This vignette shows how to generate a rectangular lattice
design using both the FielDHub Shiny App and the scripting
rectangular_lattice() from the
To generate a rectangular lattice design using the FielDHub app:
First, go to Lattice Designs > Rectangular Lattice
Then, follow the following steps where we will show how to generate a rectangular lattice design with 56 treatments and 3 reps.
If the selection is
No, that means the app is going
to generate synthetic data for entries and names of the treatment 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. The column
NAME must have a unique name
that identifies each treatment. Both
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 a rectangular lattice design, the number of
treatments must be a rectangular number, the product of two
consecutive integers. For example,
7 x 8 = 56 is a valid
entry, which we will use in this example.
Select the number of replications of these treatments with the
Input # of Full Reps box, which is
Set the number of plots in each incomplete block in the
Input # of Plots per IBlock box, which is
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 random seed in the box labeled random seed.
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 rectangular lattice 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 rectangular lattice 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 or change the location displayed. You can
also display a heatmap over the field by changing Type of
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
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:
<- rectangular_lattice( rect t = 56, r = 3, k = 7, l = 1, plotNumber = 101, locationNames = "FARGO", seed = 1235 )
t = 56is the number of treatments.
r=3is the number of replicates.
k = 7is 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 = 1235is the random seed to replicate identical randomizations.
Rectangular Lattice Design Information on the design parameters: List of 7 $ Reps : num 3 $ iBlocks : num 8 $ NumberTreatments: num 56 $ NumberLocations : num 1 $ Locations : chr "FARGO" $ seed : num 1235 $ lambda : num 0.327 10 First observations of the data frame with the rectangular_lattice field book: ID LOCATION PLOT REP IBLOCK UNIT ENTRY TREATMENT 1 1 FARGO 101 1 1 1 54 G-54 2 2 FARGO 102 1 1 2 9 G-9 3 3 FARGO 103 1 1 3 32 G-32 4 4 FARGO 104 1 1 4 21 G-21 5 5 FARGO 105 1 1 5 2 G-2 6 6 FARGO 106 1 1 6 47 G-47 7 7 FARGO 107 1 1 7 35 G-35 8 8 FARGO 108 1 2 1 3 G-3 9 9 FARGO 109 1 2 2 44 G-44 10 10 FARGO 110 1 2 3 13 G-13
rectangular_lattice() 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
rect$fieldBook is a list containing information about
every plot in the field, with information about the location of the plot
and the treatment in each plot. As seen in the output below, the field
book has columns for
<- rect$fieldBook field_book head(rect$fieldBook, 10)
ID LOCATION PLOT REP IBLOCK UNIT ENTRY TREATMENT 1 1 FARGO 101 1 1 1 54 G-54 2 2 FARGO 102 1 1 2 9 G-9 3 3 FARGO 103 1 1 3 32 G-32 4 4 FARGO 104 1 1 4 21 G-21 5 5 FARGO 105 1 1 5 2 G-2 6 6 FARGO 106 1 1 6 47 G-47 7 7 FARGO 107 1 1 7 35 G-35 8 8 FARGO 108 1 2 1 3 G-3 9 9 FARGO 109 1 2 2 44 G-44 10 10 FARGO 110 1 2 3 13 G-13
For plotting the layout in function of the coordinates
COLUMN, you can use the the generic
plot() as follows,