Monday, July 26, 2010
I use org-mode in Emacs for my work logs, for writing manuscripts, for taking notes, and, increasingly, for writing my code. I also use org-mode to write this blog. Today, I'll share how I publish a blog like mine hosted on Google's blogger.com using org-mode . Users unfamiliar with emacs can get a quick tour here. Emacs users unfamiliar with org-mode will be convinced to try it by watching this video. Org-mode increased my work efficiency greatly.
I keep my blog in a single org file: blog.org. Here is a
snippet:
#+TITLE: blog.org
#+AUTHOR: R. Todd Jobe
#+EMAIL: toddjobe@unc.edu
#+DATE: %D
#+DESCRIPTION: See Todd Jobe's thoughts about computers and ecology. R code. Arc-GIS and GRASS code. Bash scripts. Matlab code.
#+OPTIONS: H:3 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
#+OPTIONS: TeX:t LaTeX:t skip:nil d:nil todo:t pri:nil tags:not-in-toc
#+INFOJS_OPT: view:nil toc:nil ltoc:t mouse:underline buttons:0 path:http://orgmode.org/org-info.js
#+EXPORT_SELECT_TAGS: export
#+EXPORT_EXCLUDE_TAGS: noexport
#+TODO: I(i) S(s) R(r!) | Q(q!) P(p!/!) C(@/!) (todo)
* Q Extracting Raster Values from Points in R and GRASS
:PROPERTIES:
:Tags: R, GRASS, GIS
:END:
A common task in GIS analysis is to extract the value of a remotely
sensed environmental variable at a point location. For instance we
may wish to extract the elevation of a field plot from a digital
elevation model. The elevation data is a raster (i.e. grid) and the
plots are a point shapefile (or a simple text file of X, Y
locations). The command for doing this in ArcGIS is
=ExtractValuesToPoints= available in the Spatial Analyst package.
Situations may arise where ArcGIS is not the most efficient way of
extracting these values. So, here, I provide a brief overview of how to
extract raster values to points in R and GRASS.
** Extract Values to Points in R
** Extracting Values in GRASS
Extracting raster values in GRASS is somewhat faster than in R, but
it takes a little bit more planning in that you have to explicitly
create the column that the raster values will go into.
*** Data Required
- =gr= : A GRASS grid
- =pt= : A GRASS point dataset
*** The Code
The basic flow of this is that you create an empty column in the
point dataset with the right data type (i.e. =varchar(10)= string
of length 10, =double precision= floating point numbers, =int=
integers). Then, fill the column with the raster values.
#+begin_src sh -t -w 66 :results: silent
v.db.addcol map=pt columns="grval double precision"
v.what.rast vector=pt raster=gr column=grval
#+end_src
* S Posting to blogger using org-mode
I use [[http://orgmode.org/][org-mode]] in Emacs for my work logs, for writing manuscripts,
for taking notes, and, increasingly, for writing my code. I also
use org-mode to write this blog. Today, I'll share how I publish a
blog like mine hosted on Google's [[http://blogger.com/][blogger.com]] using org-mode .
Users unfamiliar with emacs can get a quick tour [[http://www.gnu.org/software/emacs/tour/][here]]. Emacs users
unfamiliar with org-mode will be convinced to try it by watching
[[http://www.youtube.com/watch?v%3DoJTwQvgfgMM][this]] video. Org-mode increased my work efficiency greatly.
I keep my blog in a single org file: ~blog.org~. Here is a
snippet:
Each blog entry
is a TODO entry. As I
blog
~blog.org~.
My [[http://toddjobe.ecology@blogspot.com][blog]] is hosted on [[http://blogger.com][blogger.com]]. This service used to allow me to
FTP my blog directly from personal website:
[[http://www.unc.edu/~toddjobe][www.unc.edu/~toddjobe/]]. Google recently ceased support for FTPing
since less than 0.5% of their users employed this feature. So, now
I have to upload directly to
*** Export region as html
*** Use Google CL and the clipboard
* S Changing the font in Carbon Emacs
My current monospaced font of choice is [[http://dejavu-fonts.org/wiki/index.php%3Ftitle%3DMain_Page][Deja Vu Sans Mono]]. It is
pretty easy to change the default font in Carbon Emacs. It is not
so easy to change the default font on Windows- or Linux-based
Emacs22, which is the current release version. It will be
relatively straightforward in Emacs23 via the ~xft~ package. But,
for your Mac folks out there...
** Installing a Font on Mac OS X
1. Download the font (Mac will accept almost any format).
2. Drag the font file into ~/System/Fonts~
** Figure out the long name of your font face in Carbon Emacs
- M-x ~mac-font-panel-mode~. Then pick your font
- M-x ~describe-font~ and copy the long name.
** Set the default font
There are a couple of ways to do this.
*** Customization
- M-x ~customize-face~ RET ~default~ RET
- Fill in the fields of the font with your
*** ~.emacs.d~ file
#+BEGIN_SRC elisp
(set-default-font "-apple-inconsolata-medium-r-normal--11-110-72-72-m-110-iso10646-1")
#+END_SRC
** Monospaced fonts for the uninitiated
Programmers tend to use different fonts for code than what we see
in books an on the web. Word processors typically use proportional
fonts, where the horizontal space allowed for narrow letters like
"l" is less than the space allowed for wide letters like "W". In
code, we want the columns of each line to be aligned. So,
programmers tend to use monospaced fonts, where each letter takes
up the same amount of horizontal space. The most commonly known
fixed width font is Courier. Another common fixed-width font for
Windows and Microsoft products in Consolas. [[http://www.codeproject.com/KB/work/FontSurvey.aspx][The Code Project]] has
an exhaustive list of monospaced fonts.
One of the key attributes to look for in a monospaced font is the
distinction between the number one and the lowercase letter "l" and
the number zero and the uppercase "O". When you are trying to read
variable names that have mixtures of numbers and letters, you will be
thankful for a font that distinguishes between these.
* I Spelling and Grammar checking in Emacs
- Grammar checking is pretty easy with ~ispell~
- The ~diction~ command line utility is a Unix classic
- An minor-mode for calling ~diction~ from Emacs is [[http://ftp2.de.freebsd.org/pub/emacs/emacs-lisp/archive/diction.el][~diction~]]
- Use ~diction-buffer~ or ~diction-region~ commands
* I Converting R tables to data frames.
as.matrix doesn't work
class(tbl) <- c("matrix")
Each blog entry
is a TODO entry. As I
blog
~blog.org~.
My [[http://toddjobe.ecology@blogspot.com][blog]] is hosted on [[http://blogger.com][blogger.com]]. This service used to allow me to
FTP my blog directly from personal website:
[[http://www.unc.edu/~toddjobe][www.unc.edu/~toddjobe/]]. Google recently ceased support for FTPing
since less than 0.5% of their users employed this feature. So, now
I have to upload directly to
*** Export region as html
*** Use Google CL and the clipboard
* I Spelling and Grammar checking in Emacs
- Grammar checking is pretty easy with ~ispell~
- The ~diction~ command line utility is a Unix classic
- An minor-mode for calling ~diction~ from Emacs is [[http://ftp2.de.freebsd.org/pub/emacs/emacs-lisp/archive/diction.el][~diction~]]
- Use ~diction-buffer~ or ~diction-region~ commands
The first thing to notice is that this org-file has custom TODO states
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