The report presents statistical procedures collected from other Environmental Monitoring and Assessment Program (EMAP) documents, as well as from Oregon State University technical reports describing data analyses for other U.S. Environmental Protection Agency (EPA) designs. By integrating the information, the manual and the EMAP design report will serve as reference sources for statisticians who implement an ecological monitoring program based on the EMAP design framework. Spatial and temporal analyses of EMAP data are not covered in this version of the report. A brief discussion of the four-point moving average, which combines data over the inter-penetrating sample, is presented in Overton et al. Algorithms listed in the report cover most design options discussed in the EMAP design report. It is expected that any further realizations of the EMAP design will also include documentation of corresponding variance estimators.