This vignette shows how to generate a completely randomized
design using both the FielDHub Shiny App and the scripting
function CRD() from the FielDHub package.
1. Using the FielDHub Shiny App
To launch the app you need to run either
FielDHub::run_app()or
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.
Inputs
-
Import entries’ list? Choose whether to import a
list with entry numbers and names for genotypes or treatments.
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.csvfile. The file must have the single columnTREATMENT, 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 ten treatments.
| TREATMENT |
|---|
| TRT_A |
| TRT_B |
| TRT_C |
| TRT_D |
| TRT_E |
| TRT_F |
| TRT_G |
| TRT_H |
| TRT_I |
| TRT_J |
Input the number of treatments in the Input # of Treatments box, which is
15in this case.Select the number of replications of these treatments with the Input # of Full Reps box. Set it as
6.Select
serpentineorcartesianin the Plot Order Layout. For this example we will use the defaultcartesianlayout.Enter the starting plot number in the Starting Plot Number box. Set it to
101.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
FARGO.To ensure that randomizations are consistent across sessions, we can set a random seed in the box labeled random seed. In this example, we will set it to
1236.Once we have entered the information for our experiment on the left side panel, click the Run! button to run the design.
Outputs
After you run a completely randomized design in FielDHub, there are several ways to display the information contained in the field book.
Field Layout
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.
Field Book
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.
2. Using the FielDHub function: CRD()
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
)Details on the inputs entered in CRD() above
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 random seed to replicate identical randomizations.
Print crd output
To print a summary of the information that is in the object
crd, we can use the generic function
print().
print(crd)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 T10Access to crd output
The 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 $ operator,
i.e. crd$layoutRandom or crd$fieldBook.
crd$fieldBook is a list containing information about
every plot in the field, with information about the location of the plot
and the treatment in each plot. As seen in the output below, the field
book has columns for ID, LOCATION,
PLOT, REP, IBLOCK,
UNIT, ENTRY, and TREATMENT.
field_book <- crd$fieldBook
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