The genosim package simulates genotypes, breeding values, and phenotypes; simulates DNA sequence read depth (numbers of A and B alleles); and resolves SNP conflicts between parent and offspring genotypes.

Genomics and Genetics

Non-dominated Sorting Genetic Algorithm-II

This code is implements the nondominated sorting genetic algorithm (NSGA-II) in the R statistical programming language. The function is theoretically applicable to any number of objectives without modification. The function automatically detects the number of objectives from the population matrix used in the function call. NSGA-II has been applied in ARS research for automatic calibration of hydrolgic models (whittaker link) and economic optimization (whittaker link).

Genomics and Genetics

Data from: Life history changes in Trogoderma variabile and T. inclusum due to mating delay with implications for mating disruption as a management tactic

Egg and progeny counts for Trogoderma variabile and Trogoderma inclusum adults with delays in mating. These data were generated to examine the effect of mating delay on life history and reproductive capacity as a cue to the use of mating disruption tactics such as pheromone lures. Survivorship was calculated as the last day egg counts were recorded for an individual. Blocks were adults that were all mated on the same day. Reps are an individual female. Control beetles are coded with either an "f" or an "m" for female and male and were never mated. Male control data was examined for similarity to female control data but was not used in further analysis and comparison. The experiment was all done at 30C, 65% relative humidity and a 16 light/8 dark photoperiod. Adults were transferred every 2 days to new vials and eggs were then counted and save for progeny counts. Trogoderma variabile populations were laboratory colonies for over 20 years. T. inclusum populations were collected in Kansas in August of 2012. We did not transform these data.

Image of Trogoderma variabile and T. inclusum

Data from: Defensive aphid symbiont Hamiltonella defensa effects on Aphelinus glycinis and Aphelinus atriplicis

Aphelinus glycinis was collected in the Peoples Republic of China under a Memorandum of Understanding between their Ministry of Agriculture and the United States Department of Agriculture (USDA). Aphelinus atriplicis was collected by employees of the USDA, Agricultural Research Service (ARS), in the Republic of Georgia with the permission of that government. The parasitoids were imported into the USDA, ARS, Beneficial Insect Introductions Research Unit containment facility in Newark, Delaware, under permits from the USDA, Animal and Plant Health Inspection Service (Permit Numbers P526P-08-02142 and P526P-09-01929). No specific permissions were required to collect Aphis craccivora or Acyrthosiphon pisum because these are cosmopolitan aphids that occur in the field throughout North America. None of the species collected or studied are endangered or protected.

Agroecosystems & Environment