Getting 90th percentile data of each plot for plant height

[Pravin Gautam]

Hi Filipe,

New in R and or any other programming. Trying to your FieldImageR for drone image analysis for plant height. Following FIeldImageR code I can get EPH mean, median or quartile of each plots. However, how do I get percentile data of each plots for plant height. I want EPH to be 90th percentile plant height rather than mean, quartile or any other function under fun=. This is important as in many crops average plant height for drone images  do not correlates with actual ground data. Its 80th percentile or more is more correlated with actual height data.

[fmatias]

Hi Pravin,

Thank you for asking. Can you adept the code below for your data and let me know if it worked, please?

PH<-extract(x = DSM, y = fieldShape)

PH90<-do.call(rbind,lapply(PH, quantile, probs = c(0.9), na.rm=TRUE))

PH90

All the best,

Filipe

[Pravin Gautam]

Filipe,

which DSM to use. There is no DSM only. It started with DSM0 and DSM1 and followed by .R, .S etc. Irrespective of which one I put it gives me following error.

Error in (function (classes, fdef, mtable)  : 

  unable to find an inherited method for function ‘extract’ for signature ‘"list", "function"’

[Pravin Gautam]

This is what I'm using.

# Estimating plant height

# Uploading files from soil base (EX_DSM0.tif) and vegetative growth (EX_DSM1.tif):

DSM0 <- stack("DSM0 HIYT 3-23.tif")

DSM1 <- stack("DSM1 HIYT 6-11.tif")

# Cropping the image using the previous shape from step 2:

DSM0.C <- fieldCrop(mosaic = DSM0,fieldShape = EX1.Crop)

DSM1.C <- fieldCrop(mosaic = DSM1,fieldShape = EX1.Crop)

# Canopy Height Model (CHM):

DSM0.R <- resample(DSM0.C, DSM1.C)

CHM <- DSM1.C-DSM0.R

plot(CHM)

# Rotating the image using the same theta from step 3:

CHM.R<-fieldRotate(CHM, theta = -0.979)

# Removing the soil using mask from step 4:

CHM.S <- fieldMask(CHM.R, mask = EX1.RemSoil$mask)

# Extracting the estimate plant height average (EPH):

EPH <- fieldInfo(CHM.S$newMosaic, fieldShape = EX1.Shape$fieldShape, fun = "mean")

EPH$plotValue

PH<-extract(x = CHM.S, y = fieldShape)

PH90<-do.call(rbind,lapply(PH, quantile, probs = c(0.9), na.rm=TRUE))

PH90

[fmatias]

Pravin,

Please try this new code:

PH90.A<-extract(x = CHM.S$newMosaic, y = EX1.Shape$fieldShape)

PH90<-do.call(rbind,lapply(PH90.A, quantile, probs = c(0.9), na.rm=TRUE))

PH90

Best,

Filipe    

[Pravin Gautam]

Thank you Filipe. It worked.

[fmatias]

Great Pravin..!!!

I just added some new code in the tutorial to extract 10% and 90% quantile: https://github.com/OpenDroneMap/FIELDimageR#P10 

Hope it helps.

All the best,

Filipe