Homework 10
You will fill out the following questionnaire for each program and submit the answers as your final homework. You will also share your questionnaire with the group that created the program by the end of discussion.
The Readme
1. Is the Readme file the first document displayed upon lading the Github? Does this Readme page include a title, and the name and contact information for all project members?

PITA (Plants in Trait Analysis)-Yes, readme is displayed first and the tile and author names/contact are provided

2. Is the purpose of this program clear from the Introduction? What -in your own words- is the motivation behind the program.

PITA (Plants in Trait Analysis)-Yes, the program aims to take data from TR8 and reorganize it so a researcher is able to locate data about a specific plant species particularly DNA.

3. Is there a program workflow and is it easy to understand? What -in your own words- is the program workflow?
MCA (Microridege Curviness Anaysis)- Yes, the program contains three main scrips and one wrapper script to run them all. The scripts match points along the ridges and uses these to calculate acceleration and slope which are used to calculate curvature. The ouput results in a csv file with the calculated curvature for each image.

PITA (Plants in Trait Analysis)- Yes, program reads an input file and deliminates by removing semicolons and blanks replacing those with tabs, all information other than genus and species is deleted as are duplicates, new information and specific information pertaining to the user are organized in a table

4. Are the dependencies indicated in the workflow? If there are Hoffman2 specific requirements are they indicated?

PITA (Plants in Trait Analysis)-Yes, and the dependences are indicated including the Hoffman (R also here)

5. Are there instructions for running the program? Do the instructions make sense? What would you do to improve the instructions?

PITA (Plants in Trait Analysis)- Yes, the instructions are chronological and I was able to follow them. I would just put a tab on the bullet parts of the instructions to help with visual organization.

6. Is there a section that indicates the files and directories produced by the program?

PITA (Plants in Trait Analysis)-Yes

7. Are the research programs / motivations for the program cited? Are the dependencies cited?
PITA (Plants in Trait Analysis)- Yes all are cited and provided
The Scripts
8. Is there a directory that contains all of the program scripts?

PITA (Plants in Trait Analysis)- Yes

9. Do these programs generate a run log?
XXXXX
The Vignette
10. Is there a directory called Vignette and does it include a test set, the commands used to run the program and the expected output databases?

PITA (Plants in Trait Analysis)- Yes these are included, they are in markdown files however

11. Where you able to run the Vignette using the small test dataset? If not what errors did you get? If so was it easy to run the dataset? Where the instructions clear.
PITA (Plants in Trait Analysis)-Yes, I was able to get everything running I didn't have any issues with it.

12. Where you able to reproduce the expected output? If not what was different.
PITA (Plants in Trait Analysis)- Yes

General
13. Give at least two suggestions for ways to improve the GitHub page or the operation of the program.


PITA (Plants in Trait Analysis)-I would change the formating at the beginning so that the authors and their contact info are not in paragraph form but in a list form for readability. Instructions could use some more clarity but overall good job.
