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We present a detailed analysis of ALMA Bands 7 and 9 data of CO, HCO+, HCNand CS, augmented with Plateau de Bure Interferometer (PdBI) data of the ~ 200pc circumnuclear disk (CND) and the ~ 1.3 kpc starburst ring (SB ring) ofNGC~1068, a nearby (D = 14 Mpc) Seyfert 2 barred galaxy. We aim at determiningthe physical characteristics of the dense gas present in the CND and whetherthe different line intensity ratios we find within the CND as well as betweenthe CND and the SB ring are due to excitation effects (gas density andtemperature differences) or to a different chemistry. We estimate the columndensities of each species in Local Thermodynamic Equilibrium (LTE). We thencompute large one-dimensional non-LTE radiative transfer grids (using RADEX) byusing first only the CO transitions, and then all the available molecules inorder to constrain the densities, temperatures and column densities within theCND. We finally present a preliminary set of chemical models to determine theorigin of the gas. We find that in general the gas in the CND is very dense (>10^5 cm^-3) and hot (T> 150K), with differences especially in the temperatureacross the CND. The AGN position has the lowest CO/HCO+, CO/HCN and CO/CScolumn density ratios. RADEX analyses seem to indicate that there is chemicaldifferentiation across the CND. We also find differences between the chemistryof the SB ring and some regions of the CND; the SB ring is also much colder andless dense than the CND. Chemical modelling does not succeed in reproducing allthe molecular ratios with one model per region, suggesting the presence ofmulti-gas phase components. The LTE, RADEX and chemical analyses all indicatethat more than one gas-phase component is necessary to uniquely fit all theavailable molecular ratios within the CND.

Molecular line emission in NGC1068 imaged with ALMA: II. The chemistry of the dense molecular gas