A method for determining national crop yields during a growing season is accomplished using a server computer system that receives observed agricultural data records for a specific geo-location at a specific time. The server calculates weather index values from the agricultural data records that represent crop stress on plants. Geo-specific weather indices are generated from the weather index values, which then are aggregated to generate aggregated weather index data series. Representative features are selected from each aggregated weather index data series to create a covariate matrix for each geographic area. Crop yield for the geographic area is calculated using a linear regression model based on the covariate matrix for the specific geographic area. The server determines a national crop yield for the specific year as a sum of the crop yields for the specific geographic areas nationally adjusted using national yield adjustment instructions.