In FielDHub: A Shiny App for Design of Experiments in Life Sciences

library(FielDHub)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = NA,
  fig.path = "man/figures/README-",
  out.width = "100%"
)

FielDHub 1.2.0

Photo by Vackground on Unsplash

2022/08/04

FielDHub

Didier Murillo

I am very happy to announce the release of FielDHub v1.2.0. It has been more than 12 months of hard work and commitment. This new version comes with many changes, new features, and a better graphical user interface design in the shiny app.

Changelog

Shiny App

Added a help menu option in the app that connect you directly to the documentation available in our GitHub repository.
Added vignettes and help documentation for all standard functions and modules available for all designs in the app.
Added capability for making multiple randomizations across different locations to the unreplicated, partially replicated, lattice, RCBD, factorial, split-plot, split-split-plot, strip-plot, IBD, and RCD designs.
Added capability to produce heatmap visualizations of simulated data for all experimental designs.
Added action buttons to copy and save field maps and field book outputs to Excel.
Added factorization options that aid users in the creation of randomizations and mapping layouts for the unreplicated and partially replicated designs. Previous version required users to do the * mathematical calculation a priori.
Added filters and search boxes for the field book tables.
Updated UI/UX design for home page.
Grouped single diagonal arrangement, multiple diagonal arrangement, optimized arrangement and augmented RCB designs under one single module.
Added action run button to all experimental designs to prevent reactivity issues with the application.
Improved and standardized user experience features and readability access.
Improved error logging messages. Added features to inform end-users on the utilization of correct input data file formats and associated metadata/columns, checking for duplicate values in input files, as well as data type verification.
Added additional field layout visualization/map options to all experimental designs. Previous version only had mapping options for unreplicated and p-rep designs.
Added a drop-down menu to display a multiple layout mapping option shown by entry number and by plot for all experimental designs. This means, that now you can visualize each randomization layout option for each of the locations you input.
Added an option for repeating whole entries/experiments in the unreplicated diagonal arrangement design with multiple experiments (previously called decision blocks).
Added a check box feature in the Augmented RCB design to allow for the creation of nurseries with the option of randomizing experimental entries or not. If user decides to leave this option unchecked, only the checks will be randomized, and the experimental entries will be shown in consecutive order.
Added a check box option to the RCB design to allow for a continuous plot numbering independently of the rep or block number. Previous version coded the replication into the plot number (i.e., 101 =rep1, 201=rep2, etc.).
Fixed a restriction in the RCBD mapping layout to allow for the use of more than 25 entries. PS: There are better designs when the number of entries is higher than 25 (for more info go to: FIELD PLOT DESIGN I).

Standalone Functions in `FielDHub` Package

partially_replicated() now generates randomization across multiple locations/sites.
diagonal_arrangement() now generates randomization across multiple locations/sites.
optimized_arrangement() now generates randomization across multiple locations/sites.
partially_replicated() now allows that all entries/treatments have replicates. Before, it required at least some unreplicated entries.
Functions optimized_arrangement(), diagonal_arrangement() and partially_replicated() now return feedback if the input dimensions nrows and ncols are incorrect.
RCBD() now includes an argument (continuous) to manage the way it sets up the plotting number.
RCBD_augmented() now allows customization of the field dimensions by inputting the number of rows and columns through nrows and ncols arguments.
RCBD_augmented() now returns feedback if the input dimensions nrows and ncols do not match the data entered.
RCBD_augmented() when random = FALSE now allows only randomizing the checks/controls if the user wants.
Fixed a bug in full_factorial() for the CRD factorial design that prevented the option of including all possible factorial combinations.
Added a method print() of class fieldLayout. See print().
Added a method plot() of class FieldHub that returns an object of class fieldLayout. See plot(). The method plot() can plot a field layout for any of the designs output. It is possible to pass arguments such as the location, layout order and others. For more detail see plot(), print() and summary() methods in FielDHub.
Fixed a bug in diagonal_arrangement() when kindExpt = DBUDC. The problem affected the random distribution of the checks for the case of unbalanced control plot numbers for each experiment.
Fixed a bug in diagonal_arrangement() when kindExpt = DBUDC. The problem affected merging data between the user data and randomization data when users wanted replicated entries across experiments.

Acknowledgements

FielDHub v1.2.0 has been a long time coming, and it wouldn’t have been possible without all the effort and contribution from Matthew Seefeldt. Thank you Johan Aparicio for the bugs you reported. Thank you Ana María Heilman for your support and leadership.