Homework Submission

Produce a Report

Create a new R markdown document. Name it: lastName-firstInitial-week5.Rmd Within your .Rmd document, include the plots listed below. When you are done with your report, use knitr to convert it to html format. Submit both the .Rmd file and the .html file. Be sure to name your files as instructed above!

Use knitr Code Chunk Arguments

In your final report, use the following knitr code chunk arguments to hide messages and warnings and code as you see fit.

• message = FALSE, warning = FALSE Hide warnings and messages in a code chunk
• echo = FALSE Hide code and just show code output
• fig.cap = "caption here" Add a caption to a figure. When you do this, each figure needs to be in it’s own code chunk!

Answer Questions Below in Your Report

1. Write at least 2 paragraphs: In this class you learned the relationship between lidar derived canopy height models and measured tree height. Use that plots that you create below, the readings and the course lessons to answer the following questions
   • Which lidar tree height metric, (max vs. mean height) more closely relates to human measured tree height?
   • What sources of uncertainty (as discussed in class and the readings) may impact relationship between lidar vs human measured tree height?
   • Do you notice any differences in the relationship between the lidar vs human measured tree height between SJER vs SOAP field sites? Explain.
2. Write at least 1 paragraph: List a minimum of 3 sources of uncertainty associated with the lidar derived tree heights and 3 sources of uncertainty associated with in situ measurements of tree height. For each source of uncertainty, specify whether it is a random or systematic error. Be sure to reference the plots and readings as necessary.

Include the Plots Below

Be sure to describe what each plot shows in your final report. Your plots do not need to be in the order below. I just listed them this way to make it easier to keep track of and grade!

Plots 1 - 2

Overlay the field site point locations on top of the canopy height model for both the SJER and the SOAP field sites.

Plots 3 - 6: Scatterplots

For both the SJER and SOAP field sites, create scatter plots that compare:

• MAXIMUM canopy height model height in meters, extracted within a 20 meter radius, compared to MAXIMUM tree height derived from the in situ field site data.
• AVERAGE canopy height model height in meters, extracted within a 20 meter radius, compared to AVERAGE tree height derived from the in situ field site data.

Plot 7 - 10 Difference Bar Plots

For both the SJER and SOAP field sites, create barplots that show the DIFFERENCE between:

• Extracted lidar max canopy height model height compared to measured max height per plot.
• Extracted lidar average canopy height model compared to measured average height per plot.

Graduate Students Only

Add a regression line to each scatterplot. For both plots write a thoughtful paragraph describing what the regression relationship tells you about the relationship between lidar and measured vegetation height. Does the comparison between lidar and measured average height look stronger? Or Maximum height? Why might one be “better” or a strong relationship than the other.

IMPORTANT: For All Plots

• Label x and y axes appropriately - include units
• Add a title to your plot that describes what the plot shows
• Add a brief, 1-3 sentence caption below each plot that describes what it shows HINT: you can use the knitr argument fig.cap = "Caption here" if you are knitting to pdf to automatically add captions.

Homework Due: Monday October 9th 2017 @ 8am.

Submit your report in both .Rmd and .html format to the D2l dropbox. Once again you are welcome to submit a .pdf instead of .html if you wish!