UOA-MEDSCI-736 / nbir012-diptera-morpho

1 stars 1 forks source link

Readme

Project Name

Geometric morphometric analysis

Project Overview

To use insect wing venation to assist in the taxonomic classification of specimens

Format of Input Data

Data should be in a csv file and be composed of species (independent variable) and centroid values for the landmarks (dependent variables) you wish to analyse.

Please note that the species name can be in any format e.g. Genus species, G. species, species, g. species etc.

The first row should contain titles for the column with column one being X and column 2, 3 and 4 being Landmark1, Landmark2, Landmark3.

An example csv data file would look like the following:

X Landmark1 Landmark2 Landmark3
D. bartletti 76.7 29.5 7.5
D. bartletti 60.5 32.1 6.3
D. bartletti 96.1 40.7 4.2
D. bartletti 88.1 45.1 4.9
D. bartletti 50.2 34.1 11.7
D. bartletti 55 31.1 6.9
D. bartletti 65.4 21.6 4.3
D. bartletti 65.7 27.7 5.3
D. costa 67.3 48.3 5.5
D. costa 61.3 28.9 6.9
D. costa 58.2 42.5 4.8
D. costa 76.9 20.4 3
D. costa 66.9 23.9 1.1
D. costa 55.4 29.1 5
D. costa 50.5 18 4.8
D. costa 64.1 14.5 3.7
D. maui 62.8 25.9 2.9
D. maui 45 15.9 1.2
D. maui 47.8 36.1 4.1
D. maui 75.6 27.7 6.3
D. maui 46.6 46.9 3.6
D. maui 50.6 29.7 4.7
D. maui 45.7 27.6 6.2
D. maui 68.4 35.3 1.9
D. corsa 52.5 39 3.1
D. corsa 80 54.2 4
D. corsa 54.7 32.1 5.7
D. corsa 63.5 25.6 3
D. corsa 46.3 31.8 7.4
D. corsa 61.5 16.8 1.9
D. corsa 62.9 25.8 2.4
D. corsa 49.3 39.4 5.2

Key requirements: That the data is presented in a comma delimited csv file.

Instructions

Download [nbir012-diptera-morpho] (https://github.com/nbir012/nbir012-diptera-morpho) and save to your computer.

Instructions With Dummy Data

  1. Within the downloaded project, navigate to the folder named Data/
  2. open normal_morpho.csv
  3. Ensure data is showing as a comma delimited csv file, there are four columns and 33 rows (including titles) and column 1 is labeled X and column 2,3 & 4 are labeled Landmark1, Landmark2 and Landmark3
  4. Close data file if all is correct, or convert data to the correct format (refer to format of input data).
  5. Go up one folder level and navigate into Code/
  6. Open up morphoManova.R
  7. Run line two of the code, a pop up will appear prompting you to select the data, navigate to the folder "Data/" in the project folder and select the normal_morpho.csv
  8. select line 3 through to 66 of the code (so these lines are all highlighted) and select run. The packages required will automatically download, the assumption tests will check the selected data and the output will present a range of statistical analyses with some annotations to help the user interpret their output.
  9. A wild manova output appears at the end.

Instructions with user supplied data

  1. Within the downloaded project navigate to the folder named Data/
  2. Save your user data as a csv file (refer to format of input data)
  3. Ensure data is showing as a comma delimited csv file, there are four columns and 33 rows (including titles) and column 1 is labeled X and column 2,3 & 4 are labeled Landmark1, Landmark2 and Landmark3
  4. Close data file if all is correct, or convert data to the correct format (refer to format of input data).
  5. Go up one folder level and navigate into Code/
  6. Open up morphoManova.R
  7. Run line two of the code, a pop up will appear prompting you to select the data, navigate to the folder "Data/" in the project folder and select your csv file
  8. select line 3 through to 66 of the code (so these lines are all highlighted) and select run. The packages required will automatically download, the assumption tests will check the selected data and the output will present a range of statistical analyses with some annotations to help the user interpret their output.
  9. Run code
  10. A wild manova output appears at the end.

Expected Output

The expected output should look similar to the below but with values that are different:

Df Pillai approx F num Df den Df Pr(>F)
data$C 3 1.85017 699.75 6 340 < 2.2e-16 ***
data$V 3 0.24953 8.08 6 340 0.000000036 ***
data$C:data$V 9 0.31746 3.56 18 340 0.000001954 ***

Known Limitations

Licence

[The Unlicence] (https://github.com/nbir012/nbir012-diptera-morpho/blob/master/Documents/Licence.txt) - applies to all code and text. and data (other than the DMP template supplied by UoA) The data contained in the [figshare repo] (https://figshare.com/projects/nbir012-diptera-morpho/16794) contains its own licencing information. Please refer directly to this.

Contributors

Neil Birrell - Developer

Greg Holwell - product owner

Zeeshan - scrum master

UoA Medsci736 teaching staff