Computational protocol: Increasing Cropping System Diversity Balances Productivity, Profitability and Environmental Health

Similar protocols

Protocol publication

[…] The experiment was arranged in a randomized complete block design, with all entry points of the three crop rotations (i.e. all crops within each of the rotations) represented in four replicate blocks in each year of the study, for a total of 36 plots. Cropping system effects in time series data were analyzed using hierarchical linear mixed effects repeated measures models, modeling temporally correlated errors with an ARMA (auto-regressive moving average) correlation structure in the nlme package of R v.2.14.1 , . Fixed effects included cropping system and experimental phase (startup = 2003 to 2005; established = 2006 to 2011), and random effects included replicate block nested within cropping system and year. Partial correlations were estimated using the corpcor package in R v.2.14.1. In contrast to data for quantitative observations (e.g. crop yield or weed biomass) that varied by replicate block and year, data for input variables, such as synthetic fertilizer or herbicides and associated environmental toxicity metrics, did not vary among blocks for a particular rotation entry point in a given year, but did vary among years. Therefore, site-year was treated as the source of experimental replication for these latter variables in our statistical tests for effects of cropping system and experimental phase. This led to contrasting degrees of freedom in reported F-tests for these two data types. Finally, for variables with non-constant variance among cropping systems over time (crop biomass and profit), we used the ‘varIdent’ variance function within the nlme package to explicitly model differences in variances among cropping systems for these variables within our mixed effects models. […]

Pipeline specifications

Software tools lme4, nlme
Application Mathematical modeling
Organisms Zea mays, Glycine max, Bos taurus
Diseases Drug-Related Side Effects and Adverse Reactions