LeBauer:Notebook/Protocols

From OpenWetWare

Lab

• Enzyme Assay
• PLFA

Extracting Data From a Figure

To extract data from a jpg file in R using the digitize package:

   library('digitize')
   calpts <- ReadAndCal('Image.jpg') 
   ## click on xaxis min (x1), xaxis max (x2), yaxis min(y1), yaxis max (y2)
   pts <- DigitData(col='red',type='p',n=8)
   ## set n = to the number of points to collect 
   data <- Calibrate(pts, calpts, x1, x2, y1, y2)
   ## x1, x2, y1, and y2 are the min and max of the x and y axes, respectively.
   write.csv(data, 'authorYYYYabc_figX.csv')

Phenology

Codes used to monitor Phenology at the EBI Novel Woody Biofuel trials

Spring Survey

• 0 all leaves fallen except remnants on beech winter condition
• 1 bud swelling noticeable
• 2 small leaves or flowers visible initial stages of leaf expansion leaves about 1 cm long
• 3 leaves 1/2 of final length leaves 5 cm long leaves obscure 1/2 of sky as seen through crowns
• 3.5 leaves 3/4 expanded sky mostly obscured through crown crowns not yet in summer condition
• 4 canopy appears in summer condition leaves fully expanded little sky visible through crowns

Fall Survey

• 0 all leaves fallen except remnants on beech winter condition
• 0.5 most leaves fallen
• 1 no more green in canopy half of leaves have fallen leaves still obscure half of sky as seen through crown
• 2 most leaves yellow or red few leaves have fallen leaves still obscure most of sky as seen through crowns
• 3 many leaves have noticeable reddening or yellowing much green still present
• 4 canopy appears in summer condition only scattered leaves or branches have any color change

Sap Flux

Based on work by John Drake learned from Oren Lab. Contact me for more protocol.