Agricolae - Ten years of an open source statistical tool for experiments in breeding, agriculture and biology

Plant breeders and educators working with the International Potato Center (CIP) needed freely available statistical tools. In response, we created first a set of scripts for specific tasks using the open source statistical software R. Based on this we eventually compiled the R package agricolae as it covered a niche. Here we describe for the first time its main functions in the form of an article. We also review its reception using download statistics, citation data, and feedback from a user survey. We highlight usage in our extended network of collaborators. The package has found applications beyond agriculture in fields like aquaculture, ecology, biodiversity, conservation biology and cancer research. In summary, the package agricolae is a well established statistical toolbox based on R with a broad range of applications in design and analyses of experiments also in the wider biological community .

[1]  P. Portmann,et al.  Field plot technique , 1997 .

[2]  Peter R. Nelson,et al.  Multiple Comparisons: Theory and Methods , 1997 .

[3]  M. Kenward,et al.  An Introduction to the Bootstrap , 2007 .

[4]  James H. Torrie,et al.  Principles and procedures of statistics: a biometrical approach (2nd ed) , 1980 .

[5]  José Crossa,et al.  Statistical analyses of multilocation trials , 1990 .

[6]  U. Schickhoff,et al.  Transition to agroforestry significantly improves soil quality: A case study in the central mid-hills of Nepal , 2015 .

[7]  A. Magurran Ecological Diversity and Its Measurement , 1988, Springer Netherlands.

[8]  Foster B. Cady,et al.  Field Plot Technique. , 1963 .

[9]  G. C. Yencho,et al.  Sweetpotato Grown from Root Pieces Displays a Significant Genotype × Environment Interaction and Yield Instability , 2014 .

[10]  S. T. Buckland,et al.  An Introduction to the Bootstrap. , 1994 .

[11]  Jianxin Pan,et al.  High arsenic in rice is associated with elevated genotoxic effects in humans , 2013, Scientific Reports.

[12]  F. Delgado Una herramienta de análisis estadístico para la investigación agrícola , 2009 .

[13]  M. Lindegarth,et al.  Testing the potential for improving quality of sediments impacted by mussel farms using bioturbating polychaete worms , 2017 .

[14]  H. Piepho,et al.  The area under the disease progress stairs: calculation, advantage, and application. , 2012, Phytopathology.

[15]  N. Sabaghnia,et al.  The use of an AMMI model and its parameters to analyse yield stability in multi-environment trials , 2008, The Journal of Agricultural Science.

[16]  Peter Dalgaard,et al.  R Development Core Team (2010): R: A language and environment for statistical computing , 2010 .

[17]  R. K. Singh,et al.  Biometrical methods in quantitative genetic analysis , 1978 .

[18]  Manjit S. Kang,et al.  Simultaneous selection for yield and stability in crop performance trials: consequences for growers , 1993 .

[19]  L. Mueller,et al.  Trait Diversity and Potential for Selection Indices Based on Variation Among Regionally Adapted Processing Tomato Germplasm , 2012 .

[20]  R Fisher,et al.  Design of Experiments , 1936 .

[21]  Douglas C. Montgomery Diseño y análisis de experimentos , 1991 .

[22]  D. F. Cox,et al.  Statistical Procedures for Agricultural Research. , 1984 .

[23]  Xinwei Deng,et al.  Experimental design , 2012, WIREs Data Mining Knowl. Discov..

[24]  J. I The Design of Experiments , 1936, Nature.

[25]  J. Purchase Parametric analysis to describe genotype x environment interaction and yield stability in winter wheat , 1997 .

[26]  W. Fry,et al.  Phenotypic stability of resistance to late blight in potato clones evaluated at eight sites in the United States , 1998, American Journal of Potato Research.

[27]  A. Scariot,et al.  Land use and management affects the demography and conservation of an intensively harvested Cerrado fruit tree species , 2015 .