The second tack of their argument （主语）is to compare （谓语）the sort of effect seen in biology-based models of where malaria might spread （宾语，内含seen... 作后置定语修饰effect，其中又包含of where malaria might spread 作后置定语修饰models, 所以不多余）

with both models of and data on the effects direct intervention against the disease can have.（方式状语，其中both models of and data on the effects 是介词with 宾语，direct intervention against the disease can have为前面省略that的定语从句修饰effects.

这句话的大致意思是：他们的第二种观点是将基于生物学的疟疾可能传播的模型与直接干预疟疾所产生的效果的模型和数据进行比较。