BioCro

BioCro is an R package that was inspired by an earlier mechanistic crop model: WIMOVAC (Windows Intuitive Model of Vegetation response to Atmospheric & Climate Change). WIMOVAC was written in Visual Basic and it is freely available from the link on the left. Details about WIMOVAC can be found in that website. BioCro is mostly written in C and it incorporated optimization routines as well as parameter estimation tools.   

I will have the R package here soon as well as some examples and tutorials. I'm also planning to host some free workshops for those interested in using it. Sometime in the future a user interface for the package will also be available.

 

Discussion on Biophysical Models

“Discussion on Biophysical Models for Biomass Crops”


In this workshop I introduced the issues when discussing modeling of biomass crops such as switchgrass and miscanthus. The slides have virtually no information since they were basically used to guide the discussion. I've been working on BioCro for a while and I hope I can release it soon. It still needs somework, but I'm getting there.

ASA talk on NLME

“Using Non-linear Mixed Models for Agricultural Data”


Here I presented the approach of using Non-Linear Mixed-Effects Models for analysis of agricultural data. There are data and code on the left. Part of the objective was to explain the methodology used in the Miscanthus meta-analysis paper. I'm also interested in comparing the results with those of similar statistical functions in other software, such as the NLMIXED procedure in SAS and GenStat.
 

ESA talk on Parameter Estimation

“Parameter Estimation in Biomass Crop Models”


At the Ecological Society of America meetings I gave a talk about my research on parameter estimation in crop models. At that time I was trying out a method which I'm not using any more. This talk is more about the problems I was having than about any conclusive results. Hopefully, my new approach will be polished soon and made into a manuscript. The meetings were great because I gave some more thought to my work and was inspired by the work of others which resulted in an improved approach to the problem of estimating parameters in crop models.
 

Miscanthus Meta-analysis

“Meta-analysis of the effects of management factors on Miscanthus × giganteus growth and biomass production”


The corrected proof of this article apeared on-line May 9th. This was the first chapter of my PhD thesis where I looked at the effect of management practices on the dry biomass production and growth patterns of Miscanthus. On the left you can be directed to the link. If you don't have access to the pdf file e-mail me for a copy. The database used in the paper and the R code to analyze the data can be downloaded. 

README: The file 'MiscanthusDatabase.csv' contains the main dataset which has a lot more data than what was used in the paper. The column titles are more or less clear. If they are not contact me and I will be happy to answer any questions. The file 'Comb(w-season).csv' has the data for the within growing season analysis. The third file 'MiscAnaly.r'  has the R code that was used to analyze the data along with the graphs which appear in the paper. The first section is for the analysis of the 'MiscanthusDatabase.csv' file and the second for the 'Comb(w-season).csv' file.

Biofuels (Biocombustibles--in spanish)

“Biocombustibles. Fernando E. Miguez y Fernando H. Miguez.”


I was asked to write a chapter about Biofuels (Biocombustibles) for a book in spanish. This book will be used to teach a class in environmental sciences at the University of Buenos Aires in Argentina. I'm Fernando E. Miguez and Fernando H. Miguez is my dad. I was supposed to write the chapter, but fortunately my Dad helped and he ended up writing a huge chunk of it.

Cover Crops Meta-analysis 

“Review of Corn Yield Response under Winter Cover Cropping Systems Using Meta-Analytic Methods”


README: This note serves as a readme for the file CoverCropsMetaAnalysis.tar.gz.  The original database is an Excel spreadsheet (.xls) which contains the 'complete' data that I collected to conduct the meta-analysis. The file Meta-analysis.csv is a reduced version of the complete database, which contained a very clear outlier (read the text for an explanation). The final analysis in the paper was done on the Meta-analysis(no outlier).csv. An additional analysis was conducted on the Meta-analysis(REG).csv file using the Meta-regression.sas file. Clearly, for the .sas files to work the correct directory must be specified in the infile statement.

Cover Crops field study 

“Winter Cover Crops in Illinois: Evaluation of Ecophysiological  Characteristics of Corn”

This study was my first research in Illinois. The objective of the research was to evaluate the performance of cereal rye and hairy vetch as winter cover crops for a corn soybean rotation. The link on the left has the PDF.