This vignette shows how to generate a completely randomized
design using both the FielDHub Shiny App and the scripting
CRD() from the
To launch the app you need to run either
Once the app is running, go to Other Designs > Completely Randomized Design (CRD)
Then, follow the following steps where we show how to generate this kind of design by an example with 15 treatments and 6 reps each.
If the selection is
No, that means the app is going
to generate synthetic data for entries and names of the
treatment/genotypes based on the user inputs.
If the selection is
Yes, the entries list must
fulfill a specific format and must be a
.csv file. The file
must have the single column
TREATMENT, containing a list of
unique names that identify each treatment. Duplicate values are not
allowed, all entries must be unique. In the following table, we show an
example of the entries list format. This example has an entry list with
Input the number of treatments in the Input # of
Treatments box, which is
15 in this case.
Select the number of replications of these treatments with the
Input # of Full Reps box. Set it as
cartesian in the
Plot Order Layout. For this example we will use the
Enter the starting plot number in the Starting Plot
Number box. Set it to
Enter a name for the location of the experiment in the
Input Location box. A completely randomized design can
only be run in a single location at a time. Set it to
To ensure that randomizations are consistent across sessions, we
can set a seed number in the box labeled Seed Number.
In this example, we will set it to
Once we have entered the information for our experiment on the left side panel, click the Run! button to run the design.
After you run a completely randomized design in FielDHub, there are several ways to display the information contained in the field book.
When you first click the run button on a completely randomized
design, FielDHub displays the Field Layout tab, which shows the entries
and their arrangement in the field. In the box below the display, you
can change the layout of the field. You can also display a heatmap over
the field by changing Type of Plot to
Heatmap. To view a heatmap, you must first simulate an
experiment over the described field with the Simulate!
button. A pop-up window will appear where you can enter what variable
you want to simulate along with minimum and maximum values.
The Field Book displays all the information on the experimental design in a table format. It contains the specific plot number and the row and column address of each entry, as well as the corresponding treatment on that plot. This table is searchable, and we can filter the data in relevant columns. If we have simulated data for a heatmap, an additional column for that variable appears in the Field Book.
You can run the same design with a function in the FielDHub package,
CRD(). We can enter the information describing the above
design like this:
<- CRD( crd t = 15, reps = 6, plotNumber = 101, locationName = "FARGO", seed = 1236 )
The description for the inputs that we used to generate the design,
t = 15is the number of treatments.
reps = 6is the number of replications for each treatment.
plotNumber = 101is the starting plot number.
locationNames = "FARGO"is an optional name for the location.
seed = 1234is the seed number to replicate identical randomizations.
To print a summary of the information that is in the object
crd, we can use the generic function
Completely Randomized Design (CRD) Information on the design parameters: List of 5 $ numberofTreatments: num 15 $ treatments : chr [1:15] "T1" "T2" "T3" "T4" ... $ Reps : num 6 $ locationName : chr "FARGO" $ seed : num 1236 10 First observations of the data frame with the CRD field book: ID LOCATION PLOT REP TREATMENT 1 1 FARGO 101 4 T9 2 2 FARGO 102 4 T12 3 3 FARGO 103 2 T5 4 4 FARGO 104 3 T9 5 5 FARGO 105 6 T13 6 6 FARGO 106 5 T10 7 7 FARGO 107 5 T5 8 8 FARGO 108 2 T10 9 9 FARGO 109 2 T8 10 10 FARGO 110 3 T10
CRD() function returns a list consisting of all the
information displayed in the output tabs in the FielDHub app: design
information, plot layout, plot numbering, entries list, and field book.
These are accessible by the
crd$fieldBook is a list containing information about
every plot in the field, with information about the location of the plot
and the treatment in each plot. As seen in the output below, the field
book has columns for
<- crd$fieldBook field_book head(crd$fieldBook, 10)
ID LOCATION PLOT REP TREATMENT 1 1 FARGO 101 4 T9 2 2 FARGO 102 4 T12 3 3 FARGO 103 2 T5 4 4 FARGO 104 3 T9 5 5 FARGO 105 6 T13 6 6 FARGO 106 5 T10 7 7 FARGO 107 5 T5 8 8 FARGO 108 2 T10 9 9 FARGO 109 2 T8 10 10 FARGO 110 3 T10
For plotting the layout in function of the coordinates
COLUMN, you can use the the generic
plot() as follow,