This vignette shows how to generate a incomplete block
design using both the FielDHub Shiny App and the scripting
incomplete_blocks() from the
To launch the app you need to run either
Once the app is running, go to Other Designs > Incomplete Block Design (IBD)
Then, follow the following steps where we show how to generate this kind of design by an example with 28 treatments and 4 reps. We will run this experiment in just one location.
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 columns
ENTRY column must have a unique entry integer number for
each treatment/genotype. The column
NAME must have a unique
name that identifies each treatment/genotype. Both ENTRY and NAME must
be unique, duplicates are not allowed. In the following table, we show
an example of the entries list format. This example has an entry list
with 12 treatments.
Input the number of treatments in the Input # of
Treatments box. In the alpha lattice design, the number of
treatments must be a composite number. In this case, Set it to
Select the number of replications of these treatments with the
Input # of Full Reps box. Set it to
Set the number of plots in each incomplete block in the
Input # of Plots per IBlock box. Set it to
Enter the number of locations in Input # of
Locations. We will run this experiment over a single location,
so set it to
cartesian in the
Plot Order Layout. For this example we will use the
Enter the starting plot number in the Starting Plot
Number box. If the experiment has multiple locations, you must
enter a comma separated list of numbers the length of the number of
locations for the input to be valid. Set it to
Enter a name for the location of the experiment in the
Input Location box. If there are multiple locations,
each name must be in a comma separated list. 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 an incomplete block design in FielDHub, there are several ways to display the information contained in the field book.
When you first click the run button on an incomplete block 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
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,
First, you need to load the
FielDHub package typing,
Then, you can enter the information describing the above design like this:
<- incomplete_blocks( ibd t = 28, r = 4, k = 4, l = 1, seed = 1243 )
The description for the inputs that we used to generate the design,
t = 28is the number of treatments.
r=4is the number of replicates.
k = 4is the number of plots per incomplete block.
l = 1is the number of locations
plotNumber = 101is the starting plot number.
locationNames = "FARGO"is an optional name for each location.
seed = 1243is the seed number to replicate identical randomizations.
Incomplete Blocks Design Information on the design parameters: List of 7 $ Reps : num 4 $ iBlocks : num 7 $ NumberTreatments: num 28 $ NumberLocations : num 1 $ Locations : int 1 $ seed : num 1243 $ lambda : num 0.444 10 First observations of the data frame with the incomplete_blocks field book: ID LOCATION PLOT REP IBLOCK UNIT ENTRY TREATMENT 1 1 1 101 1 1 1 14 G-14 2 2 1 102 1 1 2 9 G-9 3 3 1 103 1 1 3 28 G-28 4 4 1 104 1 1 4 19 G-19 5 5 1 105 1 2 1 2 G-2 6 6 1 106 1 2 2 10 G-10 7 7 1 107 1 2 3 8 G-8 8 8 1 108 1 2 4 27 G-27 9 9 1 109 1 3 1 11 G-11 10 10 1 110 1 3 2 26 G-26
incomplete_blocks() 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
ibd$fieldBook is a list containing information about
every plot in the field, with information about the location of the plot
and the treatment in each plot. As seen in the output below, the field
book has columns for
<- ibd$fieldBook field_book head(ibd$fieldBook, 10)
ID LOCATION PLOT REP IBLOCK UNIT ENTRY TREATMENT 1 1 1 101 1 1 1 14 G-14 2 2 1 102 1 1 2 9 G-9 3 3 1 103 1 1 3 28 G-28 4 4 1 104 1 1 4 19 G-19 5 5 1 105 1 2 1 2 G-2 6 6 1 106 1 2 2 10 G-10 7 7 1 107 1 2 3 8 G-8 8 8 1 108 1 2 4 27 G-27 9 9 1 109 1 3 1 11 G-11 10 10 1 110 1 3 2 26 G-26
For plotting the layout in function of the coordinates
COLUMN, you can use the the generic
plot() as follow,