Free, open access repository of research software produced and developed by CIMMYT scientists.
Research Software Repository
Studies: 17
BIO-R (Biodiversity analysis with R for Windows) Version 1.0by Pacheco, Ángela; Alvarado, Gregorio; Rodríguez, Francisco; Burgueño, Juan
Abstract:

BIO-R is a set of R programs that do biodiversity analysis of molecular data, in order to calculate heterozygosity, diversity among and within groups, shannon index, number of effective allele, percent of polymorphic loci, Rogers distance, Nei distance, cluster analysis and multidimensional scaling 2D plot and 3D plot. You can included external groups for colored the dendogram or MDS plots, and additionally you can obtain a Core Subset using molecular data and also phenotypic, geographical and any source of data. BIO-R was designed because to do biodiversity analysis easily.

hdl:11529/10820
306 downloads
Last Released: Aug 31, 2017
ACBD-R. Augmented Complete Block Design with R for Windows. Version 3.0by Francisco Rodríguez; Gregorio Alvarado; Ángela Pacheco; Juan Burgueño
Abstract:

ACBD-R is a software to simplify the creation and analysis of augmented complete block designs using R (statistical software). ACBD-R provides an interface to set easily the experimental parameters to create a new augmented complete block design. ACBD-R also provides an interface to load a data set and select the experimntal parameters and response variables to perform an analysis in an easy way.

hdl:11529/10855
500 downloads
Last Released: Aug 1, 2017
Use of High-Resolution Image Data Outperforms Vegetation Indices in Prediction of Maize Yield: Supplementary Methodsby Fernando Aguate; Samuel Trachsel; Lorena González-Pérez; Juan Burgueño; José Crossa; Mónica Balzarini; David Gouache; Matthieu Bogard; Gustavo de los Campos
Abstract:

This is the supplementary methods of "Use of High-Resolution Image Data Outperforms Vegetation Indices in Prediction of Maize Yield" published in Crop Science · May 2017, DOI: 10.2135/cropsci2017.01.0007. It includes the raw data in R format and the R-code for the analysis.

hdl:11529/10972
24 downloads
Last Released: Jun 27, 2017
META-R (Multi Environment Trail Analysis with R for Windows) Version 6.01by Alvarado, Gregorio; López, Marco; Vargas, Mateo; Pacheco, Ángela; Rodríguez, Francisco; Burgueño, Juan; Crossa, José
Abstract:

META-R is a set of R programs that performs statistical analyses to calculate BLUEs, BLUPs, genetic correlations among locations and genetic correlations between variables, broad-sense heritability, and other statistics for breeding trials are given too, in order to make boxplots and histograms. Analyses may be performed by location, across management conditions or across all locations. META-R contains a graphical JAVA interface that helps the user to easily choose input files, which analysis to implement, and which variables to analyze.

hdl:11529/10201
3517 downloads
Last Released: Jun 7, 2017
AGD-R (Analysis of Genetic Designs with R for Windows) Version 4.0by Rodríguez, Francisco; Alvarado, Gregorio; Pacheco, Ángela; Crossa, José; Burgueño, Juan
Abstract:

A major objective of biometrical genetics is to explore the nature of gene action in determining quantitative traits. This also includes determination of the number of major genetic factors or genes responsible for the traits. Diallel Mating Designs have been designed to deal with the type of genetic experiments that help assess variability in observed quantitative traits arising from genetic factors, environmental factors, and their interactions. Some Diallel Mating Designs are North Carolina Designs, Line by Tester Designs and Diallel designs. AGD-R is a set of R programs that performs statistical analyses to calculate Diallel, Line by Tester, North Carolina. AGD-R contains a graphical JAVA interface that helps the user to easily choose input files, which analysis to implement, and which variables to analyze.

hdl:11529/10202
2828 downloads
Last Released: Feb 15, 2017
PED-R. Pedigree Matrix with R for Windows. Version 1.0by Francisco Rodríguez; Paulino Pérez; Gregorio Alvarado; Ángela Pacheco; José Crossa; Juan Burgueño
Abstract:

PED-R is a software to calculate easily the Pedigree matrix using R (statistical software). PED-R provides the Pedigree matrix in csv format and txt format which can be used by GAP software to show heatmaps. Also a heatmap is provided in pdf format. Another file provided is in format gexf which can be seen in Gephi software to visualize relations.

hdl:11529/10856
229 downloads
Last Released: Jan 17, 2017
STAD-R Descriptive statistics for experimental designsby Ángela Pacheco; Francisco Rodríguez; Gregorio Alvarado; Mateo Vargas; Marco López; José Crossa; Juan Burgueño
Abstract:

STAD-R is a set of R programs that performs descriptive statistics, in order to make boxplots and histograms. STAD-R was designed because is necessary before than the thing, check if the dataset have the same number of repetitions, blocks, genotypes, environments, if we have missing values, where and how many, review the distributions and outliers, because is important to be sure that the dataset is complete and have the correct structure for do and other kind of analysis.

hdl:11529/10853
339 downloads
Last Released: Jan 17, 2017
Eval_LxT. Evaluation of Line by Tester Experiments with R for Windows. Version 1.0by Francisco Rodríguez; Thanda Dhliwayo; Samuel Trachsel; Gregorio Alvarado; Ángela Pacheco; Juan Burgueño
Abstract:

Eval_LxT is a software designed to evaluate the analyzed essays in AGD-R [1] and get the best genotypes that satisfy certain characteristics of different traits. It allows to include the pedigree information related to the codes of lines. Also its posible to identify the checks to compare the lines versus checks. Three posible main criteria are posible: Specific Values, Check Values and Fix Number of Lines. The results includes an Excel file with information of lines that satisfy the criteria, and tables to identify the number of testers or locations where lines were tested. It also includes a boxplot and scatterplot of all traits that are included in the criteria.

hdl:11529/10858
379 downloads
Last Released: Jan 17, 2017
ADEL-R. Analysis and design of experiments with R for Windows. Version 1.0by Ángela Pacheco; Francisco Rodríguez; Gregorio Alvarado; Juan Burgueño
Abstract:

ADEL-R is a set of R programs that create and analyze experimental designs, in order to make field books and map fields when you create a design and if you analyze a design you can obtain the ANOVA table and comparison means graph. ADEL-R analyze designs like: random complete block design, random incomplete block design, augmented design, splitplot design, factorial design, striplot design. ADEL-R was designed because is necessary to create and analyze experimental design easily. ADEL-R contains a graphical JAVA interface that helps the user to easily.

hdl:11529/10857
369 downloads
Last Released: Jan 17, 2017
RIndSel Selection indeces for plant breedingby Ángela Pacheco; Sergio Pérez; Gregorio Alvarado; Jesús Cerón; Francisco Rodríguez; José Crossa; Juan Burgueño
Abstract:

A genomic selection index (GSI) is a linear combination of genomic estimated breeding values that uses genomic markers to predict the net genetic merit and select parents from a nonphenotyped testing population. RIndSel is a software that calculated some different index like: Eigen Selection Index Method (ESIM), Restrictive Kempthorne Nordskog Selection Index (KN), Lande and Thompson Selection Index (LT), Molecular Eigen Selection Index Method (MESIM), Restrictive Eigen Selection Index Method (RESIM) and Smith Selection Index; easily and efficiently.

hdl:11529/10854
228 downloads
Last Released: Jan 16, 2017