This vignette shows how to generate a partially replicated
design using both the FielDHub Shiny App and the scripting
partially_replicated() from the
FielDHub R package.
Partially replicated designs are commonly employed in early generation field trials. This type of design is characterized by replication of a portion of the entries, with the remaining entries only appearing once in the experiment. Commonly, the part of treatments with reps is due to an arbitrary decision by the research, also in some cases, it is due to technical reasons. In this design, it is recommended to replicate at least 1/3 of the treatments.
In this design you can set the number of entries that will have reps, as well as the number of entries that will only appear once. You can also choose to run the same experiment over multiple locations.
Consider a plant breeding field trial with 300 plots containing 75 entries appearing two times each, and 130 entries only appearing once. This field trial is arranged in a field of 15 rows by 20 columns. In this case, the breeder decided to replicate the genotypes that do not share significant generic information with each other (75), as well as leave with just one copy the genotypes that are siblings (130).
To launch the app you need to run either
Once the app is running, go to the tab Partially Replicated Design
Then, follow the following steps where we will show how to generate a partially replicated design.
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
REPS column must have an integer
number for the replications of the groups. 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
four treatments/genotypes that will appear twice and 8 that appear just
Enter the number of entries per replicate group in the #
of Entries per Rep Group box as a comma separated list. In our
example we will have 2 groups with 85 and 130 entries. So, we enter
75, 130 in the box for our sample experiment.
Enter the number of replications per group in the # of
Rep per Group box. In our example we will have 2 and 1
replications for the 2 groups, so we enter
2, 1 in this
Enter the number of locations in Input # of
Locations. We will run this experiment over a single location,
so set Input # of Locations to
cartesian in the
Plot Order Layout. For this example we will use the
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
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.
Once we have entered the information for our experiment on the left side panel, click the Run! button to run the design.
You will then be prompted to select the dimensions of the field
from the list of options in the drop down in the middle of the screen
with the box labeled Select dimensions of field. In our
case, we will select
15 x 20.
Click the Randomize! button to randomize the experiment with the set field dimensions and to see the output plots. If you change the dimensions again, you must re-randomize.
If you change any of the inputs on the left side panel after running an experiment initially, you have to click the Run and Randomize buttons again, to re-run with the new inputs.
After you run a single diagonal arrangement in FielDHub and set the dimensions of the field, there are several ways to display the information contained in the field book. The first tab, Get Random, shows the option to change the dimensions of the field and re-randomize, as well as a reference guide for experiment design.
On the second tab, Data Input, you can see all the entries in the randomization in a list, as well as a table of the checks with the number of times they appear in the field. In the list of entries, the reps for each check is included as well.
The Randomized Field tab displays a graphical representation of the randomization of the entries in a field of the specified dimensions. The checks are the green colored cells, with the The display includes numbered labels for the rows and columns. You can copy the field as a table or save it directly as an Excel file with the Copy and Excel buttons at the top.
On the Plot Number Field tab, there is a table display of the field with the plots numbered according to the Plot Order Layout specified, either serpentine or cartesian. You can see the corresponding entries for each plot number in the field book. Like the Randomized Field tab, you can copy the table or save it as an Excel file with the Copy and Excel buttons.
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.
You can run the same design with the function
partially_replicated() in the
First, you need to load the
FielDHub package typing,
Then, you can enter the information describing the above design like this:
<- partially_replicated( prep nrows = 15, ncols = 20, repGens = c(75,150), repUnits = c(2,1), planter = "serpentine", plotNumber = 101, l = 1, exptName = "Expt1", locationNames = "PALMIRA", seed = 1245, )
The description for the inputs that we used to generate the design,
nrows = 15is the number of rows in the field.
ncols = 20is the number of columns in the field.
repGens = c(75,150)are the values for the groups to replicate
repUnits = c(2,1)are the values for representing respective replicates of each group.
planter = "serpentine"is the layout order.
plotNumber = 101is the starting plot number for the experiment.
l = 1is the number of locations.
exptName = "Expt1"is an optional name for experiment.
locationNames = "PALMIRA"is the optional name for the locations.
seed = 1245is the seed number to replicate identical randomizations.
To print a summary of the information that is in the object
prep, we can use the generic function
Partially Replicated Design Information on the design parameters: List of 7 $ rows : num 15 $ columns : num 20 $ treatments_with_reps : int 75 $ treatments_with_no_reps: int 150 $ locations : num 1 $ planter : chr "serpentine" $ seed : num 1245 10 First observations of the data frame with the partially_replicated field book: ID EXPT LOCATION YEAR PLOT ROW COLUMN CHECKS ENTRY TREATMENT 1 1 Expt1 PALMIRA 2022 101 1 1 49 49 G49 2 2 Expt1 PALMIRA 2022 102 1 2 47 47 G47 3 3 Expt1 PALMIRA 2022 103 1 3 15 15 G15 4 4 Expt1 PALMIRA 2022 104 1 4 0 146 G146 5 5 Expt1 PALMIRA 2022 105 1 5 59 59 G59 6 6 Expt1 PALMIRA 2022 106 1 6 5 5 G5 7 7 Expt1 PALMIRA 2022 107 1 7 0 136 G136 8 8 Expt1 PALMIRA 2022 108 1 8 29 29 G29 9 9 Expt1 PALMIRA 2022 109 1 9 0 102 G102 10 10 Expt1 PALMIRA 2022 110 1 10 0 177 G177
partially_replicated() 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
prep$fieldBook is a list containing information about
every plot in the field, with information about the location of the plot
and the treatment in each plot. As seen in the output below, the field
book has columns for
Let us see the first 10 rows of the field book for this experiment.
<- prep$fieldBook field_book head(field_book, 10)
ID EXPT LOCATION YEAR PLOT ROW COLUMN CHECKS ENTRY TREATMENT 1 1 Expt1 PALMIRA 2022 101 1 1 49 49 G49 2 2 Expt1 PALMIRA 2022 102 1 2 47 47 G47 3 3 Expt1 PALMIRA 2022 103 1 3 15 15 G15 4 4 Expt1 PALMIRA 2022 104 1 4 0 146 G146 5 5 Expt1 PALMIRA 2022 105 1 5 59 59 G59 6 6 Expt1 PALMIRA 2022 106 1 6 5 5 G5 7 7 Expt1 PALMIRA 2022 107 1 7 0 136 G136 8 8 Expt1 PALMIRA 2022 108 1 8 29 29 G29 9 9 Expt1 PALMIRA 2022 109 1 9 0 102 G102 10 10 Expt1 PALMIRA 2022 110 1 10 0 177 G177
For plotting the layout in function of the coordinates
COLUMN in the field book object we can
use the generic function
plot() as follow,
In the figure above, green plots contain replicated entries, and gray plots contain entries that only appear once.