A set of FORTRAN programs to implement a multiple-trait Gibbs sampling algorithm for (co)variance component inference in animal models (MTGSAM).
A set of programs for estimation of genetic (co)variances using multiple-trait derivative-free restricted maximum likelihood.
Yield Editor is a tool which allows the user to select, apply and analyze a variety of automated filters and editing techniques used to process and clean yield data. The software imports either AgLeader advanced or Greenstar text file formats, and exports data in a delimited ASCII format.
Cligen is a stochastic weather generator which produces daily estimates of precipitation, temperature, dewpoint, wind, and solar radiation for a single geographic point, using monthly parameters (means, SD's, skewness, etc.) derived from the historic measurements. Unlike other climate generators, it produces individual storm parameter estimates, including time to peak, peak intensity, and storm duration, which are required to run the WEPP and the WEPS soil erosion models.
Data from: Assessment of town and park characteristics related to physical activity in the Lower Mississippi Delta
The Delta Neighborhood Physical Activity Study was an observational study designed to assess characteristics of neighborhood built environments associated with physical activity. It was an ancillary study to the Delta Healthy Sprouts Project and therefore included towns and neighborhoods in which Delta Healthy Sprouts participants resided. The 12 towns were located in the Lower Mississippi Delta region of Mississippi. Data were collected via electronic surveys between August 2016 and September 2017 using the Rural Active Living Assessment (RALA) tools and the Community Park Audit Tool (CPAT). Scale scores for the RALA Programs and Policies Assessment and the Town-Wide Assessment were computed using the scoring algorithms provided for these tools via SAS software programming.
Data from: Starch and dextrose at 2 levels of rumen-degradable protein in iso-nitrogenous diets: Effects on lactation performance, ruminal measurements, methane emission, digestibility, and nitrogen balance of dairy cows.
This feeding trial was designed to investigate two separate questions. The first question is, “What are the effects of substituting two non-fiber carbohydrate (NFC) sources at two rumen-degradable protein (RDP) levels in the diet on apparent total-tract nutrient digestibility, manure production and nitrogen (N) excretion in dairy cows?”. This is relevant because most of the N ingested by dairy cows is excreted, resulting in negative effects on environmental quality. The second question is, “Is phenotypic residual feed intake (pRFI) correlated with feed efficiency, N use efficiency, and metabolic energy losses (via urinary N and enteric CH4) in dairy cows?”. The pRFI is the difference between what an animal is expected to eat, given its level of productivity, and what it actually eats. The goal was to determine whether production of CH4, urinary N or fecal N is a driver of pRFI.
Data from: Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design
The type 2 modified augmented design (MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_tools/MADPipeline/index.html).
Spatial Modeling for Resources Framework (SMRF) was developed at the USDA Agricultural Research Service (ARS) in Boise, ID, and was designed to increase the flexibility of taking measured weather data and distributing the point measurements across a watershed.
Automated Water Supply Model (AWSM) was developed at the USDA Agricultural Research Service in Boise, ID, to streamline the workflow used to forecast the water supply of multiple water basins.
This dataset contains all documents, the text and the pdf files, as well as the code used to carry out a term analysis of agriculturally relevant organisms in the Global Biodiversity Information Facility (GBIF).