GerminaQuant for R allows make the calculations for germination indices incredibly easy in an interactive web applications build in R (R Core Team, 2020), based in GerminaR (Lozano Isla et al., 2020) and Shiny R package (Chang et al., 2020). GerminaQuant app is reactive!. Outputs change instantly as users modify inputs. The principal features of the application allows to calculate the principal germination indices, statistical analysis and easy way to plot the results.

App modules

The application is compound for different tabs that allow to make the analysis very easy.

Description of each module in GerminaQuant to evaluate and analyze the germination process.
Module Description
Presentation Presentation of the package and the application with their principal characteristics and information
Fieldbook Interface to upload the data from germination data and choose the parameter for the analysis. Allows to upload the data from google sheet or excel file
Germination Table with the indices calculated from the germination data
Exploratory Interface to explore your data and their distribution using boxplot graphics
Statistics Interface to perform the statistical análisis according the experimental design. Allows to calculate the analysis of variance, summary statistics, mean comparison table and model diagnostic
Graphics Plot the mean comparison table from the Statistics module. Allows to customized the results using bar or line plot
InTime Plot the germination process in time selecting one of the factor from your experiment. Allows to customized the results using line plot
Tools Tool for calculate the osmotic potential for any salt or PEG solution

Data processing

Fieldbook

When you have your fieldbook, you can access to the app GerminaQuant for R and go “Fieldbook” tab.

Fieldbook interface for import your data

Fieldbook interface for import your data

You can paste a Google spread sheet URL or upload a local file in xlsx format. In “Seeds (col name)” you have to write the name of the column containing the information of the number of seed sown in each experimental unit, for “Evaluations (prefix)” you have to put the prefix of the names for the evaluated days from the germination time lapse.

Germination

If the parameter in the “Fieldbook” tab are correct, in “Germination” tab will be performed and the values of the germination indices will be shown maintaining the experimental design. GerminaQuant allows to copy or downloading the information in “csv” or “xlsx” format.

Dowload option for the calculated variables

Dowload option for the calculated variables

Statistics

The GerminaQuant application can perform analysis for experimental design in a Complete Randomize Design (CRD), Randomize Complete Block Design (RCBD), Latin Square Design (LSD) or factorial designs, allowing calculate the analysis of variance (AOV) and the mean differences through Student Newman Keuls (SNK), Tukey or Duncan test.

Statitical analysis with ANOVA and mean comparison test

Statitical analysis with ANOVA and mean comparison test

Graphics

Automatically after performed the statistical analysis the application will generate the graphs for the variable chosen with the mean comparison test. The app interface allows customized the graphics in a bar or line plot and export in “tiff” format for publication quality.

Customized interface for bar or line plot

Customized interface for bar or line plot

InTime

This Tab allows to visualize the germination process according one of the experimental factors. The app interface allows customized the graphic.

Germination in time plot

Germination in time plot

The application allows to plot two type of graphics, the first is the germination percentage in time lapse, and the second the relative germination that calculates the germination according the total number of germinated seeds.

References

Chang, W., Cheng, J., Allaire, J., Xie, Y., & McPherson, J. (2020). Shiny: Web application framework for r. https://shiny.rstudio.com
Lozano Isla, F., Benites Alfaro, O., & Pompelli, M. F. (2020). GerminaR: Indices and graphics for assess seed germination process. https://CRAN.R-project.org/package=GerminaR
R Core Team. (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org/