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Split-Split Plot Design

Source: vignettes/split_split_plot.Rmd
split_split_plot.Rmd

This vignette shows how to generate a split-split plot design using both the FielDHub Shiny App and the scripting function split_plot() 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 > Split-Split Plot Design

Then, follow the following steps where we show how to generate this kind of design by an example with 3 whole plots, 2 sub-plots, 4 sub-sub plots and 3 reps. We will run this experiment in just one location.

Inputs

  1. Import entries’ list? Choose whether to import a list with entry numbers and names for treatments.

    • 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 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, we show an example of the entries list format. This example has an entry list with 10 treatments.

WHOLEPLOT SUBPLOT SUB_SUB_PLOT
0 0 0
1 1 1
2 2 2
3 3
4

  1. Choose whether to use the split-plot design in a RCBD or CRD with the Select SPD Type box.

  2. Set the number of whole-plots in the design with the Whole-plots box. Set it to 3.

  3. Set the number of sub-plots contained with the Sub-plots Within Whole-plots box. Set it to 2.

  4. Set the number of sub-sub plots contained with the Sub-Sub-plots within Sub-plots box. Set it to 4.

  5. Select the number of replications of these treatments with the Input # of Full Reps box. Set it to 3.

  6. Enter the number of locations in Input # of Locations. We will run this experiment over a single location, so set it to 1.

  7. Select serpentine or cartesian in the Plot Order Layout. For this example we will use the default serpentine layout.

  8. 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. For this case, set it to 101.

  9. 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 "FARGO".

  10. 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 1238.

  11. 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 split-split-plot 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 split-split-plot 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: split_split_plot()

You can run the same design with a function in the FielDHub package, split_split_plot().

First, you need to load the FielDHub package typing,

Then, you can enter the information describing the above design like this:

sspd <- split_split_plot(
  wp = 3, 
  sp = 2,  
  ssp = 4,  
  reps = 3,  
  type = 2,   
  l = 1, 
  plotNumber = 101,
  locationNames = "FARGO",
  seed = 123
)
Details on the inputs entered in split_split_plot() above

The description for the inputs that we used to generate the design,

  • wp = 3 is the number of whole-plots.
  • sp = 2 is the number of sub-plots.
  • ssp = 4 is the number of sub-sub-plots.
  • reps = 3 is the number of reps
  • type = 2 CRD or RCBD, 1 or 2 respectively
  • l = 1 is the number of locations.
  • plotNumber = 101 is the starting plot number.
  • locationNames = "FARGO" is an optional name for each location.
  • seed = 1240 is the random seed to replicate identical randomizations.
print(sspd)
Split-Split Plot Design 

Information on the design parameters: 
List of 6
 $ Whole.Plots  : int [1:3] 1 2 3
 $ Sub.Plots    : int [1:2] 1 2
 $ Sub.Sub.Plots: int [1:4] 1 2 3 4
 $ Locations    : num 1
 $ typeDesign   : chr "RCBD"
 $ seed         : num 123

 10 First observations of the data frame with the split_split_plot field book: 
   ID LOCATION PLOT REP WHOLE_PLOT SUB_PLOT SUB_SUB_PLOT TRT_COMB
1   1    FARGO  101   1          3        1            2    3|1|2
2   2    FARGO  101   1          3        1            3    3|1|3
3   3    FARGO  101   1          3        1            4    3|1|4
4   4    FARGO  101   1          3        1            1    3|1|1
5   5    FARGO  101   1          3        2            2    3|2|2
6   6    FARGO  101   1          3        2            3    3|2|3
7   7    FARGO  101   1          3        2            4    3|2|4
8   8    FARGO  101   1          3        2            1    3|2|1
9   9    FARGO  102   1          1        2            1    1|2|1
10 10    FARGO  102   1          1        2            3    1|2|3

Access to sspd object

The split_split_plot() 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. sspd$layoutRandom or sspd$fieldBook.

sspd$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, WHOLE_PLOT, SUB_PLOT, SUB_SUB_PLOT, and TRT_COMB.

field_book <- sspd$fieldBook
head(field_book,10)
   ID LOCATION PLOT REP WHOLE_PLOT SUB_PLOT SUB_SUB_PLOT TRT_COMB
1   1    FARGO  101   1          3        1            2    3|1|2
2   2    FARGO  101   1          3        1            3    3|1|3
3   3    FARGO  101   1          3        1            4    3|1|4
4   4    FARGO  101   1          3        1            1    3|1|1
5   5    FARGO  101   1          3        2            2    3|2|2
6   6    FARGO  101   1          3        2            3    3|2|3
7   7    FARGO  101   1          3        2            4    3|2|4
8   8    FARGO  101   1          3        2            1    3|2|1
9   9    FARGO  102   1          1        2            1    1|2|1
10 10    FARGO  102   1          1        2            3    1|2|3

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 follows,

plot(sspd)