Initial Region Masking map

There are many ways to break up the global into regions.
Already spent hours trying to find ways of classification of create regions
Already spent hours trying to locate shape files, geoTiffs, or any GIS compatible sources

Waste of time, the data exists, others have it. Need to work out who to ask and gain the confident to ask.

Need to focus on the process

Josh O'Brien
So from http://stackoverflow.com/questions/20146809/how-can-i-plot-a-continents-map-with-r
SRES are IPCC Emission Scenario Regions


Same code tweaked.

library(rworldmap)
library(rgeos)

sPDF <- getMap()
sres <-
    sapply(levels(sPDF$SRES),
           FUN = function(i) {
               ## Merge polygons within a continent
               poly <- gUnionCascaded(subset(sPDF, SRES==i))
               ## Give each polygon a unique ID
               poly <- spChFIDs(poly, i)
               ## Make SPDF from SpatialPolygons object
               SpatialPolygonsDataFrame(poly,
                                        data.frame(SRES=i, row.names=i))
           },
           USE.NAMES=TRUE)

## Bind the 11 SRES-level SPDFs into a single SPDF
sres <- Reduce(spRbind, sres)

## Plot to check that it worked
plot(sres, col=heat.colors(nrow(sres)))

## Check that it worked by looking at the SPDF's data.frame
## (to which you can add attributes you really want to plot on)
data.frame(sres)

Save for future use. Use  .RData for faster loading in the future.
> class(sres)
[1] "SpatialPolygonsDataFrame"
attr(,"package")
[1] "sp"
> proj4string(sres)
[1] "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"


> setwd("~/Projects/R/test")
> getwd()
[1] "/Volumes/Data/Users/fmacgill/Projects/R/test"

> sres <- data_name
> plot(sres, col=heat.colors(nrow(sres)))
> data_name <- sres
> save(data_name, file="SRESGlobal.RData" )

Clear Variables and check retrieval

> sres <- 1
> data_name <- 1
> load("SRESGlobal.RData")
> sres <- data_name
> plot(sres, col=heat.colors(nrow(sres)))

Download Data

Downloaded some simple time series data.

How do I keep the data, the source, and crap together?

Metadata

What Metadata do I need?

I don't know.

Starting with

• source / url
• units
• location
• type
• startDate
• endDate
• increment

Going to save a matlab struct per time series. 

This is not going to be an optimal solution, but better than nothings, and better than doing nothing.

Python

I need to work with netCDF files

Currently I know Java, am familiar  with MATLAB

Java is clunking with numbers.

I have found MATLAB difficult to produce reusable code with.

R sounds appealing, but python has more support in the college, for netCDF and GIS applications

--> Introducing myself to python, 

1. Download and install iPython
2. Watch intro to iPython 
3. Download zip from Unidata Training Workshop from GitHub
   https://github.com/Unidata/tds-python-workshop
4. Unzip in directory
5. Start ipython in this directory
   ipython notebook --pylab inline

This went nowhere.

Talked with my supervisors going elsewhere at the moment

Submitted Abstract to Conference

Today I submitted an abstract to a conference.

The research was from my masters. It felt good to have something out there even if it is not related to my current research.

Wiki

Did a mini Wiki  Demo last week for supervisor.
Good support

Already in soft release. Multiple people using the 'Getting Started' Printer setup page.

Continuing to add pages and information for release to the group next week.

New Machine

Software

Matlab 2013b
Google Chrome

Google Drive
Evernote
Evernote Web Clipper for Chrome
Endnote V7
Spotify

Google Chrome

• Linked mainly to my PhD Google+ account. 
• Will know that I also have a Google Account
• Will never be used for Banking, PayPal, government interactions.

Online Backup

One of the extra tasks I have taken on for the group is to look at storage and online backup. 

Storage

Document Storage

Options

1.     GoogleDrive / GoogleDoc through GoogleApps

2.     University hosted file sever costing 250  per 1Tb

Recommendation

1. GoogleDrive / GoogleDoc through GoogleApps             

·      Currently provided by GoogleDoc and Google Drive.

·      Everyone seems confortable with.

·      Main issue  is there is no encryption security provided

Large data set storage

Currently students using the largest Datasets. They have access to a Earth Science hosted database for their work. Leave for later date.

Version Control Repository

Why – good practice to store versions of software.

Options

1.     Git:

             GitHub

·      Uni has a evangelist, who would help with introduction

·      I have used it.

·      Private Repository hosted in the Cloud by reputable GitHub available to education groups free, but further investigation shows there are quite a few hoops

Bitbucket

·      Uni has a evangelist, who would help with introduction

·      BitBucket allows unlimited Private Repositories with up to 5 users

·      Other Departments use it.

2.     Subversion :

·      PIK uses it

·      I can administer it

·      We would need have a box,

o   Upfront costs

o   Location issues.

Recommendation

1.  BitBucket unless likely to have more than 5 users.

Wiki

            Why – great way to communicate with in the Phd group.

Particularly as a single point for new comers to get established, record any issue or work arounds

           

Recommendation

Google Sites included as part of GoogleApps Education

Laptop Backup

Important Consideration

·      Off Site

·      Cost

·      Size

·      Encryption Security

·      Longevity

·      Ease of Use

·      OS Support (Windows , Mac, Linux)

·      Organisation Solution

 Uni does not support or have a recommended solution

Dual solutions provide best disaster plan.

            Regular Manual Hard disk / USB backup

            Online Automated Backup

Reasonable bandwidth

Ability to turn off when in a low bandwidth situation.

Non Free Solutions

            SpiderOak     

~$5 per month per user  200Gb (e)

            iDrive             

from $25 per year for 150Gb (e) individuals

 also org. pricing need further investigation,

start with 5Gb free

            CrashPlan     

~ $5 per month per user 

                        need to investigate educational discounts

                       start with 2Gb free

           

Free

	Mega	GoogleDrive	iDrive
Size	50Gb	30Gb	5
Encryption	No	No	Yes
Longevity	Unknown / Could be issue	Good	Good
Windows	yes	yes	Yes
OSx	no	yes	Yes
Linux	no	yes	Yes
Org Sol	no	somewhat	Upgrade
Location Choice	yes	no	Yes

 

Distributed Computing (CPU) power

Not Considered