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A numerical toolset to help in understanding physical processes in the electron cyclotron resonance charge breeder (ECRCB) and further to help optimization and design of current and future machines is presented. The toolset consists of three modules (Monte Carlo charge breeding code, generalized electron cyclotron resonance ion source modeling, and ion extraction), each modeling different processes occurring in the ECRCB from beam injection to extraction. The toolset provides qualitative study, such as parameter studies, and scaling of the operation, and physical understanding in the ECRCB. The methodology and a sample integrated modeling are presented.