Completely Randomized Design

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()

library(FielDHub)
run_app()

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 .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 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 15 in this case.
Select the number of replications of these treatments with the Input # of Full Reps box. Set it as 6.
Select serpentine or cartesian in the Plot Order Layout. For this example we will use the default cartesian layout.
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 seed number in the box labeled Seed Number. 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 = 15 is the number of treatments.
reps = 6 is the number of replications for each treatment.
plotNumber = 101 is the starting plot number.
locationNames = "FARGO" is an optional name for the location.
seed = 1234 is the seed number 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       T10

Access 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

Plot the field layout

For plotting the layout in function of the coordinates ROW and COLUMN, you can use the the generic function plot() as follow,

plot(crd)