiteNames <- c(\"Agulhas Plains\", \"Cape Peninsula\", \"Outeniqua\")\nleg= end(\n x =3D \"topright\",\n legend =3D c( siteNames, \"\", \"per al= l cells\", \"per invaded cells\"),\n fill =3D c(\"green\", \"red\", \= "blue\", NA, \"black\", \"black\"),\n border =3D c(\"black\", \"black\"= , \"black\", NA, \"black\", \"black\"),\n density =3D c(-1, -1, -1, NA, = -1, 30)\n)\n#+end_src\n\n#+RESULTS: fig-Budgets\n[[file:fig-Budgets.pdf]]\n= \n\n** DONE Calculate dc\n#+begin_src R :results output :tangle ./package/A= SMOptimPaper/inst/scripts/analysis.calculate.dc.R :eval never \n<>\n= dc <- getDc( new =3D TRUE, cores =3D 6 )\n#+end_src\n\n#+RESULTS:\n#+begin_= example\nLoading ASMOptimPaper\nLoading required package: sp\nLoading requi= red package: raster\nLoading required package: rgrass7\nLoading required pa= ckage: XML\nGRASS GIS interface loaded with GRASS version: (GRASS not runni= ng)\nLoading required package: magrittr\n\nAttaching package: =E2=80=98magr= ittr=E2=80=99\n\nThe following object is masked from =E2=80=98package:raste= r=E2=80=99:\n\n extract\n\nLoading required package: parallel\ngisdbase = ./inputdata \nlocation simASM \nmapset grassAnalysis \nrows = 210 \ncolumns 790 \nnorth 6263000 \nsouth 6242000 \nwest= 574000 \neast 653000 \nnsres 100 \newres 100 \np= rojection +proj=3Dutm +south +zone=3D34 +a=3D6378137 +rf=3D298.257223563 += no_defs\n+towgs84=3D0.000,0.000,0.000 +to_meter=3D1.0\n#+end_example\n\n** = TODO Examples of some simulations :noexport:\n= #+begin_src R \nua <- getUaWide(site =3D \"Agulhas\", strategy=3D\"Consensu= s\", species =3D \"all\")\n\ndcs <- split(\n dc, dc$run\n)\nmatplot(x = =3D dc$year, dc[as.character(1:7)])\nua <- rowSums(dc[as.character(1:7)])\n= \nplot(ua)\n\nua <- getUa(site =3D \"Agulhas\", budget=3D\"None\", species = =3D \"all\", proportion=3DTRUE)\nplot(ua$cl)\nb\n#+end_src\n** CHECK Figure= s --- =3Dsimulation sets=3D by site\n:PROPERTIES:\n:header-args+: :epilogue= rm(ST, SI)\n:END:\n\n:CODESNIPPETS:\n#+NAME: plotScenarios\n#+begin_src R = :eval never\n<>\npar(\n mfcol =3D c(length(STRATEGIES)-1, 1),\n = mar =3D c(1.2, 4.1, 1.1, 0.1),\n cex =3D 0.7\n)\nfor (i in 1:(leng= th(STRATEGIES)-1)) {\n if (i =3D=3D length(STRATEGIES)-1) {\n par= (\n mar =3D c(4.2, 4.1, 1.1, 0.1)\n ) \n }\n = plotScenario( site =3D SI, strategy =3D STRATEGIES[i])\n}\n#+end_src\n:E= ND:\n\n#+NAME: fig-ScenAgulhas\n#+HEADER: :var SI=3D\"Agulhas\"\n#+begin_sr= c R :exports results :file-ext pdf :results graphics :width 7 :height 7\n<<= plotScenarios>>\n#+end_src\n\n#+RESULTS: fig-ScenAgulhas\n[[file:fig-ScenAg= ulhas.pdf]]\n\n\n#+NAME: fig-ScenCapePeninsula\n#+HEADER: :var SI=3D\"CapeP= eninsula\"\n#+begin_src R :exports results :file-ext pdf :results graphics = :width 7 :height 7\n<>\n#+end_src\n\n#+RESULTS: fig-ScenCape= Peninsula\n[[file:fig-ScenCapePeninsula.pdf]]\n\n\n#+NAME: fig-ScenOuteniqu= a\n#+HEADER: :var SI=3D\"Outeniqua\"\n#+begin_src R :exports results :file-= ext pdf :results graphics :width 7 :height 7\n<>\n#+end_src\= n\n\n#+RESULTS: fig-ScenOuteniqua\n[[file:fig-ScenOuteniqua.pdf]]\n\n{{{cle= arpage}}}\n\n** CHECK Figures --- Proportion reaching Management Goal\n#+NA= ME: fig-CritBudProp\n#+begin_src R :exports results :file-ext pdf :results = graphics :width 7 :height 7\n<>\npar(\n mfcol =3D c(length(SITES)= , 1),\n mar =3D c(1.2, 4.1, 1.1, 0.1),\n cex =3D 0.7\n)\nfor (i i= n 1:length(SITES)) {\n if (i =3D=3D length(SITES)) {\n par(\n = mar =3D c(4.2, 4.1, 1.1, 0.1)\n ) \n }\n plot= CritBud( \n site =3D SITES[i],\n ylab =3D \"Prop Man. Goal\",= \n dx =3D 0.6,\n xlim =3D c(0, 150)\n )\n}\n#+end_src\n\n#= +RESULTS: fig-CritBudProp\n[[file:fig-CritBudProp.pdf]]\n\n** CHECK Plot of= Critical Budgets[[ comment:Here is something not right and needs to be che= cked. It could be the functions?]] :noexport:\n#+NAME: fig-BcOverview\n#+be= gin_src R :exports results :file-ext pdf :results graphics :width 7 :height= 4.5\n<>\ncb <- getCriticalBudget(species =3D \"all\")\n\n\nplot(\n = bc$budgetPerCell ~ bc$tmg.mean,\n xlab =3D \"mean time until manageme= nt goal is achieved at critical budget\",\n ylab =3D \"critical budget b= er cell\",\n cex =3D 1,\n col =3D as.factor(bc$strategy),\n pch = =3D as.integer(as.factor(bc$site))\n)\n\nsite <- unique(bc$site)\nstrategy = <- unique(bc$strategy)\nlegend(\n \"bottomright\",\n legend =3D c(\n = site,\n \"\",\n strategy\n ),\n pch =3D c(\n = as.integer(as.factor(site)),\n 1,\n rep(15, length(strate= gy))\n ),\n col =3D c(\n rep(\"black\", length(site)),\n = \"white\",\n as.factor(strategy)\n )\n)\n\npar(op)\n#+end_src\n= \n#+RESULTS: fig-BcOverview\n[[file:fig-BcOverview.pdf]]\n\n* Results\n** = =3Dsimulation sets=3D by Site\n\n#+CAPTION: Proportion label:fig-ScenAgulha= s of cells under aliens for the different strategies at *Agulhas Plains*. H= orizontal line at y =3D 0.05 indicates the management target.\n{{{if-latex-= else([[file:fig-ScenAgulhas.pdf]], [[file:fig-ScenAgulhas.png]])}}}\n\n#+CA= PTION: Proportion label:fig-ScenCapePeninsula of cells under aliens for the= different strategies at *Cape Peninsula*. Horizontal line at y =3D 0.05 in= dicates the management target.\n{{{if-latex-else([[file:fig-ScenCapePeninsu= la.pdf]], [[file:fig-ScenCapePeninsula.png]])}}}\n\n#+CAPTION: Proportion l= abel:fig-ScenOuteniqua of cells under aliens for the different strategies a= t *Outeniqua*. Horizontal line at y =3D 0.05 indicates the management targe= t.\n{{{if-latex-else([[file:fig-ScenOuteniqua.pdf]], [[file:fig-ScenOuteniq= ua.png]])}}}\n\n*** #### clearpage #### = :ignoreheading:\n{{{clearpage}}}\n\n** Proportion reaching Management Goal= \n#+CAPTION: label:fig-CritBudProp Proportion of five simulation runs whic= h reached the Management Goal. Colors depict different sites. Horizontal li= ne at y =3D 0.05 indicates the critical budget $\\bc$\n{{{if-latex-else([[f= ile:fig-CritBudProp.pdf]], [[file:fig-CritBudProp.pdf]])}}}\n\n*** #### cle= arpage #### :ignoreheading:\n{{{clearpa= ge}}}\n\n* Discussion\n- Based on Figure ref:fig-CritBudProp, it is clear t= hat the choice of\n strategy is heavily site dependent. E.g. for Cape Peni= nsula, it\n really doesn't matter what strategy is used - just go in and c= lear\n what you see. While in the case of Agulhas Plains and Outeniqua, th= ere are\n considerable differences with for Agulhas Plains =3DFuture=3D an= d =3DRandom=3D\n being the worst, this is not true for Outeniqua, where = =3DFuture=3D and\n =3DConsensus=3D is the worst.\n\n- No clear pattern whi= ch one is better - heavily site dependent\n\n- Random is not necessarily th= e worst - sometimes better than wrong choice\n\n- ???\n\n* Acknowledgements= \n* References\nbibliographystyle:plainnat\n# <>\nbiblio= graphy:asmOptim.bib\n\n \n* Appendix\n\\appendix\n* Simulations\nSimulation= s are differentiated by their =3Dsite=3D, =3Dstrategy=3D and\n=3Dbudget=3D = (see Table ref:tab-simulations for the different\ncombinations).\n\n#+CAPTI= ON: Parameter label:tab-simulations sets used forthe different simulations.= \n| =3Dsite=3D | =3Dstrategy=3D | =3Dbudget=3D |\n|---------------= +------------+------------|\n| | Consensus | depends |\n|= Agulhas | Future | on |\n| CapePeninsula | Past | = =3Dsite=3D |\n| Outeniqua | Present | and |\n| = | Random | =3Dstrategy=3D |\n| | | = |\n|---------------+------------+------------|\n\n* Budget\n#+CAPTION: = label:tab-Budgets Different budget factors and their actual values per cell= .\n| budget | Agulhas | | CapePeninsula | | Outeniqua= | |\n| factor | R/Cell | R/Cell_inv | R/Cell | R/Cell_i= nv | R/Cell | R/Cell_inv |\n|--------+---------+------------+-----------= ----+------------+-----------+------------|\n| 0.1 | 1.709 | 2.58= 8 | 13.504 | 34.721 | 3.358 | 3.372 |\n| 0.2 | = | | 27.008 | 69.442 | 6.716 | 6.744 |\n| = 0.3 | | | 40.512 | 104.163 | 10.074 | = 10.116 |\n| 0.4 | | | 54.016 | 138.884 | = 13.432 | 13.488 |\n| 0.5 | | | 67.52 |= 173.605 | 16.79 | 16.86 |\n| 0.6 | | | = 81.024 | 208.326 | 20.148 | 20.232 |\n| 0.7 | | = | 94.528 | 243.047 | 23.506 | 23.604 |\n| 0.= 8 | | | 108.032 | 277.768 | 26.864 | 26.= 976 |\n| 0.9 | | | 121.536 | 312.489 | 30= .222 | 30.348 |\n| 1. | 17.09 | 25.88 | 135.04 | = 347.21 | 33.58 | 33.72 |\n| 1.1 | | | = | | | |\n| 1.2 | 20.508 | 3= 1.056 | | | | |\n| 1.3 | = | | 175.552 | 451.373 | 43.654 | 43.836 |= \n| 1.4 | | | | | = | |\n| 1.5 | 25.635 | 38.82 | 202.56 | 520.81= 5 | 50.37 | 50.58 |\n| 1.6 | | | = | | | |\n| 1.7 | 29.053 | 43.996= | 229.568 | 590.257 | 57.086 | 57.324 |\n| 1.8 | = | | | | | |\n| = 1.9 | | | | | | = |\n| 2. | 34.18 | 51.76 | 270.08 | 694.42 | = 67.16 | 67.44 |\n| 2.2 | 37.598 | 56.936 | | = | | |\n| 2.5 | 42.725 | 64.7 | = | | | |\n| 3. | 51.27 | = 77.64 | | | | |\n| 3.5= | 59.815 | 90.58 | | | | = |\n| 4. | 68.36 | 103.52 | | | = | |\n| 4.5 | 76.905 | 116.46 | | = | | |\n| 5. | 85.45 | 129.4 | = | | | |\n| 5.5 | 93.995 | 14= 2.34 | | | | |\n| 6. | 1= 02.54 | 155.28 | | | | |\= n\n\n* Figures and tables for pandoc\n\n{{{pandoc(\\\\section*{List of Figu= res})}}}\n\n\n{{{pandoc(FiguresHere\\\\par)}}}\n\n{{{pandoc(\\\\section*{Li= st of Tables})}}}\n\n\n{{{pandoc(TablesHere\\\\par)}}}\n\n\n* Some initial = plots of histograms :noexport:\n\n#+begin_s= rc R \n<>\n\nsim <- getDir(\n type =3D \"csv\",\n site =3D \"C= apePeninsula\",\n strategy =3D \"Consensus\",\n budget =3D \"CapePe= ninsula_1_0\",\n run =3D 1)\n\nh <- read.csv(file.path(sim, \"all_dc_his= t.csv\"))\n#+end_src\n\n#+RESULTS:\n\n* Results from Simulations = :noexport:\n** Directory structure = :noexport:\n*** Example\n#+begin_example\n= ./inputdata/csv/ASM_Optimization/\n=E2=94=94=E2=94=80=E2=94=80 Simulations\= n =E2=94=9C=E2=94=80=E2=94=80 Agulhas\n =E2=94=82=C2=A0=C2=A0 =E2=94= =94=E2=94=80=E2=94=80 simASM\n =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94= =80=E2=94=80 Consensus\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0= =E2=94=9C=E2=94=80=E2=94=80 Agulhas_0_1\n =E2=94=82=C2=A0=C2=A0 =E2= =94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 Agulha= s\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2= =A0 =E2=94=9C=E2=94=80=E2=94=80 47835.1\n =E2=94=82=C2=A0=C2=A0 = =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80= 47835.2\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2= =A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80 47835.3\n =E2=94=82=C2=A0=C2= =A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80= =E2=94=80 47835.4\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2= =94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 47835.5\n =E2=94=82= =C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80 Agulhas_= 2_5\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2= =A0 =E2=94=94=E2=94=80=E2=94=80 ...\n =E2=94=82=C2=A0=C2=A0 =E2=94= =82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94=80 Agulhas_5_0\n =E2=94=82=C2= =A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94= =80=E2=94=80 ...\n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2= =94=9C=E2=94=80=E2=94=80 Agulhas_5_5\n =E2=94=82=C2=A0=C2=A0 =E2=94= =82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 ...\n = =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80= Agulhas_6_0 \n =E2=94=82=C2=A0=C2=A0 =E2=94=82=C2=A0=C2=A0 =E2= =94=94=E2=94=80=E2=94=80 ...\n =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94= =80=E2=94=80 Future\n =E2=94=82=C2=A0=C2=A0 =E2=94=9C=E2=94=80=E2=94= =80 Past ...\n =E2=94=82=C2=A0=C2=A0 =E2=94=94=E2=94=80=E2=94=80 Pre= sent ...\n =E2=94=9C=E2=94=80=E2=94=80 CapePeninsula ...\n =E2=94=9C= =E2=94=80=E2=94=80 Outeniqua ...\n =E2=94=94=E2=94=80=E2=94=80 log\n#+en= d_example\n\n./inputdata/*csv*/SITE/simASM/STRATEGY/BUDGET/FIRE/RUN\n\n*** = R functions\nsee package ASMOptimPaper for the functions used in the analys= is. \n\n** GRASS simASM input data\n*** Mapset name structure\nThe [[file:i= nputdata/simASM/][GRASS location]] contains the following mapsets:\n- [[fil= e:inputdata/simASM/PERMANENT/][PERMANENT]] mapset - read-only :: which cont= ains the South Africa wide data used in the simulations\n- [[file:inputdata= /simASM/grassAnalysis/][grassAnalysis]] - read-write :: which can be used f= or analysis\n- [[file:inputdata/simASM/simASM.Outeniqua.Random.Outeniqua_2_= 0.Outeniqua.41719.5/][simulations]] :: about 530 mapsets whose names are bu= ild as follow:\n\n {{{if-latex-else(simASM.\\\\texttt{SITE}.\\\\texttt{= STRATEGY}.\\\\texttt{BUDGET}.\\\\texttt{FIREREGIME}.\\\\texttt{JOBID}.\\\\t= exttt{ARRAYID}, simASM . =3DSITE=3D . =3DSTRATEGY=3D . =3DBUDGET=3D . =3DFI= REREGIME=3D . =3DJOBID=3D . =3DARRAYID=3D)}}}\n #+CAPTION: Simulations = conducted and combination of different parameter values. =3Df=3D is the fac= tor which, multiplied with the yearly original budget of year 2006 [[commen= t:Check!]] becomes the initial budget of the simulation. The factor f is wr= itten with underscore ({{{us}}}) instead of the decimal point (e.g. 1.5 bec= omes 1{{{us}}}1).\n | =3DSITE=3D | =3DSTRATEGY=3D | =3DBUDGET=3D= | =3DFIREREGIME=3D | =3DJOBID=3D | =3DARRAYID=3D |\n |--= -------------+------------+------------------------+--------------+--------= -+-----------|\n | | Consensus | = | | | 1 |\n | Agulhas | Future |= =3DSITE=3D {{{us}}}f | | | 2 |\n | = CapePeninsula | Past | | =3DSITE=3D | nu= mber | 3 |\n | Outeniqua | Present | none = | | | 4 |\n | | Random = | | | | 5 |\n |= ---------------+------------+------------------------+--------------+------= ---+-----------|\n\n*** Map name structure in the =3Dsimulation=3D mapsets\= nUsing =3DsimASM.CapePeninsula.Random.CapePeninsula_1_0.CapePeninsula.xxx.5= =3D as an exapmle.\n**** Static data\n#+begin_src R :colnames yes :exports = results\n<>\nx <- getMapNames(\n site =3D \"CapePeninsula\",\= n strategy =3D \"Random\",\n budget =3D \"CapePeninsula_1_0\",\n = run =3D 5,\n type =3D \"raster\",\n pattern =3D \"*\",\n = fullMapNames =3D FALSE\n) %>%\n strsplit(split=3D\"_\") %>%\n subse= t(sapply(., FUN=3D\"length\") =3D=3D 1) %>%\n sapply(FUN=3D\"[[\", 1) %>= %\n unique()\nx <- c(x, \"SPECIES\\{{{us}}}suitability\")\ndata.frame(\"= names\" =3D x)\n#+end_src\n\n#+RESULTS:\n| names = |\n|-------------------------------------|\n| MASK = |\n| NBALs |\n| TPI = |\n| ignitionRisk |\n| region = |\n| vegetationID |\n| vege= tationStatus |\n| SPECIES{{{us}}}suitability |\n\n**** D= ynamic, i.e. over time changing, raster maps\nThe maps have the following n= aming structure:\n\n# =3DSPECIES=3D {{{us}}} =3DTYPE=3D {{{us}}} =3DYEAR=3D= \n\n\\texttt{SPECIES}{{{us}}}\\texttt{TYPE}{{{us}}}\\texttt{YEAR}\n\n\nBloc= ks of combinations are separated by ------ and all combinations are availab= le for all =3DYEAR=3D\n\n#+begin_src R :colnames yes :exports results\n<>\nx <- getMapNames(\n site =3D \"CapePeninsula\",\n strategy= =3D \"Random\",\n budget =3D \"CapePeninsula_1_0\",\n run =3D= 5,\n type =3D \"raster\",\n pattern =3D \"*\",\n fullMapName= s =3D FALSE\n) %>%\n strsplit(split=3D\"_\") %>%\n subset(sapply(., F= UN=3D\"length\") =3D=3D 3) %>%\n data.frame(stringsAsFactors =3D FALSE) = %>%\n t() %>%\n data.frame(stringsAsFactors =3D FALSE)\n##\nrownames(= x) <- NULL\n\n##\nSP <- x$X1 %in% c(\"ACyclops\", \"HSericea\", \"PPinaster= \")\nALL <- x$X1 %in% \"all\"\nOTHER <- !SP & !ALL\n\n##\nxsp <- x[SP,] %>%= \n lapply(unique)\nyears <- sort(xsp[[3]])\nmn <- max(sapply (xsp[-3], l= ength))\nxsp <- lapply(\n xsp[-3],\n function(y) {\n y <- c(so= rt(y), rep(\"\", mn - length(y)))\n }\n)\n\n##\nxall <- x[ALL,] %>%\n = lapply(unique)\nmn <- max(sapply (xall[-3], length))\nxall <- lapply(\n = xall[-3],\n function(y) {\n y <- c(sort(y), rep(\"\", mn - lengt= h(y)))\n }\n)\n\n##\nxother <- x[OTHER,] %>%\n lapply(unique)\nmn <- = max(sapply (xother[-3], length))\nxother <- lapply(\n xother[-3],\n f= unction(y) {\n y <- c(sort(y), rep(\"\", mn - length(y)))\n }\n)\= n\n##\n\nx <- list(\n SPECIES =3D c( xsp$X1, \"------------\", xall$X1, = \"------------\", xother$X1),\n TYPE =3D c( xsp$X2, \"---------------= -----\", xall$X2, \"--------------------\", xother$X2)\n)\nx$YEAR <- c(year= s, rep(\"\", length(x$SPECIES)-length(years)))\ndata.frame(x)\n#+end_src\n\= n#+CAPTION: Names label:tab-MapNames of the rastermaps in the simulations. = They have the structure \\texttt{SPECIES}{{{us}}}\\texttt{TYPE}{{{us}}}\\te= xttt{YEAR}\n#+RESULTS:\n| SPECIES | TYPE | YEAR |\n|--= ------------+----------------------+------|\n| ACyclops | age = | 2006 |\n| HSericea | ageClass | 2007 |\n| PPinast= er | ageClassFire | 2008 |\n| | clearingCost = | 2009 |\n| | dc | 2010 |\n| = | dcEstablished | 2011 |\n| | dcFire | 20= 12 |\n| | dcSeedlings | 2013 |\n| | dist= urbances | 2014 |\n| | fuelModel | 2015 |\n= | | individuals | 2016 |\n| | noEstablis= hed | 2017 |\n| | noSeedlings | 2018 |\n| = | personDay | 2019 |\n| | pGerm = | 2020 |\n| | seedsDisperse | 2021 |\n| = | seedsPlant | 2022 |\n| | seedsProduced |= 2023 |\n| | seedsSoil | 2024 |\n| ------------ | -= ------------------- | 2025 |\n| all | cleared | 2026 = |\n| | clearingCosts | 2027 |\n| | dc = | 2028 |\n| | fuelModel | 2029 |\n| = | personDay | 2030 |\n| | prioStand = | 2031 |\n| ------------ | -------------------- | 2032 |\n| clearin= g | 1h | 2033 |\n| fire | count = | 2034 |\n| ignition | fuelModel | 2035 |\n| moisture = | last | 2036 |\n| NatVeg | live | 20= 37 |\n| | Points | |\n| | stag= e | |\n| | | |\n= \n* Tool Functions :noexp= ort:\n#+begin_src sh :results output \nmogrify -format png -density 300 -qu= ality 100 ./fig-*.pdf \n#+end_src\n\n#+RESULTS:\n#+begin_example\n12\n3\n1\= n17541\n0\n3\n0\n3\n17541\n(3 0 obj\\350\\262}\\303\\327\\330\\312\\334\\33= 0-\\336\\017m8\\223\\337p\\)i\\302\\257\\304h\\267\\376-\\267\\024-\\370\\2= 25\\030,\\365\\370\\226\\237\\203&\\374R\\2642\\222\\215\\276\\301\\302=3D\= \013`\\303\\225h\\355\\t\\351\\316o\\370=3Dh\">\\032c\\321\\241\\205\\177\\= 374\\364\\377\\000\\t\\235\\273\\207endstream\\331\\177\\305\\315\\262\\365= \\317\\255\\360\\272\\320\\312z\\267|\\376\\033\\355\\367\\347Vx]h\\305\\25= 7\\313\\327\\256\\356q~n\\205\\327\\205V~\\372\\272\\234\\341\\272l\\317BR\= \303u\\331\\3721\\226\\247p]\\276v\\353FZL+\\274.\\264\\342\\327\\3457\\337= }e\\222\\370\\365\\337\\265W}}\\367o\\257:\\327\\260\\242\\177\\231\\\\\\35= 3\\004t\\355Y\\310\\237@\\362\\273\\357_\\277\\250\\003...)\n65535\n21250\n= 12\n4\n1\n17624\n0\n4\n0\n4\n17624\n(4 0 obje /Pages /Kids [ 7 0 R ] /Count= 1 /MediaBox [0 0 504 324] >>=3Dh\">\\032c\\321\\241\\205\\177\\374\\364\\3= 77\\000\\t\\235\\273\\207endstream\\331\\177\\305\\315\\262\\365\\317\\255\= \360\\272\\320\\312z\\267|\\376\\033\\355\\367\\347Vx]h\\305\\257\\313\\327= \\256\\356q~n\\205\\327\\205V~\\372\\272\\234\\341\\272l\\317BR\\303u\\331\= \3721\\226\\247p]\\276v\\353FZL+\\274.\\264\\342\\327\\3457\\337}e\\222\\37= 0\\365\\337\\265W}}\\367o\\257:\\327\\260\\242\\177\\231\\\\\\353\\004t\\35= 5Y\\310\\237@\\362\\273\\357_\\277\\250\\003...)\n65535\n21250\n12\n5\n1\n1= 7747\n0\n5\n0\n5\n17747\n(5 0 objpace << /sRGB 5 0 R >> >>/Count 1 /MediaBo= x [0 0 504 324] >>=3Dh\">\\032c\\321\\241\\205\\177\\374\\364\\377\\000\\t\= \235\\273\\207endstream\\331\\177\\305\\315\\262\\365\\317\\255\\360\\272\\= 320\\312z\\267|\\376\\033\\355\\367\\347Vx]h\\305\\257\\313\\327\\256\\356q= ~n\\205\\327\\205V~\\372\\272\\234\\341\\272l\\317BR\\303u\\331\\3721\\226\= \247p]\\276v\\353FZL+\\274.\\264\\342\\327\\3457\\337}e\\222\\370\\365\\337= \\265W}}\\367o\\257:\\327\\260\\242\\177\\231\\\\\\353\\004t\\355Y\\310\\23= 7@\\362\\273\\357_\\277\\250\\003...)\n65535\n21250\n12\n6\n1\n17780\n0\n6\= n0\n6\n17780\n(6 0 objsed 6 0 R]RGB 5 0 R >> >>/Count 1 /MediaBox [0 0 504 = 324] >>=3Dh\">\\032c\\321\\241\\205\\177\\374\\364\\377\\000\\t\\235\\273\\= 207endstream\\331\\177\\305\\315\\262\\365\\317\\255\\360\\272\\320\\312z\\= 267|\\376\\033\\355\\367\\347Vx]h\\305\\257\\313\\327\\256\\356q~n\\205\\32= 7\\205V~\\372\\272\\234\\341\\272l\\317BR\\303u\\331\\3721\\226\\247p]\\276= v\\353FZL+\\274.\\264\\342\\327\\3457\\337}e\\222\\370\\365\\337\\265W}}\\3= 67o\\257:\\327\\260\\242\\177\\231\\\\\\353\\004t\\355Y\\310\\237@\\362\\27= 3\\357_\\277\\250\\003...)\n65535\n21250\n#+end_example\n\n\n\n* File Local= Variables :noexport:\n\n# Loca= l Variables:\n# eval: (visual-line-mode 1)\n# End:\n\n\n") (narrow-to-regio= n 1 57482) (goto-char 1)))() | org-export-copy-buffer() | org-export-as(latex nil nil nil (:output-file "./asmOptim.tex")) | org-export-to-file(latex "./asmOptim.tex" nil nil nil nil nil) | org-latex-export-to-latex(nil nil nil nil) | org-export-dispatch(nil) | funcall-interactively(org-export-dispatch nil) | call-interactively(org-export-dispatch nil nil) | command-execute(org-export-dispatch) `---- =2D-=20 Rainer M. 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