December 15th - Jan 5th

In Peru. Christmas in Lima and then travelling to Manu park in the Andes to assist on a project looking at climate change impacts on frog reproduction and growth in conjunction with Berkeley and La Mollina, Peru.

Saturday & Sunday – 12/ (05 & 06) /09

• Moving to new house in Laupahoehoe to be located closer to field site. Here we are 5 minutes from entrance to experimental forest versus 45 from Hilo.

 

Friday – 12/04/09

• Field work
• Setup and cleaned traverse
• No leaf profiles possible as we ran out of time due to extensive cleaning and traverse setup issues
• Traverse 5 is ready for quick install and profile collection on Wednesday

Thursday – 12/03/09

• Working on new house, installation, etc…

Wednesday – 12/02/09

• Scanning leaf area at IPIF
• Entering questionnaires

Tuesday – 12/01/09

• Leaf area profiles. 15 of 30 completed now.

Looking down at Angelica from on a traverse. She’s preparing to shoot my location in 3 dimensions using a laser rangefinder/360 compass system (Trupulse 360).

 

A few of the many tools needed to identify leaf locations at high precision in 3 dimensions. Sonic rangefinders, Trupulse 360 and lots of climbing gear.

Monday – 11/30/09

• Entering questionnaires
• Organizing field gear for tomorrow early
• Finish review for Journal Tropical Ecology (done)

Wed – 11/25/09

• entering questionnaires
• packing field gear for Friday

Tuesday – 11/24/09

• Angelica office day
• Entering questionnaires
• Finish review for Tropical forest ecology journal
• Finish entering leaf profile data (done)
• Renew laupahoehoe keys at DOFAW

Monday – 11/23/09

• Office day (Hilo).
• Enter Angelica PEN questionnaires
• Scan leaves at IPIF (done)
• Enter all leaf data and laser data into spreadsheet
• Post previous laser level to craigslist
• Finish review for Journal tropical ecology
• Complete GCEP renewal and submit for recommendation (done)
• Download remaining Costa Rica Landsat images (done)
• Review new Forest Ecology & Management article (done)

 

Misc:

• Safety check field vehicle (done)

Wed-Saturday 11/21/09

• Intensive leaf profile work – final rigging of traverses. 12 of 30 now finished.

Monday – 11/16/09

• Field work – collecting leaf area profiles
• Rained out – huge tropical storm and flash flooding present

Tuesday – 11/17/09

• Enter PEN questionnaires (Brazil)
• Download and verify Costa Rica imagery
• Resorption calculations (redo) for Bolivia article
• Get Angelica’s time sheets signed
• Return/sign-out Laup keys (done)
• Pick up HIPPNET tower keys from Bernice

Sunday – 11/15/09

• Costa Rica: Download satellite imagery and analyze defaunation using spatial data.
• Bolivia: Redo figures including this effect
• Bolivia: write up methods final and results section with new results.
• Pack all field gear for tomorrow

 

Steps for Costa Rica remote sensing analyses:

1) Identify and download imagery (in process)

2) Identify and trim images to study area

3) Georeference all imagery to base imagery

4) Identify/remove clouds (write IDL code for this)

5) Merge images (remove SLC, cloud areas, etc…) – modify my IDL code for this.

6) Import GPS points from field work

7) Classify as forest / non-forest / mangroves

8) Use same spectral classes for all images

9) De speckle (modify my IDL code for this)

10) Manual clean (modify my IDL code for this)

 

Manuel Antonio, Costa Rica – location of study

Saturday – 11/14/09

General to do list:

• Peru: Enter all land history questionnaires (2 of 90 finished)
• Angelica: Enter all PEN Brazil questionnaires (47 left)
• Hawaii: Enter all leaf area data (done)
• Hawaii: Collect all leaf area profiles (9 of 30 finished)
• Costa Rica: Download satellite imagery and analyze defaunation using spatial data.
• Bolivia: Redo niche effect analyses
• Bolivia: Redo figures including this effect
• Bolivia: write up methods final and results section with new results.
• Costa Rica: Butterfly data collaboration with INBIO, any updates?

Friday – 11/13/09

• Enter leaf area density (LAD) data into worksheet (partly done)
• Download and organize microclimate data from field laptop  (done)
• Continue entering Peru land use history questionnaires (2 of 90 entered)
• Locate and download good Costa Rica satellite imagery (for defaunation project)
• Check climbing gear drying status
• Order new batteries if necessary (charge ones we brought back from the field yesterday)  (done - 70$)
• Order new cordless drill for sensor rigging (done) (165$)

Thursday – 11/12/09

• Changed desiccant, programs and batteries on top of canopy climate stations this morning.
• Located new house to rent closer to field site.

http://honolulu.craigslist.org/big/apa/1420465260.html

• Scanned all leaves from Wednesday profiles this afternoon.

Wednesday – 11/11/09

• Heading to the field to collect leaf area profiles (6 am)
• scan leaf areas at IPIF this evening
• Change desiccant and batteries of CR-200 microclimate sensors + download data
• Success – now 9 of 30 profiles completed.

Tuesday – 11/10/09

• Finish CR-200 programs for install tomorrow
• Organize desiccant and bags and make sure 2 charged batteries are available .
• Get tower access key from Bernice (for checking BF3 status)
• Repack all field gear
• Tighten all life safety screwlink carabineers!
• Finish entering data from LAD profiles
• Enter final Brazil PEN questionnaire
• Download Costa Rica project imagery
• Journal of Tropical Forest Science review due tomorrow!
• Enter deforestation data from my Peru chapter 4. Angelica needs this info for some of her questionnaires as well.

Monday – 11/09/2009

• Field work for leaf area profiles
• Hardware failure. Had to return home early and were unable to collect any data.
• Looking for houses in Laupahoehoe rather than Hilo to save on transport time and expenses.

Sunday – 11/08/09

• Entered PEN questionnaires (1 left)
• FORECO article review completed today (finished)
• Bring in outdoor sensors (finished)
• Download and verify data from CR-10x – PAR & wind
• Complete hanging system for sensors (50% completed)
• Pack bags for field work tomorrow (repack)

 

To do list:

- need to enter all data for Chapter 4 PERU land use deforestation by year. This is necessary for part of Angelica’s study as well.

- Prep computer to install new climate programs in weather stations in Laup.

- Pick up CR-3000 key from Bernice to check BF3 data on Monday as well if we have time.

Friday – 11/06/09

• Car broke down – likely damaged during field work
• Working at home today and tomorrow while it is repaired, then we will be doing intensive field work next week to finish leaf area profiles before Christmas break.
• Entering questionnaires related to Angelica’s research

Thursday – 11/05/09

• Entering PEN questionnaires
• Learning about Dinamica landscape modeling software

Wednesday – 11/03/09

• Research errands mostly
• Mailed back broken BF3
• Returned materials to IPIF

Tuesday – 11/02/09

• Heading to the field with IPIF crew for hopefully final installation of BF3 sensor in the climate tower.
• Successfully installed a net radiometer, BF3 sensor and a PAR sensor. A quick data check showed that all was well with the BF3. Hopefully it will remain like that for the next year!!!

Monday – 11/01/09

• Traverse 2 completed
• 3 leaf area profiles collected and measured
• long day: 6 am - 10 pm in the field or lab

 

Our traverse hanging system for leaf area profile collection

 

3d laser georeferencing system with sonic rangefinder separate. used to georeference all leaf collections or ecophysiology measurements.

Sunday – 11/01/09

Objectives:

• Order additional cube for parachute cord storage (done)
• pack for Monday field work
• finish sensor hanging system (install steel bolts)
• update blog (done)
• review FORECO article
• make Bolivia d15N figures
• Write R code for feedback analyses
• enter 1 more Brazil questionnaire
• Download Landsat images for Costa Rica project
• Update Bolivia MS with new results

Saturday – 10/31/09

• Entering PEN questionnaires.
• Designing new PEN Access database.

Friday – 10/30/09

• Field work. Leaf area profiles at traverse site 2.
• Improved traverse mobility system.  New knot for primary life support allows me to be much closer to traverse lines for easier mobility.

Thursday – 10/29/09

• Entering PEN questionnaires.
• Chapter 3 statistics.
• New BF3 arrived. Testing for one week prior to tower installation planned for Wednesday Nov 4th.

Wednesday – 10/28/09

• Field work.
• First 3 of 30 leaf area profiles completed.
• 

Tuesday – 10/27/09 – 5:45 am

• Angelica work day – download and geo-reference RS satellite imagery.
• Make new biomass correlation statistics for chap. 3
• Make descriptive figure (niche width)
• Continue formatting tables
• Finalize sensor hanging array system for Wednesday field work.
• Test sensor weatherproofing – email to arrange tower installation date next week.

Monday – 10/26/09 – 8 am

• Field work cancelled due to injury
• Received new BF3!!! Will begin setup and testing if possible here at the house.
• Arrange for installation of BF3 next week if possible.
• Finalize microclimate sensor hanging system, bought the parts just need to install them.
• Collecting wood density values for all species (220 sps.) in Chapter 3.
• Continue final statistics and figures for PNAS chapter 3 article.
• Yeah, finished the biomass, wood density, and a great figure.. yeah!!!!! Here is a preliminary version below…

Saturday – 10/24/09 – 8 am

• Decide on figures and tables for Bolivia article (PNAS)
• Finalize hanging mechanisms for interior forest sensors
• Download images for Costa Rica project
• Continue geo-referencing imagery for Peru Amazon project

Thursday – 10/21/09 – 8 am

• Fighting the flu, had to cancel field work today
• Working on Bolivia chapter 3 analyses
• New BF3 shipped directly to us from England, should have it within a week.

Wednesday – 10/21/09 – 8 am

• Check all traverse gear
• Pack all equipment for LAD collection tomorrow
• Finish entering questionnaires
• Continue statistical analysis of Bolivia data

Tuesday – 10/20/09 – 5 am

• Write inter-variable correlation analysis code for Bolivia project.
• Finish writing up results section.
• Finish any missing statistical analyses.
• Make a list of figures for article vs... appendix.
• Angelica work day – enter >= 10 PEN questionnaires.
• Finish microclimate field hanging system.
• Check all traverse climbing gear and organize for tomorrow.
• Check all equipment for leaf area profiles for tomorrow.

Monday – 10/19/09 – 7:30 am

• Download microclimate data (Cr10x, HOBOs)
• Write R code for data organization / merging
• Finish sensor design/construction of installation method
• Finish statistical analysis for Bolivia project

- recheck highlighted numbers in tables

• Decide on most important figures for article

- appendix Vs. main text

• Organize family information for all trees in Bolivia structure dataset.
• Windspeed calibration successful. Differences due to different locations at the test site.

Sunday – 10/18/09 – 8 am

• Finish flow chart for Bolivia analysis
• Redo previous analyses as necessary
• Write R code for final analyses and descriptive stats
• Download all sensor data (CR-10x and HOBOs)
• Compare for climate data validity (wind, temp, rH, PAR)
• Start R code for climate data organization and merging
• Enter PEN questionnaires for Angelica

Saturday – 10/17/09 – 8 am

• Visit new future field work site – Hakalau
• Input PEN questionnaires to meet deadline.

Friday – 10/16/09 – 5 am

• Monte carlo R code (finish) 5-7 am
• Priority RS for Brazil nut sustainability project
• IDL coding for image cleaning and manipulation
• Collection of image statistics

Example classification, red = deforestation 2000-2005, Peru trans-oceanic road impacts. Logging roads are visible.

Thursday – 10/15/09 – 5 am

• Angelica PEN data entry 7-6 pm
• R scripting for Bolivia project: 5-7 am
• Delta-T identified problem with our previous 2 BF3 units. There is a seal error in the recently constructed units. I should hopefully have a new working unit within a week!

Wednesday – 10/14/09 – 5:15 am

• monte carlo R code (continue)
• finish datalogger weather storage unit
• install hobo software on field laptop
• connect sensors and check data quality
• check traverse equipment and make checklist
• laup keys return / checkout
• bf3 update (sensors status in England)
• finish sewing desiccant bags
• given time to field and download weather data, install new CR-200 programs
• Success! (11:44 am) – datalogger, sensors and HOBOs all working correctly. Collecting data now for the next 5 days for calibration/verification.

Tuesday – 10/13/09 – 6:30 am

• Angelica work day – entering PEN questionnaires

Monday – 10/12/2009 – 7 am

• Complete review for Biological Conservation (priority).
• Chap 3. Continue writing R code for primary forest age error assessment.
• Finish interior forest microclimate sensor setup and datalogger housing units.
• Finish sewing desiccant mesh bags.
• Install sensor setup outside house for rest of week to error check and inter-calibrate climate data.
• Continue readings PDFs on C & N stable isotopes
• 6 pm. construction completed on microclimate sensors!

Saturday – 09/10/2009 – 8 am

• Angelica work day – entering questionnaires
• Sewing desiccant bags
• Continue R scripting Monte Carlo error code
• Finish review for Biological Conservation
• Learning about MODIS imagery…how to download and process.

Friday – 10/09/2009 – 5:05 am

• Have initial results from phylogenetic analysis – wrote R code to enable Monte Carlo runs on errors
• Learn Phylocon v.4.1 and R picante package for phylogenetic analysis. Making big progress on this section.
• Continue coding R error code, work to include phylogenetic analysis as well as linear regressions
• Construct weather proof data logger containers for microclimate sensors.
• Continue organizing bibliography (mendeley)
• Read isotope articles and incorporate into MS

Thursday – 10/08/2009 – 6:40 am

• Angelica assistant day: enter PEN questionnaires
• Continue coding R program to check variables in Bolivia chapter.
• Design and construct datalogger weather proof shells
• Design and construct desiccant storage bags

Wednesday – 10/07/2009 – 6:20 am

• Continue analysis of species mean age Vs. leaf nutrients
• Continue writing methods for chapter 3.
• Finish construction of interior forest sensors.
• Finish migrating work from laptop to desktop
• Posted my research bibliography online for eventual use by colleagues in Latin America and elsewhere. Weblink is:

http://www.mendeley.com/collections/103232/0-All-Documents/

• Interesting updates to Bolivia succession project. See PDF download at:

http://dl.getdropbox.com/u/1447763/Broadbent_Chap_3_Bolivia_Succesion_Update_100709.pdf

• New report on illegal logging worldwide featuring Asnerlab selective logging / forest degradation research. See link below for PDF:

http://dl.getdropbox.com/u/1447763/Global%20Witness_2009_Vested%20Interests_Industrialloggingandcarbonintropicalforests.pdf

Tuesday - 10/06/2009 – 8 am

• Working at home – Angelica assistant day
• Review due for Biological Conservation Journal
• Continue organizing / writing Bolivia article (chap. 3)
• Most of today: entering PEN questionnaires from Peru
• Continuing work on interior forest microclimate sensor construction.

Monday – 10/05/2009 – 6:30 am

• Work hours: 6:30 am – 6 pm
• Dealing with broken BF3, the third one. Finally figured out the design issue which Delta-T will hopefully resolve and send me a new one promptly.
• Fix problem with bibliographic software. (solved, 7:20 am)
• Read articles on stable nitrogen isotopes. Many new ones downloaded.
• Continue designing tower climbing safety & rescue course for IPIF. This is necessary for Angelica and I to get certified so we can maintain and fix issues with the BF3 sunshine sensor.
• Continue data analysis for Bolivia chapter 3. Rachel is helping with the phylogenetic analysis which should be done within a week.
• Finish designing and constructing interior forest hanging array. Half completed today (6 pm).
• Download link for Bolivia succession research update:

http://dl.getdropbox.com/u/1447763/Broadbent_Chap_3_Bolivia_Succesion_Update_092709.pdf

Saturday - 10/03/2009 – 5:45 am

• Work hours: 5:40 am – 8 pm
• made  dataset for phylogenetic analyses with Rachel
• Modified CR20o code for Vaisalas, trying to get their data equivalent with the tower bucket data. However, I learned the tower bucket is not calibrated so will trust the Vaisala data.
• Entered Angelica’s questionnaires into Access.
• Refined bibliographic software and database.
• Dealing with 2nd broken BF3 sunshine sensor. Apparently a problem in the batch with the weatherproofing. See photo below for what 7 days with only slight rain did to to the 2800$ unit.