Background: Disease or mortality rate map, geographically is desired for public health officials and epidemiologists. Point Poisson Kriging and Empirical Bayesian methods are used in estimating the map parameters. The aim of this study was to compare the precision of the methods in mapping of gastrointestinal cancer incidence in Iran. Methods: This study was application/ecology. The methodology was illustrated using gastrointestinal cancer data recorded in the ministry of health and medical education (in the non-infectious diseases management center) of Iran in years 2003-2007 from 336 counties. Poisson Kriging model was used to estimate the parameters of the map. Spacestat, OpenBUGS and ArcGIS9.3 softwares were used for analysing the data and drawing maps. Findings: Mean incidence rate according to Empirical Bayesian method was 12.99 and based on Point Poisson Kriging method was estimated 12.64. Mean incidence rate variance using the Empirical Bayesian method was 2.83 and based on Point Poisson Kriging method was estimated 3.85. Maximum incidence rate according to Empirical Bayesian method was 42.23 with variance of 2.16 related to Sari county and minimum incidence rate was 0.48 with variance of 0.08 related to Sarbaz County. Maximum incidence rate using the Point Poisson Kriging method was estimated 40.35 with variance of 0.79 related to Sari county and minimum incidence rate of 0.30 with variance of 2.54 related to Sarbaz County. Poisson Kriging estimation method yields smaller standard error compared to Empirical Bayesian model. Conclusion: The Poisson Kriging method was recommended for estimation of disease mapping parameters since it generates less smoothing and yields smaller standard error.

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