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Re: [O] Bug: can not evaluate any code blocks after enabling additional
|
From: |
Rainer M Krug |
|
Subject: |
Re: [O] 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 |
|
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/24.5 (darwin) |
Kyle Meyer <address@hidden> writes:
> Rainer M Krug <address@hidden> writes:
>
>> Nicolas Goaziou <address@hidden> writes:
>>
>>> Hello,
>>>
>>> Rainer M Krug <address@hidden> 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-initialize).
>>
>> 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=102882.
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]
org-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
mode-class)) (put (quote 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
(standard-syntax-table)))) nil (set-char-table-parent org-mode-syntax-table
(syntax-table)))) (if (or (abbrev-table-get org-mode-abbrev-table :parents) (eq
org-mode-abbrev-table local-abbrev-table)) nil (abbrev-table-put
org-mode-abbrev-table :parents (list local-abbrev-table)))) (use-local-map
org-mode-map) (set-syntax-table org-mode-syntax-table) (setq local-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-remove
outline-mode-menu-hide))) (define-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 (quote 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)) org-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 (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 (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-variable (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 org-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-local-variable (quote
indent-line-function)) (quote org-indent-line)) (set (make-local-variable
(quote indent-region-function)) (quote org-indent-region)) (org-setup-filling)
(org-setup-comments-handling) (org-element-cache-reset) (set
(make-local-variable (quote beginning-of-defun-function)) (quote
org-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 (quote
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) (quote org-block-todo-from-children-or-siblings-or-parent)))
(if org-enforce-todo-checkbox-dependencies (add-hook (quote org-blocker-hook)
(quote org-block-todo-from-checkboxes)) (remove-hook (quote org-blocker-hook)
(quote org-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-variable (quote
pcomplete-command-completion-function)) (quote org-pcomplete-initial)) (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-name "Org") (progn (if (get (quote outline-mode) (quote mode-class)) (put
(quote 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-mode-syntax-table (syntax-table)))) (if (or
(abbrev-table-get org-mode-abbrev-table :parents) (eq org-mode-abbrev-table
local-abbrev-table)) nil (abbrev-table-put org-mode-abbrev-table :parents (list
local-abbrev-table)))) (use-local-map org-mode-map) (set-syntax-table
org-mode-syntax-table) (setq local-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-remove outline-mode-menu-hide))) (define-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 (quote 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)) org-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 (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 (vconcat
(mapcar (function ...) (if ... 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-variable (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
org-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-local-variable (quote indent-line-function)) (quote org-indent-line))
(set (make-local-variable (quote indent-region-function)) (quote
org-indent-region)) (org-setup-filling) (org-setup-comments-handling)
(org-element-cache-reset) (set (make-local-variable (quote
beginning-of-defun-function)) (quote org-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 (quote 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) (quote org-block-todo-from-children-or-siblings-or-parent)))
(if org-enforce-todo-checkbox-dependencies (add-hook (quote org-blocker-hook)
(quote org-block-todo-from-checkboxes)) (remove-hook (quote org-blocker-hook)
(quote org-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-variable (quote
pcomplete-command-completion-function)) (quote org-pcomplete-initial)) (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-inhibit-startup t)) (org-mode)) (set (make-local-variable (quote
org-table-may-need-update)) (quote t)) (set (make-local-variable (quote
org-latex-and-related-regexp)) (quote "")) (set (make-local-variable (quote
org-todo-line-tags-regexp)) (quote "^\\(\\*+\\)\\(?:
+\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\\|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)\\)?\\(?:
+\\(.*?\\)\\)??\\(?:[ ]+\\(:[[:alnum:]:address@hidden:\\)\\)?[
]*$")) (set (make-local-variable (quote org-complex-heading-regexp-format))
(quote "^\\(\\*+\\)\\(?:
+\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\\|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)\\)?\\(?:
+\\(\\[#.\\]\\)\\)?\\(?: +\\(?:\\[[0-9%%/]+\\] *\\)*\\(%s\\)\\(?:
*\\[[0-9%%/]+\\]\\)*\\)\\(?:[ ]+\\(:[[:alnum:address@hidden:]+:\\)\\)?[
]*$")) (set (make-local-variable (quote org-complex-heading-regexp))
(quote "^\\(\\*+\\)\\(?:
+\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\\|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)\\)?\\(?:
+\\(\\[#.\\]\\)\\)?\\(?: +\\(.*?\\)\\)??\\(?:[
]+\\(:[[:alnum:address@hidden:]+:\\)\\)?[ ]*$")) (set
(make-local-variable (quote org-todo-line-regexp)) (quote "^\\(\\*+\\)\\(?:
+\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\\|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)\\)?\\(?:
+\\(.*?\\)\\)?[ ]*$")) (set (make-local-variable (quote
org-not-done-heading-regexp)) (quote "^\\(\\*+\\)\\(?:
+\\(C\\(?:HECK\\|ODE\\)\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)\\)\\(?:
+\\(.*?\\)\\)?[ ]*$")) (set (make-local-variable (quote
org-not-done-regexp)) (quote
"\\(C\\(?:HECK\\|ODE\\)\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)")) (set
(make-local-variable (quote org-todo-regexp)) (quote
"\\(C\\(?:ANCELED\\|HECK\\|ODE\\)\\|DONE\\|EXECUTE\\|T\\(?:EXT\\|ODO\\)\\|WAIT\\)"))
(set (make-local-variable (quote org-not-done-keywords)) (quote ("TODO" "WAIT"
"CHECK" "EXECUTE" "CODE" "TEXT"))) (set (make-local-variable (quote
org-todo-log-states)) (quote nil)) (set (make-local-variable (quote
org-todo-sets)) (quote (("TODO" "WAIT" "CHECK" "EXECUTE" "CODE" "TEXT" "DONE"
"CANCELED")))) (set (make-local-variable (quote org-todo-heads)) (quote
("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 99 101 111
121 100 120))) (set (make-local-variable (quote org-todo-key-alist)) (quote
((:startgroup) ("TODO" . 116) ("WAIT" . 119) ("CHECK" . 99) ("EXECUTE" . 101)
("CODE" . 111) ("TEXT" . 121) ("DONE" . 100) ("CANCELED" . 120) (:endgroup))))
(set (make-local-variable (quote org-todo-kwd-alist)) (quote (("TODO" sequence
"TODO" "DONE" "CANCELED") ("WAIT" sequence "TODO" "DONE" "CANCELED") ("CHECK"
sequence "TODO" "DONE" "CANCELED") ("EXECUTE" sequence "TODO" "DONE"
"CANCELED") ("CODE" sequence "TODO" "DONE" "CANCELED") ("TEXT" sequence "TODO"
"DONE" "CANCELED") ("DONE" sequence "TODO" "DONE" "CANCELED") ("CANCELED"
sequence "TODO" "DONE" "CANCELED")))) (set (make-local-variable (quote
org-hide-block-startup)) (quote t)) (set (make-local-variable (quote
org-use-sub-superscripts)) (quote t)) (set (make-local-variable (quote
org-table-formula-constants-local)) (quote nil)) (set (make-local-variable
(quote org-file-properties)) (quote (("header-args:R" . ":session test
:comments link") ("header-args" . ":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/Projects/ASM_Optimization/asmOptim.org")) (set
(make-local-variable (quote default-directory)) (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, Núria Roura-Pascual &
David M. Richardson\n#+EMAIL:
address@hidden:\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#+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_OPTIONS:
[a4paper,usenames,dvipsnames,table]\n\n#+LATEX_HEADER:
\\lstset{%\n#+LATEX_HEADER: basicstyle=\\ttfamily\\footnotesize, %
the font that is used for the code\n#+LATEX_HEADER: tabsize=4,
% sets default tabsize to 4 spaces\n#+LATEX_HEADER: numbers=left,
% where to put the line numbers\n#+LATEX_HEADER:
numberstyle=\\tiny, % line number font size\n#+LATEX_HEADER:
stepnumber=0, % step between two line
numbers\n#+LATEX_HEADER: breaklines=true, %!! don't break
long lines of code\n#+LATEX_HEADER: showtabs=false, % show
tabs within strings adding particular underscores\n#+LATEX_HEADER:
showspaces=false, % show spaces adding particular
underscores\n#+LATEX_HEADER: showstringspaces=false, % underline
spaces within strings\n#+LATEX_HEADER:
keywordstyle=\\color{blue},\n#+LATEX_HEADER:
identifierstyle=\\color{black},\n#+LATEX_HEADER:
stringstyle=\\color{ForestGreen},\n#+LATEX_HEADER:
commentstyle=\\color{red},\n#+LATEX_HEADER:
backgroundcolor=\\color{light-gray}, % sets the background
color\n#+LATEX_HEADER: columns=fullflexible, \n#+LATEX_HEADER:
basewidth={0.5em,0.4em}, \n#+LATEX_HEADER: captionpos=b,
% sets the caption position to `bottom'\n#+LATEX_HEADER:
extendedchars=false %!?? workaround for when the listed file is in
UTF-8\n#+LATEX_HEADER: }\n\n#+LATEX_HEADER:
\\usepackage[round,semicolon,authoryear]{natbib}\n\n#+LATEX_CLASS_OPTIONS:
[colorlinks=true]\n\n#+LATEX_HEADER:
\\usepackage[section]{placeins}\n#+LATEX_HEADER:
\\usepackage{subcaption}\n\n#+LATEX_HEADER: \\usepackage{bm}\n\n#+LATEX_HEADER:
%% \\usepackage{showframe}\n#+LATEX_HEADER:
\\usepackage{float}\n\n#+LaTeX_header: \\usepackage{amsmath}\n\n#+LaTeX_header:
\\usepackage{todonotes}\n\n#+LaTeX_header: \\usepackage{soul}\n# See
[[http://tex.stackexchange.com/a/139500/6941]] for why\n#+LaTeX_header:
\\soulregister\\cite7\n#+LaTeX_header: \\soulregister\\citep7\n#+LaTeX_header:
\\soulregister\\citet7\n#+LaTeX_header:
\\soulregister\\emph7\n\n:END:\n:HTMLHEADER:\n#+SETUPFILE:
/Users/rainerkrug/.emacs.d/org-html-themes/setup/theme-readtheorg.setup\n:END:\n:MATHMACROS:\n#+LATEX_HEADER:
\\newcommand{\\cua}{\\mathit{a} (t)}\n#+LATEX_HEADER:
\\newcommand{\\cov}{\\mathit{cov} (t)}\n#+LATEX_HEADER:
\\newcommand{\\ac}{\\mathit{c} (t)}\n#+LATEX_HEADER:
\\newcommand{\\bpc}{\\mathit{b}}\n#+LATEX_HEADER:
\\newcommand{\\bpci}{\\mathit{b_{inv}}}\n\n#+LATEX_HEADER:
\\newcommand{\\tmg}{\\mathit{t_{95}}}\n#+LATEX_HEADER:
\\newcommand{\\bmg}{\\mathit{B_{95}}}\n\n#+LATEX_HEADER:
\\newcommand{\\pmg}{\\mathit{p_{95}}}\n\n#+LATEX_HEADER:
\\newcommand{\\bc}{\\mathit{\\hat{b}}}\n#+LATEX_HEADER:
\\newcommand{\\bci}{\\mathit{\\hat{b}_{inv}}}\n\n#+LATEX_HEADER:
\\newcommand{\\idb}{\\mathit{I^{b}_{95}}}\n#+LATEX_HEADER:
\\newcommand{\\idt}{\\mathit{I^{t}_{95}}}\n\n:END:\n:MACROS:\n#+INCLUDE:
~/.emacs.d/org-macros/org-macros.setup\n\n#+MACRO: us (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"\\\\textunderscore{}\" \"＿\" ))\n#+MACRO: clearpage (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"\\\\clearpage\" \"\" ))\n#+MACRO: img (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"[[file:$1.pdf]]\" \"[[file:$1.png]]\"))\n#+MACRO: sc (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"\\\\textsc{$1}\" \"$1\"))\n\n#+MACRO: pandoc (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"@@latex:%forPandoc%$1@@\" \"$1\"))\n:END:\n:BABEL:\n#+PROPERTY: header-args
:tangle-mode (identity #o444)\n#+PROPERTY: header-args+ :tangle
no\n#+PROPERTY: header-args+ :mkdirp yes\n#+PROPERTY: header-args+ :exports
both\n#+PROPERTY: header-args+ :padline no\n#+PROPERTY: header-args+ :eval
never-export \n#+PROPERTY: header-args+ :noweb yes\n\n#+PROPERTY: header-args:R
:session test\n#+PROPERTY: header-args:R+ :comments link\n\n#+Bind:
org-babel-use-quick-and-dirty-noweb-expansion \"t\"\n:END:\n\n# #+LaTeX_header:
\\usepackage[]{endfloat}\n\n* List Of Figures
:ignoreheading:\n{{{if-latex-else(\\\\listoffigures, \"\")}}}\n\n*
List Of Tables
:ignoreheading:\n{{{if-latex-else(\\\\listoftables, \"\")}}}\n* List Of TODOs
:ignoreheading:\n{{{if-latex-else(\\\\listoftodos, \"\")}}}\n\n\n\n* Version
src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION} \n:PROPERTIES:\n:header-args:
:exports results\n:header-args+: :tangle no\n:END:\nVersion src_sh{sed -n
'/^Version: /s///p' ./DESCRIPTION}\n\n* #### clearpage ####
:ignoreheading:\n{{{clearpage}}}\n\n\n\n*
Abstract\n#+begin_abstract\nNeeds top be written\n#+end_abstract\n\n\n* TODO
DESCRIPTION File
:noexport:\n:PROPERTIES:\n:header-args: :comments no\n:header-args+: :padline
no\n:header-args+: :no-expand TRUE\n:header-args+: :eval
never\n:END:\n\n#+begin_src RDescr :tangle ./DESCRIPTION\nPackage:
ASMOptim\nType: Paper\nTitle: Analysis transcripts and Paper Alanysis\nVersion:
0.2.0.+\nAuthor: Rainer M. Krug\nMaintainer: Rainer M Krug
<address@hidden>\nDepends: ASMOptimPackage (>= 0.2.0)\n#+end_src\n\n\n* TODO
Setup .Rprofile file :noexport:\nThis
file will only be used when R is not started with --vanilla!!!!\n#+begin_src R
:tangle
./.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 lEnergyBalance
and WindProfilePaper packages\n#+NAME: initR\n#+begin_src R\n\n##
<initR>\nlibrary(devtools)\n## install_bitbucket(repo=\"rkrug/WindProfiles\",
ref=\"v_0.7.0\", auth_user=\"rkrug\",
password=\"\")\nload_all(\"./package/ASMOptimPaper/ASMOptimPaper.org/\")\n##
gInit()\n## </initR>\n\n#+end_src\n\n** getMapsetTypes\nThis is a template to
be remembered and to be used as a base for getting the results types from a
simulation.\n\n#+NAME: getMapsetTypes\n#+begin_src R \n getMapNames(\n
site = \"CapePeninsula\",\n strategy = \"Consensus\",\n
budget = \"CapePeninsula_1_0\",\n run = 5,\n type =
\"raster\",\n pattern = \"*\",\n fullMapNames = FALSE\n )
%>%\n strsplit(split=\"_\") %>%\n subset(sapply(.,
FUN=\"length\") == 2) %>%\n sapply(FUN=\"[[\", 2) %>%\n
unique()\n\n#+end_src\n* emails
:noexport:\n[[notmuch:id:address@hidden from Núria Roura-Pascual: RE:
Missing piece ...]]\n\n* Data preparation
:noexport:\n** Split complete data into different
types\n:PROPERTIES:\n:heade-args: :eval never-export\n:END:\n- csv
::\n#+begin_src sh :session data :results none\nmkdir ./inputdata/csv/ \nrsync
-avz --include=\"*/\" --include=\"*.csv\" --exclude=\"*\"
/Volumes/Seagate_1TB/HomeExternal/Documents/ASM_Optimization ./inputdata/csv/
\nfind . -type f -name \"*.asc\" -exec gzip -v {} \\;\nrsync -avz
--include=\"*/\" --include=\"*.csv\" --exclude=\"*\"
address@hidden:~/clusterResults/clusterResults/simASM/RandomClearingPaper/results/simASMRightFire
./inputdata/csv/\n#+end_src\n\n- png ::\n#+begin_src sh :session data :results
none\nmkdir ./inputdata/png// \nrsync -avz --include=\"*/\"
--include=\"*.png\" --exclude=\"*\"
/Volumes/Seagate_1TB/HomeExternal/Documents/ASM_Optimization ./inputdata/png/
\nrsync -avz --include=\"*/\" --include=\"*.png\" --exclude=\"*\"
/Volumes/Home\\ on\\
Pogoplug/clusterResults/clusterResults/simASM/RandomClearingPaper/results/simASMRightFire/
./inputdata/csv/\nrsync -avz --include=\"*/\" --include=\"*.png\"
--exclude=\"*\"
address@hidden:~/clusterResults/clusterResults/simASM/RandomClearingPaper/results/simASMRightFire
./inputdata/png/\n#+end_src\n\n** Merge directory structure
into\n./inputdata/csv/ASM_Otimization/Simulations/SITE/simASM/STRATEGY/BUDGET/FIRE/RUN\n\n*
Bash scripts for data preparation and handling
:noexport:\n** tar2grass - extract grass/simulation directories and create
single grass location\n:PROPERTIES:\n:header-args:sh: :tangle
./tar2grass\n:header-args:sh: :comments no\n:header-args:sh+: :tangle-mode
(identity #o755)\n:END:\nThis script extracts the =grass/simulation= directory
from a tar.gz\nfile of the simulation and moves it into the folder =./simASM=
folder\nand renames it to the name of the =tar.gz= without the
=.tar.gz=.\n\nAfter adding the \n#+begin_src sh \nTAR=\"$1\"\necho $TAR
...\ntar -xvzf $TAR --include='*/grass/simulation/*'\nmkdir -p simASM\ncd
tmp\ncd $(ls)\nSIM=$(ls)\ncd $(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 =PERMANENT= from =./inputdata/PERMANENT= into
the location and\nadds the link to a mapset =./../grassAnalysis= which can be
used for\nwrite access outside 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_src\n\n#+begin_src sh :tangle no\nmksquashfs
./simASM ./simASM.squashfs -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 .squashfs files\nin the current directory. It should be run in the
./input directory.\n\n*** Extract .tar.gz simulation but exclude certain
redundant files\n#+begin_src sh\nTAR=\"$1\"\ntar -xvzf $TAR
--exclude='*/output/*' --exclude='input.tar.gz'
--exclude='output.tar.gz'\n#+end_src\n\n*** Climb in dirrectory into single
unique directory\n#+begin_src sh \ncd tmp\ncd `ls`\n#+end_src\n\n*** Replace
link to =PERMANENT= with link to existing =PERMANENT= \n#+begin_src sh \nfind .
-type \"link\" -name \"PERMANENT\" -exec ln -fhs ./../../PERMANENT {}
\\;\n#+end_src\n\n*** Create squashfs in base folder and delete original
folder\n#+begin_src sh \nNAME=$(ls)\nmksquashfs $NAME ./../../$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:header-args:sh+:
:tangle-mode (identity #o755)\n:END:\n#+begin_src sh
\nDEST=./DEST$$\nGRASS=./GRASS$$/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/PERMANENT $GRASS/\nfor F in ./inputdata/simASM.*.squashfs; do \n
BN=$(basename $F)\n DN=$(dirname $F)\n DIR=\"${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/$DIR\"\n mv \"./$DEST/grass/simulation\" \"$GRASS\"\n
mv \"$GRASS/simulation\" \"$GRASS/$DIR\"\n echo Deleting \"$DEST\"\n rm
-rf \"$DEST\"\n echo \">>>>>\"\ndone \necho Create link $GRASS/analysis out
of the squashfs for editable mapset\nln -s \"./../../grassAnalysis\"
\"$GRASS/analysis\"\necho Making SquashFS ./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 #o755)\n:END:\n#+begin_src sh
\nDIR=./inputdata/simASM\nSFS=./inputdata/simASM.grass.squashfs\nFN=./umountSimASM\necho
\"#!/bin/sh\" > $FN\necho \"umount $DIR\" >> $FN\necho \"rm $DIR/NOT_MOUNTED\"
>> $FN\necho \"rmdir $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:header-args:sh+: :tangle-mode
(identity #o755)\n:END:\n#+begin_src sh \nFN=./umountsimASM\necho \"#!/bin/sh\"
> $FN\nchmod +x umountsimASM\nfor F in ./inputdata/simASM.*.squashfs; do \n
BN=$(basename $F)\n DN=$(dirname $F)\n DIR=$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 environment and society. They are known to cause
significant changes in species, communities and ecosystems citep:Vila2011 and
to be responsible for major economic losses citep:Pimentel2005. Economic
expenses are in the form of losses 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 eradication is not always an option and the
maintenance and effectiveness of control measures are largely uncertain.
Economics are known to play an important role in clearing operations
citep:Higgins1997a,Marais2004a.\n \n[[comment:Needs to be reworded.][For
example, cite:Odom2005 showed that investment in managing the Scotch broom
(/Cytisus scoparius/) is economically justified and that higher budgets yield
higher value for the society. citep:Cacho2008 used a decision model based on
economic analysis to identify the most 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 more eradication oriented
goals.]]\n\nBesides the overreaching importance of budget, the effectivity of
management actions is also constrained by the characteristics 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 clearing programs citep:Krug2010_rmk. The
maintenance of management measures over time is, however, not exempt of
nuances. [[comment:TAlk about the problems associated with clearing the same
site over time][TALK ABOUTTHE PROBLEMS ASSOCIATED 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 guidelines for use in fiscal and policy
decisions of IAP management. \n\nThis study builds on our previous work that
examined the impact of different budget scenarios on the effectivity of
clearing actions on a selected prioritization strategy citep:Krug2010_rmk, but
instead of focusing on a single prioritization strategy we also examine the
effect of several prioritization strategies. In particular, we aim to identify
the optimal combination of elements –budget and clearing strategy– that ensures
the effective 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’s 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 expansion 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
simulations for this study are based on three study sites within South Africa’s
Cape Floristic Region: Agulhas Plain, Cape Peninsula and Outeniqua (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 Peninsula and Outeniqua
regions have large areas of natural or seminatural vegetation, the Agulhas
Plains consists of a mosaic of agricultural landscapes and conservation areas.
All sites are invaded by IAPs, albeit by different 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 woody plants, particularly species
of /Acacia/, /Hakea/ and /Pinus/
citep:Richardson1986_rmka,Richardson1992_rmk,Richardson1994_rmk,Wilgen1994_rmk,Richardson2008_rmk
[[comment:Further References needed?]]). \n\nDifferent usage and management
pattern as well as topography of the three sites result in different fire
patterns, e.g. with respect to the average area burned per year 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 = 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 under different management
strategies, we used the spatio-temporal explicit 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 found 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:Krug2010_rmk, by
incorporating spatial population dynamics (seed production, seed dispersal,
germination and establishment), fire dynamics and the clearing of IAPs based on
a certain prioritization strategy, the costs of clearing actions and the budget
available per year. The aim is to assess the effectiveness of different
clearing strategies and budget scenarios over time. \n\nThe model
{{{sc(SpreadSim)}}} was written in R citep:R2008_rmk, (with additional packages
by
cite:Pebesma2005_rmk,Petzoldt2007_rmk,Bivand2009_rmk,James2009_rmk,Keitt2009_rmk,Lewin-Koh2009_rmk,Urbanek_rmk)
and uses GRASS citep:GRASS2007 for the storage of the spatial results and
spatial calculations. 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-Model for the flowchart of the model). Each module contains
parameter controlling the stochastic spread and management of IAPs of the
genera /Acacia/, /Hakea/ and /Pinus/ citep:Krug2010_rmk. \n\nDue to the
stochastic nature of the model, each *simulation* (defined by the =site=,
prioritization =strategy= and =budget=) was repeated five times. For further
analysis, we defined a *simulation set* as different =budget= scenarios for the
same =site= and clearing =strategy=.\n\nThe input data for the simulations was
provided by the relevant nature conservation agencies and Working for Water
(see cite:Roura-Pascual2009_rmkb,Roura-Pascual2009_rmkc for details
[[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 step of one year.
\n\n#+ATTR_LATEX: :caption \\caption{\\label{fig-Model} from
\\protect\\cite{Krug2010_rmk}} \\todo[inline]{If we need this here, I will redo
it - just let me know.}\n{{{if-latex-else([[file:fig-Model.pdf]],
[[file:fig-Model.png]])}}}\n\n\n** Prioritization =strategy=\n\nThe
prioritization =strategy= 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:Krug2010_rmk). \n\nThe strategies are based on weights and consider the
following 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:fig-Strategies):\n\n- =consensus= :: this strategy was developed through a
participatory 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 =strategies= are based on the
=consensus strategy= and were modified based on certain aims.\n- =maintain
follow-ups= :: (aka =past=) aims at prioritizing areas based on previous
clearing operations, i.e. giving higher priority to areas which have been
cleared already or in follow-ups. It relies on accurate information of fire and
clearing history of the site citep:Roura-Pascual2009_rmkc;\n- =keep clean= ::
(aka =present=) 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 accurate information of the
present, i.e. present density of the IAPs and spread potential based on
topography citep:Roura-Pascual2009_rmkc;\n- =water production= :: (aka
=future=)is orientated towards increasing water production in the future, with
higher priority given to riparian areas in lower 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- =random= :: is a
null-strategy which does not require any knowledge about the past and randomly
assigns priorities citep:Krug2010_rmk.\n\nA visualization of these
prioritization strategies can be seen in Fig.
ref:fig-Strategies.\n\n#+ATTR_LATEX: :caption \\caption{\\label{fig-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\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 are specified in South African Rand (R) as
$\\boldmath\\bpc$ (IAP clearing budget per year per cell) and
$\\boldmath\\bpci$ (IAP clearing budget per year per invaded cell).\n\nThe
actual budgets were multiplied with a factor ranging from 0.1 to 6.0 to obtain
14 to 15 different budget scenarios for each simulation set defined by a =site=
and a =strategy= (see Figure ref:fig-Budgets and Table ref:tab-Budgets in the
Appendix for values from cite: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 :: $\\bpc =$ 17.09 R/cell, $\\bpci
=$ 25.88 R/cell\n - Consensus, Maintain Follow Ups, 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 ::
$\\bpc =$ 135.047 R/cell, $\\bpci =$ 347.21R/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 :: $\\bpc =$ 33.58R/cell, $\\bpci =$ 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: 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.pdf]],
[[file:fig-Budgets.png]])}}}\n\n** TODO Analysis\nThe analysis follows the
analysis done in cite:Krug2010_rmk and uses very similar measures and
indicators to assess the efficiency of the different strategies. We therefore
calculated for each individual =simulation= run (i.e. five per
=simulation=)\n\n# - $\\cua$ :: number of cells covered by IAPs per year, where
*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. all cells for
which the density class of aliens is higher\n than *rare*). $\\cov = 0$
indicates no alien infestation and $\\cov\n = 1$ indicates complete cover
of IAPs. (From cite:Krug2010_rmk) \n# - $\\ac$ :: number of cells cleared of
IAPs in year $t$\n\nTo assess the effectiveness of the =simulation= run, we
defined a\n- management goal :: as to be having 95% of the area (cells) alien
free (density class of aliens smaller or equal *rare*), i.e. $\\cov \\leq
0.95$\nwhere each individual simulation run is regarded as successful after
reaching the *management goal*.\n\nIf the *management goal* was reached, we
calculated for each =simulation= run\n- $\\tmg$ :: as the time when we reached
the management goal\n- $\\bmg$ :: as the cumulative budget needed to achieve
the management goal\n\nFor each =simulation= (i.e. over the five simulation
runs) we then calculated\n+ $\\pmg$ :: proportions of all the runs (here five
simulation runs) in one =simulation= which reached the *management goal*\n\nTo
accumulate over each =simulation set=, i.e. one =site= and one =strategy= and
multiple =budget=s, we calculated\n- $\\bc$ :: the *critical budget* is the
lowest budget at which more than 50% of all simulations resulted in achieving
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 =site= and =strategy= a\n# - budget index ::
$\\bm{\\idb} = \\frac{\\bpc}{\\bc}$\n# - time index :: $\\bm{\\idt} =
\\frac{\\tmg(\\bc)-1}{\\mathit{mean}\\left(\\tmg(\\bc)-1\\right)}$ [[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: area 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 ‘‘rare’’, is called cov(t). cov(t) =
0 indicates no alien infestation and cov(t) = 1 indicates complete cover of
IAPs.\n\n# We set our ‘‘management goal’’ arbitrarily at clearing 95% (and for
some scenarios 90%) of the area of IAPs. This ‘‘management goal’’ represents
the threshold cover, below which the management is considered as being
successful. An eradication 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 ‘‘management goal’’, we determined the year in which it occurred
(tnf95) and the cumulative costs per cell up to tnf95 (BPC 95). Note that BPC
95 <= bPC·tnf95 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
‘‘critical budget’’ (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
calculated by dividing the actual budget bPC by the critical budget ^ bPC.
Consequently, 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
tnf95 we achieved that the lowest value of the index is zero, while 1
represents the average tnf95ð ^ bPCÞ.\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 |
104.163 | 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 | 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 |
42.725 | 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#+NAME:
fig-Budgets\n#+begin_src R :var BUDGET=tabBudgets :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 \"Agulhas\", \"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(decreasing = 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 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 = c(4.1, 0.3,
0.1, 0.8)\n)\nbarplot(\n x,\n xlab = \"Budget per cell\",\n xlim =
c(0, 700),\n names.arg = \"\",\n horiz = TRUE,\n col = cols,\n
density = dens\n)\nsiteNames <- c(\"Agulhas Plains\", \"Cape Peninsula\",
\"Outeniqua\")\nlegend(\n x = \"topright\",\n legend = c( siteNames,
\"\", \"per all cells\", \"per invaded cells\"),\n fill = c(\"green\",
\"red\", \"blue\", NA, \"black\", \"black\"),\n border = c(\"black\",
\"black\", \"black\", NA, \"black\", \"black\"),\n density = 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/ASMOptimPaper/inst/scripts/analysis.calculate.dc.R :eval never
\n<<initR>>\ndc <- getDc( new = TRUE, cores = 6
)\n#+end_src\n\n#+RESULTS:\n#+begin_example\nLoading ASMOptimPaper\nLoading
required package: sp\nLoading required package: raster\nLoading required
package: rgrass7\nLoading required package: XML\nGRASS GIS interface loaded
with GRASS version: (GRASS not running)\nLoading required package:
magrittr\n\nAttaching package: ‘magrittr’\n\nThe following object is masked
from ‘package:raster’:\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 \nprojection +proj=utm +south +zone=34 +a=6378137
+rf=298.257223563 +no_defs\n+towgs84=0.000,0.000,0.000
+to_meter=1.0\n#+end_example\n\n** TODO Examples of some simulations
:noexport:\n#+begin_src R \nua <- getUaWide(site =
\"Agulhas\", strategy=\"Consensus\", species = \"all\")\n\ndcs <- split(\n
dc, dc$run\n)\nmatplot(x = dc$year, dc[as.character(1:7)])\nua <-
rowSums(dc[as.character(1:7)])\n\nplot(ua)\n\nua <- getUa(site = \"Agulhas\",
budget=\"None\", species = \"all\",
proportion=TRUE)\nplot(ua$cl)\nb\n#+end_src\n** CHECK Figures --- =simulation
sets= 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<<initR>>\npar(\n mfcol = c(length(STRATEGIES)-1, 1),\n mar =
c(1.2, 4.1, 1.1, 0.1),\n cex = 0.7\n)\nfor (i in 1:(length(STRATEGIES)-1))
{\n if (i == length(STRATEGIES)-1) {\n par(\n mar =
c(4.2, 4.1, 1.1, 0.1)\n ) \n }\n plotScenario( site = SI,
strategy = STRATEGIES[i])\n}\n#+end_src\n:END:\n\n#+NAME:
fig-ScenAgulhas\n#+HEADER: :var SI=\"Agulhas\"\n#+begin_src 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-ScenAgulhas.pdf]]\n\n\n#+NAME:
fig-ScenCapePeninsula\n#+HEADER: :var SI=\"CapePeninsula\"\n#+begin_src R
:exports results :file-ext pdf :results graphics :width 7 :height
7\n<<plotScenarios>>\n#+end_src\n\n#+RESULTS:
fig-ScenCapePeninsula\n[[file:fig-ScenCapePeninsula.pdf]]\n\n\n#+NAME:
fig-ScenOuteniqua\n#+HEADER: :var SI=\"Outeniqua\"\n#+begin_src R :exports
results :file-ext pdf :results graphics :width 7 :height
7\n<<plotScenarios>>\n#+end_src\n\n\n#+RESULTS:
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<<initR>>\npar(\n mfcol = c(length(SITES), 1),\n mar
= c(1.2, 4.1, 1.1, 0.1),\n cex = 0.7\n)\nfor (i in 1:length(SITES)) {\n
if (i == length(SITES)) {\n par(\n mar = c(4.2, 4.1, 1.1,
0.1)\n ) \n }\n plotCritBud( \n site = SITES[i],\n
ylab = \"Prop Man. Goal\",\n dx = 0.6,\n xlim = 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 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 = \"all\")\n\n\nplot(\n bc$budgetPerCell ~
bc$tmg.mean,\n xlab = \"mean time until management goal is achieved at
critical budget\",\n ylab = \"critical budget ber cell\",\n cex = 1,\n
col = as.factor(bc$strategy),\n pch =
as.integer(as.factor(bc$site))\n)\n\nsite <- unique(bc$site)\nstrategy <-
unique(bc$strategy)\nlegend(\n \"bottomright\",\n legend = c(\n
site,\n \"\",\n strategy\n ),\n pch = c(\n
as.integer(as.factor(site)),\n 1,\n rep(15, length(strategy))\n
),\n col = 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** =simulation sets=
by Site\n\n#+CAPTION: Proportion label:fig-ScenAgulhas of cells under aliens
for the different strategies at *Agulhas Plains*. Horizontal line at y = 0.05
indicates the management
target.\n{{{if-latex-else([[file:fig-ScenAgulhas.pdf]],
[[file:fig-ScenAgulhas.png]])}}}\n\n#+CAPTION: Proportion
label:fig-ScenCapePeninsula of cells under aliens for the different strategies
at *Cape Peninsula*. Horizontal line at y = 0.05 indicates the management
target.\n{{{if-latex-else([[file:fig-ScenCapePeninsula.pdf]],
[[file:fig-ScenCapePeninsula.png]])}}}\n\n#+CAPTION: Proportion
label:fig-ScenOuteniqua of cells under aliens for the different strategies at
*Outeniqua*. Horizontal line at y = 0.05 indicates the management
target.\n{{{if-latex-else([[file:fig-ScenOuteniqua.pdf]],
[[file:fig-ScenOuteniqua.png]])}}}\n\n*** #### clearpage ####
:ignoreheading:\n{{{clearpage}}}\n\n** Proportion reaching
Management Goal\n#+CAPTION: label:fig-CritBudProp Proportion of five
simulation runs which reached the Management Goal. Colors depict different
sites. Horizontal line at y = 0.05 indicates the critical budget
$\\bc$\n{{{if-latex-else([[file:fig-CritBudProp.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 choice 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 what you see. While in the case
of Agulhas Plains and Outeniqua, there are\n considerable differences with for
Agulhas Plains =Future= and =Random=\n being the worst, this is not true for
Outeniqua, where =Future= and\n =Consensus= is the worst.\n\n- No clear
pattern which one is better - heavily site dependent\n\n- Random is not
necessarily the worst - sometimes better than wrong choice\n\n- ???\n\n*
Acknowledgements\n* References\nbibliographystyle:plainnat\n# <<bibliography
link>>\nbibliography:asmOptim.bib\n\n \n* Appendix\n\\appendix\n*
Simulations\nSimulations are differentiated by their =site=, =strategy=
and\n=budget= (see Table ref:tab-simulations for the
different\ncombinations).\n\n#+CAPTION: Parameter label:tab-simulations sets
used forthe different simulations.\n| =site= | =strategy= | =budget=
|\n|---------------+------------+------------|\n| | Consensus |
depends |\n| Agulhas | Future | on |\n| CapePeninsula |
Past | =site= |\n| Outeniqua | Present | and |\n|
| Random | =strategy= |\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_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 |
104.163 | 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 | 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 |
42.725 | 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* Figures
and tables for pandoc\n\n{{{pandoc(\\\\section*{List of
Figures})}}}\n\n\n{{{pandoc(FiguresHere\\\\par)}}}\n\n{{{pandoc(\\\\section*{List
of Tables})}}}\n\n\n{{{pandoc(TablesHere\\\\par)}}}\n\n\n* Some initial plots
of histograms :noexport:\n\n#+begin_src R
\n<<initR>>\n\nsim <- getDir(\n type = \"csv\",\n site =
\"CapePeninsula\",\n strategy = \"Consensus\",\n budget =
\"CapePeninsula_1_0\",\n run = 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└── Simulations\n
├── Agulhas\n │ └── simASM\n │ ├── Consensus\n │ │
├── Agulhas_0_1\n │ │ │ └── Agulhas\n │ │ │ ├──
47835.1\n │ │ │ ├── 47835.2\n │ │ │ ├──
47835.3\n │ │ │ ├── 47835.4\n │ │ │ └──
47835.5\n │ │ ├── Agulhas_2_5\n │ │ │ └── ...\n │
│ ├── Agulhas_5_0\n │ │ │ └── ...\n │ │ ├──
Agulhas_5_5\n │ │ │ └── ...\n │ │ └── Agulhas_6_0 \n
│ │ └── ...\n │ ├── Future\n │ ├── Past ...\n
│ └── Present ...\n ├── CapePeninsula ...\n ├── Outeniqua ...\n
└──
log\n#+end_example\n\n./inputdata/*csv*/SITE/simASM/STRATEGY/BUDGET/FIRE/RUN\n\n***
R functions\nsee package ASMOptimPaper for the functions used in the analysis.
\n\n** GRASS simASM input data\n*** Mapset name structure\nThe
[[file:inputdata/simASM/][GRASS location]] contains the following mapsets:\n-
[[file:inputdata/simASM/PERMANENT/][PERMANENT]] mapset - read-only :: which
contains the South Africa wide data used in the simulations\n-
[[file:inputdata/simASM/grassAnalysis/][grassAnalysis]] - read-write :: which
can be used for analysis\n-
[[file:inputdata/simASM/simASM.Outeniqua.Random.Outeniqua_2_0.Outeniqua.41719.5/][simulations]]
:: about 530 mapsets whose names are build as follow:\n\n
{{{if-latex-else(simASM.\\\\texttt{SITE}.\\\\texttt{STRATEGY}.\\\\texttt{BUDGET}.\\\\texttt{FIREREGIME}.\\\\texttt{JOBID}.\\\\texttt{ARRAYID},
simASM . =SITE= . =STRATEGY= . =BUDGET= . =FIREREGIME= . =JOBID= .
=ARRAYID=)}}}\n #+CAPTION: Simulations conducted and combination of
different parameter values. =f= is the factor which, multiplied with the yearly
original budget of year 2006 [[comment:Check!]] becomes the initial budget of
the simulation. The factor f is written with underscore ({{{us}}}) instead of
the decimal point (e.g. 1.5 becomes 1{{{us}}}1).\n | =SITE= |
=STRATEGY= | =BUDGET= | =FIREREGIME= | =JOBID= | =ARRAYID= |\n
|---------------+------------+------------------------+--------------+---------+-----------|\n
| | Consensus | | |
| 1 |\n | Agulhas | Future | =SITE= {{{us}}}f |
| | 2 |\n | CapePeninsula | Past |
| =SITE= | number | 3 |\n | Outeniqua |
Present | none | | | 4 |\n
| | Random | | |
| 5 |\n
|---------------+------------+------------------------+--------------+---------+-----------|\n\n***
Map name structure in the =simulation= mapsets\nUsing
=simASM.CapePeninsula.Random.CapePeninsula_1_0.CapePeninsula.xxx.5= as an
exapmle.\n**** Static data\n#+begin_src R :colnames yes :exports
results\n<<initR>>\nx <- getMapNames(\n site = \"CapePeninsula\",\n
strategy = \"Random\",\n budget = \"CapePeninsula_1_0\",\n run =
5,\n type = \"raster\",\n pattern = \"*\",\n fullMapNames =
FALSE\n) %>%\n strsplit(split=\"_\") %>%\n subset(sapply(.,
FUN=\"length\") == 1) %>%\n sapply(FUN=\"[[\", 1) %>%\n unique()\nx <-
c(x, \"SPECIES\\{{{us}}}suitability\")\ndata.frame(\"names\" =
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. over time
changing, raster maps\nThe maps have the following naming structure:\n\n#
=SPECIES= {{{us}}} =TYPE= {{{us}}}
=YEAR=\n\n\\texttt{SPECIES}{{{us}}}\\texttt{TYPE}{{{us}}}\\texttt{YEAR}\n\n\nBlocks
of combinations are separated by ------ and all combinations are available for
all =YEAR=\n\n#+begin_src R :colnames yes :exports results\n<<initR>>\nx <-
getMapNames(\n site = \"CapePeninsula\",\n strategy = \"Random\",\n
budget = \"CapePeninsula_1_0\",\n run = 5,\n type =
\"raster\",\n pattern = \"*\",\n fullMapNames = FALSE\n) %>%\n
strsplit(split=\"_\") %>%\n subset(sapply(., FUN=\"length\") == 3) %>%\n
data.frame(stringsAsFactors = FALSE) %>%\n t() %>%\n
data.frame(stringsAsFactors = 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],
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 (xother[-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 = c( xsp$X1, \"------------\", xall$X1,
\"------------\", xother$X1),\n TYPE = c( xsp$X2,
\"--------------------\", xall$X2, \"--------------------\",
xother$X2)\n)\nx$YEAR <- c(years, rep(\"\",
length(x$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}}}\\texttt{YEAR}\n#+RESULTS:\n|
SPECIES | TYPE | YEAR
|\n|--------------+----------------------+------|\n| ACyclops | age
| 2006 |\n| HSericea | ageClass | 2007 |\n| PPinaster
| ageClassFire | 2008 |\n| | clearingCost | 2009
|\n| | dc | 2010 |\n| |
dcEstablished | 2011 |\n| | dcFire | 2012
|\n| | dcSeedlings | 2013 |\n| |
disturbances | 2014 |\n| | fuelModel | 2015
|\n| | individuals | 2016 |\n| |
noEstablished | 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| 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 Functions
:noexport:\n#+begin_src sh :results output \nmogrify
-format png -density 300 -quality 100 ./fig-*.pdf
\n#+end_src\n\n#+RESULTS:\n#+begin_example\n12\n3\n1\n17541\n0\n3\n0\n3\n17541\n(3
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0 objpace << /sRGB 5 0 R >> >>/Count 1 /MediaBox [0 0 504 324]
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0 objsed 6 0 R]RGB 5 0 R >> >>/Count 1 /MediaBox [0 0 504 324]
>>=h\">\\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:address@hidden)\n65535\n21250\n#+end_example\n\n\n\n*
File Local Variables
:noexport:\n\n# Local Variables:\n# eval: (visual-line-mode 1)\n# End:\n\n\n")
(narrow-to-region 1 57482) (goto-char 1))
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(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, Núria Roura-Pascual &
David M. Richardson\n#+EMAIL:
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CANCELED(x)\n:END:\n:LATEXHEADER:\n#+LaTeX_CLASS_OPTIONS:
[a4paper,usenames,dvipsnames,table]\n\n#+LATEX_HEADER:
\\lstset{%\n#+LATEX_HEADER: basicstyle=\\ttfamily\\footnotesize, %
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% sets default tabsize to 4 spaces\n#+LATEX_HEADER: numbers=left,
% where to put the line numbers\n#+LATEX_HEADER:
numberstyle=\\tiny, % line number font size\n#+LATEX_HEADER:
stepnumber=0, % step between two line
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stringstyle=\\color{ForestGreen},\n#+LATEX_HEADER:
commentstyle=\\color{red},\n#+LATEX_HEADER:
backgroundcolor=\\color{light-gray}, % sets the background
color\n#+LATEX_HEADER: columns=fullflexible, \n#+LATEX_HEADER:
basewidth={0.5em,0.4em}, \n#+LATEX_HEADER: captionpos=b,
% sets the caption position to `bottom'\n#+LATEX_HEADER:
extendedchars=false %!?? workaround for when the listed file is in
UTF-8\n#+LATEX_HEADER: }\n\n#+LATEX_HEADER:
\\usepackage[round,semicolon,authoryear]{natbib}\n\n#+LATEX_CLASS_OPTIONS:
[colorlinks=true]\n\n#+LATEX_HEADER:
\\usepackage[section]{placeins}\n#+LATEX_HEADER:
\\usepackage{subcaption}\n\n#+LATEX_HEADER: \\usepackage{bm}\n\n#+LATEX_HEADER:
%% \\usepackage{showframe}\n#+LATEX_HEADER:
\\usepackage{float}\n\n#+LaTeX_header: \\usepackage{amsmath}\n\n#+LaTeX_header:
\\usepackage{todonotes}\n\n#+LaTeX_header: \\usepackage{soul}\n# See
[[http://tex.stackexchange.com/a/139500/6941]] for why\n#+LaTeX_header:
\\soulregister\\cite7\n#+LaTeX_header: \\soulregister\\citep7\n#+LaTeX_header:
\\soulregister\\citet7\n#+LaTeX_header:
\\soulregister\\emph7\n\n:END:\n:HTMLHEADER:\n#+SETUPFILE:
/Users/rainerkrug/.emacs.d/org-html-themes/setup/theme-readtheorg.setup\n:END:\n:MATHMACROS:\n#+LATEX_HEADER:
\\newcommand{\\cua}{\\mathit{a} (t)}\n#+LATEX_HEADER:
\\newcommand{\\cov}{\\mathit{cov} (t)}\n#+LATEX_HEADER:
\\newcommand{\\ac}{\\mathit{c} (t)}\n#+LATEX_HEADER:
\\newcommand{\\bpc}{\\mathit{b}}\n#+LATEX_HEADER:
\\newcommand{\\bpci}{\\mathit{b_{inv}}}\n\n#+LATEX_HEADER:
\\newcommand{\\tmg}{\\mathit{t_{95}}}\n#+LATEX_HEADER:
\\newcommand{\\bmg}{\\mathit{B_{95}}}\n\n#+LATEX_HEADER:
\\newcommand{\\pmg}{\\mathit{p_{95}}}\n\n#+LATEX_HEADER:
\\newcommand{\\bc}{\\mathit{\\hat{b}}}\n#+LATEX_HEADER:
\\newcommand{\\bci}{\\mathit{\\hat{b}_{inv}}}\n\n#+LATEX_HEADER:
\\newcommand{\\idb}{\\mathit{I^{b}_{95}}}\n#+LATEX_HEADER:
\\newcommand{\\idt}{\\mathit{I^{t}_{95}}}\n\n:END:\n:MACROS:\n#+INCLUDE:
~/.emacs.d/org-macros/org-macros.setup\n\n#+MACRO: us (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"\\\\textunderscore{}\" \"＿\" ))\n#+MACRO: clearpage (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"\\\\clearpage\" \"\" ))\n#+MACRO: img (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"[[file:$1.pdf]]\" \"[[file:$1.png]]\"))\n#+MACRO: sc (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"\\\\textsc{$1}\" \"$1\"))\n\n#+MACRO: pandoc (eval (if
(org-export-derived-backend-p org-export-current-backend 'latex)
\"@@latex:%forPandoc%$1@@\" \"$1\"))\n:END:\n:BABEL:\n#+PROPERTY: header-args
:tangle-mode (identity #o444)\n#+PROPERTY: header-args+ :tangle
no\n#+PROPERTY: header-args+ :mkdirp yes\n#+PROPERTY: header-args+ :exports
both\n#+PROPERTY: header-args+ :padline no\n#+PROPERTY: header-args+ :eval
never-export \n#+PROPERTY: header-args+ :noweb yes\n\n#+PROPERTY: header-args:R
:session test\n#+PROPERTY: header-args:R+ :comments link\n\n#+Bind:
org-babel-use-quick-and-dirty-noweb-expansion \"t\"\n:END:\n\n# #+LaTeX_header:
\\usepackage[]{endfloat}\n\n* List Of Figures
:ignoreheading:\n{{{if-latex-else(\\\\listoffigures, \"\")}}}\n\n*
List Of Tables
:ignoreheading:\n{{{if-latex-else(\\\\listoftables, \"\")}}}\n* List Of TODOs
:ignoreheading:\n{{{if-latex-else(\\\\listoftodos, \"\")}}}\n\n\n\n* Version
src_sh{sed -n '/^Version: /s///p' ./DESCRIPTION} \n:PROPERTIES:\n:header-args:
:exports results\n:header-args+: :tangle no\n:END:\nVersion src_sh{sed -n
'/^Version: /s///p' ./DESCRIPTION}\n\n* #### clearpage ####
:ignoreheading:\n{{{clearpage}}}\n\n\n\n*
Abstract\n#+begin_abstract\nNeeds top be written\n#+end_abstract\n\n\n* TODO
DESCRIPTION File
:noexport:\n:PROPERTIES:\n:header-args: :comments no\n:header-args+: :padline
no\n:header-args+: :no-expand TRUE\n:header-args+: :eval
never\n:END:\n\n#+begin_src RDescr :tangle ./DESCRIPTION\nPackage:
ASMOptim\nType: Paper\nTitle: Analysis transcripts and Paper Alanysis\nVersion:
0.2.0.+\nAuthor: Rainer M. Krug\nMaintainer: Rainer M Krug
<address@hidden>\nDepends: ASMOptimPackage (>= 0.2.0)\n#+end_src\n\n\n* TODO
Setup .Rprofile file :noexport:\nThis
file will only be used when R is not started with --vanilla!!!!\n#+begin_src R
:tangle
./.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 lEnergyBalance
and WindProfilePaper packages\n#+NAME: initR\n#+begin_src R\n\n##
<initR>\nlibrary(devtools)\n## install_bitbucket(repo=\"rkrug/WindProfiles\",
ref=\"v_0.7.0\", auth_user=\"rkrug\",
password=\"\")\nload_all(\"./package/ASMOptimPaper/ASMOptimPaper.org/\")\n##
gInit()\n## </initR>\n\n#+end_src\n\n** getMapsetTypes\nThis is a template to
be remembered and to be used as a base for getting the results types from a
simulation.\n\n#+NAME: getMapsetTypes\n#+begin_src R \n getMapNames(\n
site = \"CapePeninsula\",\n strategy = \"Consensus\",\n
budget = \"CapePeninsula_1_0\",\n run = 5,\n type =
\"raster\",\n pattern = \"*\",\n fullMapNames = FALSE\n )
%>%\n strsplit(split=\"_\") %>%\n subset(sapply(.,
FUN=\"length\") == 2) %>%\n sapply(FUN=\"[[\", 2) %>%\n
unique()\n\n#+end_src\n* emails
:noexport:\n[[notmuch:id:address@hidden from Núria Roura-Pascual: RE:
Missing piece ...]]\n\n* Data preparation
:noexport:\n** Split complete data into different
types\n:PROPERTIES:\n:heade-args: :eval never-export\n:END:\n- csv
::\n#+begin_src sh :session data :results none\nmkdir ./inputdata/csv/ \nrsync
-avz --include=\"*/\" --include=\"*.csv\" --exclude=\"*\"
/Volumes/Seagate_1TB/HomeExternal/Documents/ASM_Optimization ./inputdata/csv/
\nfind . -type f -name \"*.asc\" -exec gzip -v {} \\;\nrsync -avz
--include=\"*/\" --include=\"*.csv\" --exclude=\"*\"
address@hidden:~/clusterResults/clusterResults/simASM/RandomClearingPaper/results/simASMRightFire
./inputdata/csv/\n#+end_src\n\n- png ::\n#+begin_src sh :session data :results
none\nmkdir ./inputdata/png// \nrsync -avz --include=\"*/\"
--include=\"*.png\" --exclude=\"*\"
/Volumes/Seagate_1TB/HomeExternal/Documents/ASM_Optimization ./inputdata/png/
\nrsync -avz --include=\"*/\" --include=\"*.png\" --exclude=\"*\"
/Volumes/Home\\ on\\
Pogoplug/clusterResults/clusterResults/simASM/RandomClearingPaper/results/simASMRightFire/
./inputdata/csv/\nrsync -avz --include=\"*/\" --include=\"*.png\"
--exclude=\"*\"
address@hidden:~/clusterResults/clusterResults/simASM/RandomClearingPaper/results/simASMRightFire
./inputdata/png/\n#+end_src\n\n** Merge directory structure
into\n./inputdata/csv/ASM_Otimization/Simulations/SITE/simASM/STRATEGY/BUDGET/FIRE/RUN\n\n*
Bash scripts for data preparation and handling
:noexport:\n** tar2grass - extract grass/simulation directories and create
single grass location\n:PROPERTIES:\n:header-args:sh: :tangle
./tar2grass\n:header-args:sh: :comments no\n:header-args:sh+: :tangle-mode
(identity #o755)\n:END:\nThis script extracts the =grass/simulation= directory
from a tar.gz\nfile of the simulation and moves it into the folder =./simASM=
folder\nand renames it to the name of the =tar.gz= without the
=.tar.gz=.\n\nAfter adding the \n#+begin_src sh \nTAR=\"$1\"\necho $TAR
...\ntar -xvzf $TAR --include='*/grass/simulation/*'\nmkdir -p simASM\ncd
tmp\ncd $(ls)\nSIM=$(ls)\ncd $(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 =PERMANENT= from =./inputdata/PERMANENT= into
the location and\nadds the link to a mapset =./../grassAnalysis= which can be
used for\nwrite access outside 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_src\n\n#+begin_src sh :tangle no\nmksquashfs
./simASM ./simASM.squashfs -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 .squashfs files\nin the current directory. It should be run in the
./input directory.\n\n*** Extract .tar.gz simulation but exclude certain
redundant files\n#+begin_src sh\nTAR=\"$1\"\ntar -xvzf $TAR
--exclude='*/output/*' --exclude='input.tar.gz'
--exclude='output.tar.gz'\n#+end_src\n\n*** Climb in dirrectory into single
unique directory\n#+begin_src sh \ncd tmp\ncd `ls`\n#+end_src\n\n*** Replace
link to =PERMANENT= with link to existing =PERMANENT= \n#+begin_src sh \nfind .
-type \"link\" -name \"PERMANENT\" -exec ln -fhs ./../../PERMANENT {}
\\;\n#+end_src\n\n*** Create squashfs in base folder and delete original
folder\n#+begin_src sh \nNAME=$(ls)\nmksquashfs $NAME ./../../$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:header-args:sh+:
:tangle-mode (identity #o755)\n:END:\n#+begin_src sh
\nDEST=./DEST$$\nGRASS=./GRASS$$/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/PERMANENT $GRASS/\nfor F in ./inputdata/simASM.*.squashfs; do \n
BN=$(basename $F)\n DN=$(dirname $F)\n DIR=\"${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/$DIR\"\n mv \"./$DEST/grass/simulation\" \"$GRASS\"\n
mv \"$GRASS/simulation\" \"$GRASS/$DIR\"\n echo Deleting \"$DEST\"\n rm
-rf \"$DEST\"\n echo \">>>>>\"\ndone \necho Create link $GRASS/analysis out
of the squashfs for editable mapset\nln -s \"./../../grassAnalysis\"
\"$GRASS/analysis\"\necho Making SquashFS ./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 #o755)\n:END:\n#+begin_src sh
\nDIR=./inputdata/simASM\nSFS=./inputdata/simASM.grass.squashfs\nFN=./umountSimASM\necho
\"#!/bin/sh\" > $FN\necho \"umount $DIR\" >> $FN\necho \"rm $DIR/NOT_MOUNTED\"
>> $FN\necho \"rmdir $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:header-args:sh+: :tangle-mode
(identity #o755)\n:END:\n#+begin_src sh \nFN=./umountsimASM\necho \"#!/bin/sh\"
> $FN\nchmod +x umountsimASM\nfor F in ./inputdata/simASM.*.squashfs; do \n
BN=$(basename $F)\n DN=$(dirname $F)\n DIR=$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 environment and society. They are known to cause
significant changes in species, communities and ecosystems citep:Vila2011 and
to be responsible for major economic losses citep:Pimentel2005. Economic
expenses are in the form of losses 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 eradication is not always an option and the
maintenance and effectiveness of control measures are largely uncertain.
Economics are known to play an important role in clearing operations
citep:Higgins1997a,Marais2004a.\n \n[[comment:Needs to be reworded.][For
example, cite:Odom2005 showed that investment in managing the Scotch broom
(/Cytisus scoparius/) is economically justified and that higher budgets yield
higher value for the society. citep:Cacho2008 used a decision model based on
economic analysis to identify the most 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 more eradication oriented
goals.]]\n\nBesides the overreaching importance of budget, the effectivity of
management actions is also constrained by the characteristics 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 clearing programs citep:Krug2010_rmk. The
maintenance of management measures over time is, however, not exempt of
nuances. [[comment:TAlk about the problems associated with clearing the same
site over time][TALK ABOUTTHE PROBLEMS ASSOCIATED 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 guidelines for use in fiscal and policy
decisions of IAP management. \n\nThis study builds on our previous work that
examined the impact of different budget scenarios on the effectivity of
clearing actions on a selected prioritization strategy citep:Krug2010_rmk, but
instead of focusing on a single prioritization strategy we also examine the
effect of several prioritization strategies. In particular, we aim to identify
the optimal combination of elements –budget and clearing strategy– that ensures
the effective 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’s 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 expansion 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
simulations for this study are based on three study sites within South Africa’s
Cape Floristic Region: Agulhas Plain, Cape Peninsula and Outeniqua (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 Peninsula and Outeniqua
regions have large areas of natural or seminatural vegetation, the Agulhas
Plains consists of a mosaic of agricultural landscapes and conservation areas.
All sites are invaded by IAPs, albeit by different 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 woody plants, particularly species
of /Acacia/, /Hakea/ and /Pinus/
citep:Richardson1986_rmka,Richardson1992_rmk,Richardson1994_rmk,Wilgen1994_rmk,Richardson2008_rmk
[[comment:Further References needed?]]). \n\nDifferent usage and management
pattern as well as topography of the three sites result in different fire
patterns, e.g. with respect to the average area burned per year 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 = 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 under different management
strategies, we used the spatio-temporal explicit 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 found 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:Krug2010_rmk, by
incorporating spatial population dynamics (seed production, seed dispersal,
germination and establishment), fire dynamics and the clearing of IAPs based on
a certain prioritization strategy, the costs of clearing actions and the budget
available per year. The aim is to assess the effectiveness of different
clearing strategies and budget scenarios over time. \n\nThe model
{{{sc(SpreadSim)}}} was written in R citep:R2008_rmk, (with additional packages
by
cite:Pebesma2005_rmk,Petzoldt2007_rmk,Bivand2009_rmk,James2009_rmk,Keitt2009_rmk,Lewin-Koh2009_rmk,Urbanek_rmk)
and uses GRASS citep:GRASS2007 for the storage of the spatial results and
spatial calculations. 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-Model for the flowchart of the model). Each module contains
parameter controlling the stochastic spread and management of IAPs of the
genera /Acacia/, /Hakea/ and /Pinus/ citep:Krug2010_rmk. \n\nDue to the
stochastic nature of the model, each *simulation* (defined by the =site=,
prioritization =strategy= and =budget=) was repeated five times. For further
analysis, we defined a *simulation set* as different =budget= scenarios for the
same =site= and clearing =strategy=.\n\nThe input data for the simulations was
provided by the relevant nature conservation agencies and Working for Water
(see cite:Roura-Pascual2009_rmkb,Roura-Pascual2009_rmkc for details
[[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 step of one year.
\n\n#+ATTR_LATEX: :caption \\caption{\\label{fig-Model} from
\\protect\\cite{Krug2010_rmk}} \\todo[inline]{If we need this here, I will redo
it - just let me know.}\n{{{if-latex-else([[file:fig-Model.pdf]],
[[file:fig-Model.png]])}}}\n\n\n** Prioritization =strategy=\n\nThe
prioritization =strategy= 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:Krug2010_rmk). \n\nThe strategies are based on weights and consider the
following 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:fig-Strategies):\n\n- =consensus= :: this strategy was developed through a
participatory 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 =strategies= are based on the
=consensus strategy= and were modified based on certain aims.\n- =maintain
follow-ups= :: (aka =past=) aims at prioritizing areas based on previous
clearing operations, i.e. giving higher priority to areas which have been
cleared already or in follow-ups. It relies on accurate information of fire and
clearing history of the site citep:Roura-Pascual2009_rmkc;\n- =keep clean= ::
(aka =present=) 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 accurate information of the
present, i.e. present density of the IAPs and spread potential based on
topography citep:Roura-Pascual2009_rmkc;\n- =water production= :: (aka
=future=)is orientated towards increasing water production in the future, with
higher priority given to riparian areas in lower 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- =random= :: is a
null-strategy which does not require any knowledge about the past and randomly
assigns priorities citep:Krug2010_rmk.\n\nA visualization of these
prioritization strategies can be seen in Fig.
ref:fig-Strategies.\n\n#+ATTR_LATEX: :caption \\caption{\\label{fig-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\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 are specified in South African Rand (R) as
$\\boldmath\\bpc$ (IAP clearing budget per year per cell) and
$\\boldmath\\bpci$ (IAP clearing budget per year per invaded cell).\n\nThe
actual budgets were multiplied with a factor ranging from 0.1 to 6.0 to obtain
14 to 15 different budget scenarios for each simulation set defined by a =site=
and a =strategy= (see Figure ref:fig-Budgets and Table ref:tab-Budgets in the
Appendix for values from cite: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 :: $\\bpc =$ 17.09 R/cell, $\\bpci
=$ 25.88 R/cell\n - Consensus, Maintain Follow Ups, 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 ::
$\\bpc =$ 135.047 R/cell, $\\bpci =$ 347.21R/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 :: $\\bpc =$ 33.58R/cell, $\\bpci =$ 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: 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.pdf]],
[[file:fig-Budgets.png]])}}}\n\n** TODO Analysis\nThe analysis follows the
analysis done in cite:Krug2010_rmk and uses very similar measures and
indicators to assess the efficiency of the different strategies. We therefore
calculated for each individual =simulation= run (i.e. five per
=simulation=)\n\n# - $\\cua$ :: number of cells covered by IAPs per year, where
*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. all cells for
which the density class of aliens is higher\n than *rare*). $\\cov = 0$
indicates no alien infestation and $\\cov\n = 1$ indicates complete cover
of IAPs. (From cite:Krug2010_rmk) \n# - $\\ac$ :: number of cells cleared of
IAPs in year $t$\n\nTo assess the effectiveness of the =simulation= run, we
defined a\n- management goal :: as to be having 95% of the area (cells) alien
free (density class of aliens smaller or equal *rare*), i.e. $\\cov \\leq
0.95$\nwhere each individual simulation run is regarded as successful after
reaching the *management goal*.\n\nIf the *management goal* was reached, we
calculated for each =simulation= run\n- $\\tmg$ :: as the time when we reached
the management goal\n- $\\bmg$ :: as the cumulative budget needed to achieve
the management goal\n\nFor each =simulation= (i.e. over the five simulation
runs) we then calculated\n+ $\\pmg$ :: proportions of all the runs (here five
simulation runs) in one =simulation= which reached the *management goal*\n\nTo
accumulate over each =simulation set=, i.e. one =site= and one =strategy= and
multiple =budget=s, we calculated\n- $\\bc$ :: the *critical budget* is the
lowest budget at which more than 50% of all simulations resulted in achieving
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 =site= and =strategy= a\n# - budget index ::
$\\bm{\\idb} = \\frac{\\bpc}{\\bc}$\n# - time index :: $\\bm{\\idt} =
\\frac{\\tmg(\\bc)-1}{\\mathit{mean}\\left(\\tmg(\\bc)-1\\right)}$ [[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: area 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 ‘‘rare’’, is called cov(t). cov(t) =
0 indicates no alien infestation and cov(t) = 1 indicates complete cover of
IAPs.\n\n# We set our ‘‘management goal’’ arbitrarily at clearing 95% (and for
some scenarios 90%) of the area of IAPs. This ‘‘management goal’’ represents
the threshold cover, below which the management is considered as being
successful. An eradication 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 ‘‘management goal’’, we determined the year in which it occurred
(tnf95) and the cumulative costs per cell up to tnf95 (BPC 95). Note that BPC
95 <= bPC·tnf95 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
‘‘critical budget’’ (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
calculated by dividing the actual budget bPC by the critical budget ^ bPC.
Consequently, 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
tnf95 we achieved that the lowest value of the index is zero, while 1
represents the average tnf95ð ^ bPCÞ.\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 |
104.163 | 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 | 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 |
42.725 | 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#+NAME:
fig-Budgets\n#+begin_src R :var BUDGET=tabBudgets :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 \"Agulhas\", \"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(decreasing = 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 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 = c(4.1, 0.3,
0.1, 0.8)\n)\nbarplot(\n x,\n xlab = \"Budget per cell\",\n xlim =
c(0, 700),\n names.arg = \"\",\n horiz = TRUE,\n col = cols,\n
density = dens\n)\nsiteNames <- c(\"Agulhas Plains\", \"Cape Peninsula\",
\"Outeniqua\")\nlegend(\n x = \"topright\",\n legend = c( siteNames,
\"\", \"per all cells\", \"per invaded cells\"),\n fill = c(\"green\",
\"red\", \"blue\", NA, \"black\", \"black\"),\n border = c(\"black\",
\"black\", \"black\", NA, \"black\", \"black\"),\n density = 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/ASMOptimPaper/inst/scripts/analysis.calculate.dc.R :eval never
\n<<initR>>\ndc <- getDc( new = TRUE, cores = 6
)\n#+end_src\n\n#+RESULTS:\n#+begin_example\nLoading ASMOptimPaper\nLoading
required package: sp\nLoading required package: raster\nLoading required
package: rgrass7\nLoading required package: XML\nGRASS GIS interface loaded
with GRASS version: (GRASS not running)\nLoading required package:
magrittr\n\nAttaching package: ‘magrittr’\n\nThe following object is masked
from ‘package:raster’:\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 \nprojection +proj=utm +south +zone=34 +a=6378137
+rf=298.257223563 +no_defs\n+towgs84=0.000,0.000,0.000
+to_meter=1.0\n#+end_example\n\n** TODO Examples of some simulations
:noexport:\n#+begin_src R \nua <- getUaWide(site =
\"Agulhas\", strategy=\"Consensus\", species = \"all\")\n\ndcs <- split(\n
dc, dc$run\n)\nmatplot(x = dc$year, dc[as.character(1:7)])\nua <-
rowSums(dc[as.character(1:7)])\n\nplot(ua)\n\nua <- getUa(site = \"Agulhas\",
budget=\"None\", species = \"all\",
proportion=TRUE)\nplot(ua$cl)\nb\n#+end_src\n** CHECK Figures --- =simulation
sets= 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<<initR>>\npar(\n mfcol = c(length(STRATEGIES)-1, 1),\n mar =
c(1.2, 4.1, 1.1, 0.1),\n cex = 0.7\n)\nfor (i in 1:(length(STRATEGIES)-1))
{\n if (i == length(STRATEGIES)-1) {\n par(\n mar =
c(4.2, 4.1, 1.1, 0.1)\n ) \n }\n plotScenario( site = SI,
strategy = STRATEGIES[i])\n}\n#+end_src\n:END:\n\n#+NAME:
fig-ScenAgulhas\n#+HEADER: :var SI=\"Agulhas\"\n#+begin_src 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-ScenAgulhas.pdf]]\n\n\n#+NAME:
fig-ScenCapePeninsula\n#+HEADER: :var SI=\"CapePeninsula\"\n#+begin_src R
:exports results :file-ext pdf :results graphics :width 7 :height
7\n<<plotScenarios>>\n#+end_src\n\n#+RESULTS:
fig-ScenCapePeninsula\n[[file:fig-ScenCapePeninsula.pdf]]\n\n\n#+NAME:
fig-ScenOuteniqua\n#+HEADER: :var SI=\"Outeniqua\"\n#+begin_src R :exports
results :file-ext pdf :results graphics :width 7 :height
7\n<<plotScenarios>>\n#+end_src\n\n\n#+RESULTS:
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<<initR>>\npar(\n mfcol = c(length(SITES), 1),\n mar
= c(1.2, 4.1, 1.1, 0.1),\n cex = 0.7\n)\nfor (i in 1:length(SITES)) {\n
if (i == length(SITES)) {\n par(\n mar = c(4.2, 4.1, 1.1,
0.1)\n ) \n }\n plotCritBud( \n site = SITES[i],\n
ylab = \"Prop Man. Goal\",\n dx = 0.6,\n xlim = 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 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 = \"all\")\n\n\nplot(\n bc$budgetPerCell ~
bc$tmg.mean,\n xlab = \"mean time until management goal is achieved at
critical budget\",\n ylab = \"critical budget ber cell\",\n cex = 1,\n
col = as.factor(bc$strategy),\n pch =
as.integer(as.factor(bc$site))\n)\n\nsite <- unique(bc$site)\nstrategy <-
unique(bc$strategy)\nlegend(\n \"bottomright\",\n legend = c(\n
site,\n \"\",\n strategy\n ),\n pch = c(\n
as.integer(as.factor(site)),\n 1,\n rep(15, length(strategy))\n
),\n col = 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** =simulation sets=
by Site\n\n#+CAPTION: Proportion label:fig-ScenAgulhas of cells under aliens
for the different strategies at *Agulhas Plains*. Horizontal line at y = 0.05
indicates the management
target.\n{{{if-latex-else([[file:fig-ScenAgulhas.pdf]],
[[file:fig-ScenAgulhas.png]])}}}\n\n#+CAPTION: Proportion
label:fig-ScenCapePeninsula of cells under aliens for the different strategies
at *Cape Peninsula*. Horizontal line at y = 0.05 indicates the management
target.\n{{{if-latex-else([[file:fig-ScenCapePeninsula.pdf]],
[[file:fig-ScenCapePeninsula.png]])}}}\n\n#+CAPTION: Proportion
label:fig-ScenOuteniqua of cells under aliens for the different strategies at
*Outeniqua*. Horizontal line at y = 0.05 indicates the management
target.\n{{{if-latex-else([[file:fig-ScenOuteniqua.pdf]],
[[file:fig-ScenOuteniqua.png]])}}}\n\n*** #### clearpage ####
:ignoreheading:\n{{{clearpage}}}\n\n** Proportion reaching
Management Goal\n#+CAPTION: label:fig-CritBudProp Proportion of five
simulation runs which reached the Management Goal. Colors depict different
sites. Horizontal line at y = 0.05 indicates the critical budget
$\\bc$\n{{{if-latex-else([[file:fig-CritBudProp.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 choice 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 what you see. While in the case
of Agulhas Plains and Outeniqua, there are\n considerable differences with for
Agulhas Plains =Future= and =Random=\n being the worst, this is not true for
Outeniqua, where =Future= and\n =Consensus= is the worst.\n\n- No clear
pattern which one is better - heavily site dependent\n\n- Random is not
necessarily the worst - sometimes better than wrong choice\n\n- ???\n\n*
Acknowledgements\n* References\nbibliographystyle:plainnat\n# <<bibliography
link>>\nbibliography:asmOptim.bib\n\n \n* Appendix\n\\appendix\n*
Simulations\nSimulations are differentiated by their =site=, =strategy=
and\n=budget= (see Table ref:tab-simulations for the
different\ncombinations).\n\n#+CAPTION: Parameter label:tab-simulations sets
used forthe different simulations.\n| =site= | =strategy= | =budget=
|\n|---------------+------------+------------|\n| | Consensus |
depends |\n| Agulhas | Future | on |\n| CapePeninsula |
Past | =site= |\n| Outeniqua | Present | and |\n|
| Random | =strategy= |\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_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 |
104.163 | 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 | 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 |
42.725 | 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* Figures
and tables for pandoc\n\n{{{pandoc(\\\\section*{List of
Figures})}}}\n\n\n{{{pandoc(FiguresHere\\\\par)}}}\n\n{{{pandoc(\\\\section*{List
of Tables})}}}\n\n\n{{{pandoc(TablesHere\\\\par)}}}\n\n\n* Some initial plots
of histograms :noexport:\n\n#+begin_src R
\n<<initR>>\n\nsim <- getDir(\n type = \"csv\",\n site =
\"CapePeninsula\",\n strategy = \"Consensus\",\n budget =
\"CapePeninsula_1_0\",\n run = 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└── Simulations\n
├── Agulhas\n │ └── simASM\n │ ├── Consensus\n │ │
├── Agulhas_0_1\n │ │ │ └── Agulhas\n │ │ │ ├──
47835.1\n │ │ │ ├── 47835.2\n │ │ │ ├──
47835.3\n │ │ │ ├── 47835.4\n │ │ │ └──
47835.5\n │ │ ├── Agulhas_2_5\n │ │ │ └── ...\n │
│ ├── Agulhas_5_0\n │ │ │ └── ...\n │ │ ├──
Agulhas_5_5\n │ │ │ └── ...\n │ │ └── Agulhas_6_0 \n
│ │ └── ...\n │ ├── Future\n │ ├── Past ...\n
│ └── Present ...\n ├── CapePeninsula ...\n ├── Outeniqua ...\n
└──
log\n#+end_example\n\n./inputdata/*csv*/SITE/simASM/STRATEGY/BUDGET/FIRE/RUN\n\n***
R functions\nsee package ASMOptimPaper for the functions used in the analysis.
\n\n** GRASS simASM input data\n*** Mapset name structure\nThe
[[file:inputdata/simASM/][GRASS location]] contains the following mapsets:\n-
[[file:inputdata/simASM/PERMANENT/][PERMANENT]] mapset - read-only :: which
contains the South Africa wide data used in the simulations\n-
[[file:inputdata/simASM/grassAnalysis/][grassAnalysis]] - read-write :: which
can be used for analysis\n-
[[file:inputdata/simASM/simASM.Outeniqua.Random.Outeniqua_2_0.Outeniqua.41719.5/][simulations]]
:: about 530 mapsets whose names are build as follow:\n\n
{{{if-latex-else(simASM.\\\\texttt{SITE}.\\\\texttt{STRATEGY}.\\\\texttt{BUDGET}.\\\\texttt{FIREREGIME}.\\\\texttt{JOBID}.\\\\texttt{ARRAYID},
simASM . =SITE= . =STRATEGY= . =BUDGET= . =FIREREGIME= . =JOBID= .
=ARRAYID=)}}}\n #+CAPTION: Simulations conducted and combination of
different parameter values. =f= is the factor which, multiplied with the yearly
original budget of year 2006 [[comment:Check!]] becomes the initial budget of
the simulation. The factor f is written with underscore ({{{us}}}) instead of
the decimal point (e.g. 1.5 becomes 1{{{us}}}1).\n | =SITE= |
=STRATEGY= | =BUDGET= | =FIREREGIME= | =JOBID= | =ARRAYID= |\n
|---------------+------------+------------------------+--------------+---------+-----------|\n
| | Consensus | | |
| 1 |\n | Agulhas | Future | =SITE= {{{us}}}f |
| | 2 |\n | CapePeninsula | Past |
| =SITE= | number | 3 |\n | Outeniqua |
Present | none | | | 4 |\n
| | Random | | |
| 5 |\n
|---------------+------------+------------------------+--------------+---------+-----------|\n\n***
Map name structure in the =simulation= mapsets\nUsing
=simASM.CapePeninsula.Random.CapePeninsula_1_0.CapePeninsula.xxx.5= as an
exapmle.\n**** Static data\n#+begin_src R :colnames yes :exports
results\n<<initR>>\nx <- getMapNames(\n site = \"CapePeninsula\",\n
strategy = \"Random\",\n budget = \"CapePeninsula_1_0\",\n run =
5,\n type = \"raster\",\n pattern = \"*\",\n fullMapNames =
FALSE\n) %>%\n strsplit(split=\"_\") %>%\n subset(sapply(.,
FUN=\"length\") == 1) %>%\n sapply(FUN=\"[[\", 1) %>%\n unique()\nx <-
c(x, \"SPECIES\\{{{us}}}suitability\")\ndata.frame(\"names\" =
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. over time
changing, raster maps\nThe maps have the following naming structure:\n\n#
=SPECIES= {{{us}}} =TYPE= {{{us}}}
=YEAR=\n\n\\texttt{SPECIES}{{{us}}}\\texttt{TYPE}{{{us}}}\\texttt{YEAR}\n\n\nBlocks
of combinations are separated by ------ and all combinations are available for
all =YEAR=\n\n#+begin_src R :colnames yes :exports results\n<<initR>>\nx <-
getMapNames(\n site = \"CapePeninsula\",\n strategy = \"Random\",\n
budget = \"CapePeninsula_1_0\",\n run = 5,\n type =
\"raster\",\n pattern = \"*\",\n fullMapNames = FALSE\n) %>%\n
strsplit(split=\"_\") %>%\n subset(sapply(., FUN=\"length\") == 3) %>%\n
data.frame(stringsAsFactors = FALSE) %>%\n t() %>%\n
data.frame(stringsAsFactors = 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],
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 (xother[-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 = c( xsp$X1, \"------------\", xall$X1,
\"------------\", xother$X1),\n TYPE = c( xsp$X2,
\"--------------------\", xall$X2, \"--------------------\",
xother$X2)\n)\nx$YEAR <- c(years, rep(\"\",
length(x$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}}}\\texttt{YEAR}\n#+RESULTS:\n|
SPECIES | TYPE | YEAR
|\n|--------------+----------------------+------|\n| ACyclops | age
| 2006 |\n| HSericea | ageClass | 2007 |\n| PPinaster
| ageClassFire | 2008 |\n| | clearingCost | 2009
|\n| | dc | 2010 |\n| |
dcEstablished | 2011 |\n| | dcFire | 2012
|\n| | dcSeedlings | 2013 |\n| |
disturbances | 2014 |\n| | fuelModel | 2015
|\n| | individuals | 2016 |\n| |
noEstablished | 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| 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 Functions
:noexport:\n#+begin_src sh :results output \nmogrify
-format png -density 300 -quality 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\\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=\\013`\\303\\225h\\355\\t\\351\\316o\\370=h\">\\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:address@hidden)\n65535\n21250\n12\n4\n1\n17624\n0\n4\n0\n4\n17624\n(4
0 obje /Pages /Kids [ 7 0 R ] /Count 1 /MediaBox [0 0 504 324]
>>=h\">\\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:address@hidden)\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]
>>=h\">\\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:address@hidden)\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]
>>=h\">\\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:address@hidden)\n65535\n21250\n#+end_example\n\n\n\n*
File Local Variables
:noexport:\n\n# Local Variables:\n# eval: (visual-line-mode 1)\n# End:\n\n\n")
(narrow-to-region 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)
`----
--
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982
signature.asc
Description: PGP signature