1. A computer-implemented method for analyzing ionospheric slant total electron content (TEC) using global navigation satellite systems (GNSS)-based estimation comprising: estimating slant TEC for a given set of raypath geometries by fitting historical GNSS data to a specified delay model; evaluating an accuracy of the specified delay model by calculating delay estimate residuals and plotting a behavior of the delay estimate residuals; computing an ionospheric threat model based on the specified delay model, wherein the computing of the ionospheric threat model is performed in multiple stages, wherein each stage generates a distinct set of output files; computing a second ionospheric threat model with new options, by reusing one or more of the files in the distinct set of output files, wherein the second ionospheric threat model is used to protect users from effects of ionospheric irregularities; computing ionospheric grid delays (IGDs) and grid ionospheric vertical errors (GIVEs) based on the ionospheric threat model; and outputting the second ionospheric threat model, wherein the second ionospheric threat model is applied to the GNSS.