The 2018 Field Season

20180825_165216.jpg

Because I am in the last year of PhD program, I was unable to go to Western Australia for the whole field season. But I did get the chance to head to the field site in WA for a couple of short stays. I helped at the beginning of the season to move around equipment and to install some PRS probes for a side project. 

PRS Probes in the ground surrounding a plot with focal indidividuals marked with toothpicks and yarn.

PRS Probes in the ground surrounding a plot with focal indidividuals marked with toothpicks and yarn.

Then I came back in late August to collect species composition data and to help set up some other experiments that the 2018 field crew are working on. 

20180825_164823.jpg
20180825_165345.jpg
20180826_134333.jpg

I was a bit worried this year about the rains - April got 0.0mm and May got less than average. I was crossing my fingers that we would not have a drought again this year... AND June, July & August all got close to double the long-term average amount of rainfall for each month - What a relief! Upon my second visit to the field, I saw carpets of pink, white, and yellow flowers about - certainly not like last year during the drought. 

20180826_134125.jpg
IMG_20170906_121839_879.jpg

I even went back to my old haunting ground to grab a picture from the same place I had 2 years before (L to R; 2018, 2017, 2016 pictures). The 2018 picture was not exactly 1 year apart from the 2017/2016 pictures (I was short 2 weeks) but you can already tell it is quite green and flowers are starting to pop out! 

Data processing complete!

achievemtn.unloked.png

Phew... it has been a long ride (>560 days) but my data processing is finally complete!

During my 3 month field season in 2016, I mapped 100 vegetation plots and collected seed from as many of the plants in those plots as I could grab (nearly 12,000 samples). I then brought those samples back to the lab and counted the seeds from each of those samples (with lots of help from others). We had to count most samples by hand because of the level of detail of the seed count - seed per pod/head - negated the usage of digital methods (e.g. taking a picture and using imageJ would probably take just as long or longer given the few number of seeds per sample for most samples). For some samples with really tiny seeds, we used a mass-count method, weighing a set number of seeds to estimate the number of seeds for that plant. In other instances, such as for grasses, we counted bracts of the culm/panicle and multiplied it by the number of seeds held in the bract.

The final seed tally is 864,748 from 12,139 samples.

Then I went through the maps to include any information for individual plants that I wrote on the map and did not collect a sample (e.g. a note of '0 seeds' on the map in the field instead of making an empty envelope). While mapping I recorded information on number of flowers/seed heads not collected (due to time constraints) by making a note next to the point, or grouping individuals into a contour on the map, or by jotting notes in the map legend. These all are varying levels of seed count quality (with the best being actually counted and the worse being a note in the legend) but this also provides more potential information for future analyses instead of just 'NA'.

points.notes.png
contour.notes.png
legend.notes.png

Using these map notes, we can add 4,824 individuals to the seed count dataset (considering the point and contour notes).

While counting, we also made note of any seed pods that were collected to early or after dispersal (resulting in no seeds) as well as seed pods that were open ( indicating the potential for missing seed). We also had counts of number of flowers and buds still remaining on the sample. Using this data, we can estimate the number of seeds per head/pod/stem and calculate a 'corrected' seed count to use in my analyses.

So an updated count is 941,674 seeds from 13,551 individual plants (corrected for lost seed and lost potential seed - e.g. a flower still on the sample). Compared to a total of 28,579 individuals mapped across 100 plots (max=965 plants in one 50 X 50 cm plot, min=53 plants/plot, median=231 plants/plot), that is about a 47% fecundity data sampling success across the plots - not too shabby...

Now onto my analyses... 

 

Recap of Peru

IMG_1146B.JPG

Peru was AMAZING!

I arrived at the beginning of March and had a couple of days to acclimate to the altitude of Cusco (~3900m). I enjoyed walking around town and visiting local markets and the Spanish churches and Incan temples. 

IMG_1382B.JPG

The city of Cusco was beautiful - you could almost feel the history from the 17th century churches to the 12th century temples/ruins to even the cobbles of the streets! 

During the course we spent 3 days in Cusco having lectures on plant ecology, ecosystem ecology, fire ecology... many ecologies... We also got the chance to survey some of the residents of Cusco about their views of climate change. 

Photo by Erik Kusch.

Photo by Erik Kusch.

 Then we headed to the Wayqecha Research Station in the Andes. 

Photo by Erik Kusch.

Photo by Erik Kusch.

The station was beautiful - nestled on a mountain side with a view straight down onto the (often cloudy) Amazon. There was an amazing collection of orchids at the location and a number of inquisitive (and hungry) hummingbirds (Photos by Erik Kusch). 

We then spent about 10 days collecting plant samples in the Puna grasslands of the Andes.

20180316_083734B.jpg

There were such beautiful views from our field sites that they were quite distracting (when not covered in clouds and not raining/hailing on us).

(Click through the gallery below for some pictures from our adventures on the course. Photos by Brian Enquist)

After our sample collection and processing, the course travelled to Pisac where we presented short summaries of the data and proposed potential research questions that we intend to follow up on. I did not do any heavy data processing (due to lack of time) but my tablet was sufficient to help with the data cleaning and small data processing tasks. We also got a chance to visit the ruins above Pisac which were quite spectacular.

IMG_1552B.JPG

After the course many of the students spent a few days travelling around the area. I took a short trip to Machu Picchu. Then I spent my last couple of days back in Cusco collecting souvenirs and gifts for family and friends. 

IMG_1920B.JPG

I then returned to NY to visit family before heading back to Brisbane! 

Photo by Erik Kusch.

Photo by Erik Kusch.

It was a fantastic visit to Peru and a great course! I met a lot of amazing people and had the opportunity to learn some of the plants of Peru and, of course, collect some traits as well!

Photo by Erik Kusch.

Photo by Erik Kusch.

Plant Functional Trait Course, Peru

This is not Peru... but I am missing the weather in Australia... New York is cold!

This is not Peru... but I am missing the weather in Australia... New York is cold!

Hi all! 

I will be shortly heading to the 2018 Plant Functional Trait Course in Cusco, Peru. Students in the course have been working on small assignments and reading some background literature to prepare for the 3-week field component. One such assignment has been to publish two blog posts (one pre- and one post-course). Check out the blog posts from all the attendees, here! I am very excited for the opportunity to attend the course and the chance to experience the natures and culture of Peru. Look for some pictures in the near future!

Testing R on my Android tablet

IMG-20180216-WA0004.jpeg

So I was recently faced with a tough choice before heading to a field course in Peru: to I take my large, heavy, everyday laptop or take a smaller less powerful computer. The pros of taking my everyday computer is that I am comfortable with how I use it now and I have access to all my files and increased functionality. The cons are that it is large and heavy (~5lbs does not seem like much but, man can I feel a difference) and it cost me $1.5k. I am not sure I want to (1) lug it around with me and (2) risk breaking or losing a very valuable piece of equipment that is essential to my PhD. I plan to do quite a bit of hiking/trekking around and would only feel comfortable if it was on me at all times.

So I started looking for alternatives... simple netbooks and small laptops that were within what I was willing to pay (<$200, still a decent chunk of my stipend). However, I started to realize that I had something with similar enough specs that I could potentially use, my Samsung tablet (SM-P600) I bought during my master's. Its current and previous uses have been watching Netflix and reading/commenting papers, but maybe now it has a new purpose!

I did a lot of googling and browsing many sites (see here, here, and there are many more). I found that I could add something like a virtual Linux machine on my tablet without having to root it. I have tested it a bit and am pleased but the real test will be the field course (so fingers crossed and will report back after the course). For anyone who is interested and for my future reference (because I will surely forget these steps) here are the steps I did which mirror those I found on other sites:

!!!!!!!!! If you follow these steps it is at your own risk. I do not expect anything below will permanently harm a device but I do not take any responsibility for crashed or bricked tablets/phone/devices !!!!!!!!!!!!!

(1) Download both GNURoot Debian and XServer XSDL from the Google play store. I also download QuickEdit for writing code outside of the terminal.

(2) Open GNURoot Debian and run:

apt-get update
apt-get update

(3) Then run the following code to install backports version of R. As of Feb 2018 the most current version of R available is 3.4.3 but I can only get R 3.3.3 on backports (was good enough for me but check here for some potential work-arounds). This takes a while so I would just run this line and let it go.

apt-get install -t jessie-backports install r-recommended

NOTE: for some  packages I wanted in R, I also had to install some other Linux packages and dependencies. I would suggest trying to load the package in R and look at any error outputs to see what dependencies you might need. Below are a couple I have to install for "devtools" and "nloptr." Remember to update in between installing dependancies!

apt-get update
apt-get install pkg-config libssl-dev
apt-get update
apt-get install libnlopt-dev
apt-get-update

(4) Install a package in Debian so that you can send any plots or other displays to XServer. There is an example of this where you can have an entire Linux GUI on you tablet but I just wanted a screen where I can send plots to so I installed 'i3'. *People have previously gotten RStudio on their tablet but I haven't gone down that route yet, see here too.

apt-get install i3

I also found that the option for using simple text plots is also very nice in R in the Debian terminal (see NostalgiR).

Screenshot_2018-02-17-16-43-12.png

(5) Now we can work in R! First open XServer XDSL (the first time you open the app it will ask you if you want to download some extra fonts, I clicked 'yes'). You will get a blue screen (see above) with some code that you need to put into the Debian terminal (before you open R). My code is the bottom line:

export DISPLAY=:0 PULSE_SERVER=tcp:1027.0.0.1:4712

Since my tablet allows split screens, this is what I see:

Screenshot_2018-02-17-16-56-14.png

Then launch the i3 package in the Linux terminal (see above): 

i3 &

(6) Now, I open R and make a simple plot. The first time i3 comes on it is a little fussy (I probably just don't have the kinks figured out yet). For the plot to show, you have to 'click' or 'touch' the program to prompt it. Then going back to R just hit enter and you are ready for whatever next steps you want to take.

Screenshot_2018-02-17-16-58-37.png

Plotting is slower than my other computer (which is expected) but it gets the job done! You have to switch between the terminal and XServer app each time you send code to the plotting device (even when using dev.off() in R). Before exiting R, I have found that turning off the graphics devices helps with not confusing the program and XServer:

dev.off()
q()

(7) When you are out of R and completely done with the your time in Debian, turn off i3 by inputting the code below and tapping the XServer app again. 

i3 exit
Screenshot_2018-02-17-17-24-17.png

Then stop XServer via the notifications tab (see above) and go back to the terminal and type:

exit

GNURoot Debian will close, you can closer XServer, and you will be done!

 

Soooo... about $100 bucks and lots of time later, I had a device that I could enter data, analyse the data, write a report, and create some basic plots (and also create a basic presentation if need be via the PowerPoint app). It was really neat to add this to my tablet and I am excited/scared to learn more about the quirks of using this new functionality. Of course, its uses are limit so I will not be parting with my brick of a laptop anytime soon, but for the field course I am sure that it will be sufficient (yet slow). An extra plus, all of the accessories I bought can also be used on my phone or any Bluetooth and/or USB Micro device if need be.

 

Anything I missed? Suggestions to improve what I have done? Found other things to work for you? Comments? Questions (which I am unsure I can answer)? Let me know! I will update here and respond as needed!


NOTES:

(1) To 'put' files onto you Debian computer you need to put anything you want in the following file on your Android (I would think it would be similar on other devices):

20180217_172912.jpg

Go to "Device storage > GNURoot > home" and paste your file into the folder.

Screenshot_2018-02-17-17-30-51.png

Then you can find that file in GNURoot under "/home".

(2) For those that want to make .csv's on the fly, I have only found one app that will let me enter data into a spreadsheet form and save it as a ".csv", WPS Office. This way I can enter data, save it as a .csv, move it into my GNURoot directory, and do some preliminary analyses all on the same device.

(3) I have found that I can attach my 2TB external hard drive that is helpful for carrying around files in general (have yet to test how to access in GNURoot and R). It does require a piece of hardware (A) and an app (B): (A) a OTG cable with power. I choose this one but there are many others out there that have the same capability and could potentially charge your tablet at the same time as powering your external hard drive. The one I have requires external power has 4 USB import locations (one with power for my external and three without for USB flash drives) but does not charge my tablet at the same time. It also works without the power just with the USB flash drives that do not need power. (B) I have only found one app USB Media Explorer that works the way I want it to. It lets me attach ExFAT and NTFS formatted drives - this app is PAID ($3.99) and the only app I have ever actually bought so far - just used my Google Opinion Rewards so it was basically no money out of my pocket. You may have better luck finding and using one of the free apps!

(4) The use of a Bluetooth keyboard and number pad have been very helpful with increasing the functionality of my tablet. I also got a mouse but I have found it to be too cumbersome compared to using my touchscreen. I bought all 3 from Jelly Comb and have been please so far. You might find a better option out there for you. **The number pad's other usages (e.g. "Home" and "End" do not seem to work for me in the word processing app or R, but there is a key combination on the Bluetooth keyboard that works well).

For those of you struggling without a keyboard to recall text in the terminal or R (where you would have hit the up key) you need to click the Volume up button and then hit 'w' on your screen keyboard. Or install an app like Hacker's Keyboard. I also bought a collapsible stand for my tablet but the jury is out on if I like it our not... it does a decent job of getting the screen closer to eye-level but is not made for such a big device and tipping is an issue (see top pic).