Geneland : How to use the graphical interface.



Start up

Normal users:
Data files
Run
Post process
Output

Advanced users:
Simulate panmictic data
Simulate IBD data
Output

Start up

- Launch R

- Load Geneland with the command library(Geneland)

- Enter the command: Geneland.GUI()

 initial

Normal Users

Data Files

- Press the button Data Files

- Before you set the coordinates and genotypes choose the fields separator in your files, e. g.:

If your fields are separated by a spaces (tab or any amount of spaces) choose White space

You can also choose , and ;  as separator

- Press the Coordinates File, Genotypes File and Output Directory and choose the correspondent files and directories.

You will notice as soon as the files are loaded that, at bottom-left corner there will be a label telling if the coordinates and genotype files are loaded. You will need them to be loaded in order to run inference. Output label will stop blinking as soon as the output directory is well set.


Run


- Press the button Run.

- Fill the fields with adequate values. For the first run we recomend that you insert a large value for the mximum number of populations (if this value is unknown). Remember that the number in pop min (Minimum number of Populations) must always be smaller than the number pop max (Maximum number of Populations) and pop init (Initial Number of Populations) a value between pop min and pop max.
 


- When you hit the Run button at the bottom of the screen, if everything is OK, a window will appear and tell that  the inference is going on.



- After the inference is completed  a window will appear returning the status of the run.

 

Post process

- Hit Postprocess button.

- Fill the fields as desired.

- Hit bottom Run button.


 

Output

- Hit Output button.

- Hit Number of populations.


- A new window will appear. There you can decide if you want to visualize your results or save them into a file.

- In case of saving results to file press the button "Save File" to choose (or create) a file. The output file format is PostScript.

- Hit Draw


- The result for Number of populations should be something like this:

- Users should re-run several times their analysis to check consistency qcross runs.
 


Advanced Users

- Press Menu at top.

-Select Advanced Options

 

Simulate panmictic data

- Hit Panmictic data.

- Fill the fields with the desired values.

- Hit the bottom Run button.


- If you had pressed the "Save coordinates and genotypes file" box then you will be asked where to save those files.

After simulating data, a label saying that simulated data had been loaded  will appear at bottom left of the window inference may be run directly with that data. It is not possible to have more than one dataset  loaded at same time, so if there is any unsaved loaded dataset they WILL BE LOST.


Simulate IBD data

- Hit IBD data.

- Fill the fields with the desired values.

- Hit the bottom Run button.




- If you had pressed the "Save coordinates and genotypes file" box then you will be asked where to save those files.

You may notice that after simulating this datase,  it will appear at bottom left of the window a label saying that simulated data have been loaded, inference may be run directly with that dataset.

It is not possible to have more than one dataset loaded at same time, so if there is any unsaved loaded dataset it WILL BE LOST.


Output

- After simulating data (Panmictic or IBD) there will be possible to have some outputs.

- Hit Output button from Simulation part.