Build a DiseaseVars.csv File

Welcome! This shiny app instance will help you put together a DiseaseVars.csv file to use as a CDmetaPOP input file. Select any of the tabs below and change the default parameters of the simulations in order to reflect those of the system you want to test. The parameter that will be changed according to your choices is indicated for each section as parameter .

Disease
Preview Updated DiseaseVars

Define the number of states Number of States

Define the proportion of individuals to be initialized in each state, separated by semicolons Initial Conditions

Define the state considered succeptible Susceptible States

Define the state considered infected Infection States

Do you want to include a death state?

No Yes

Define the state used for mortality Death States

Initialize offspring states

Susceptible: All are born in state 0 (Default). Random: Drawn from initial conditions. Vertical_X:Y: Vertical transmission from infected mothers with mean rate X and standard deviation Y.

Define how to initialize offspring states Initial Conditions Offspring

Susceptible Random Vertical_X:Y

Define the time step to initiate disease spread. Start Disease

Define transmission mode

Direct Indirect

Do you want to include a disease resistance genotype?

No Yes

Define the transition rate(s) modified by the resistance genotype.

Do you want to include a disease tolerance genotype?

No Yes

Define the transition rate(s) modified by the tolerance genotype.

Build a DiseaseVars.csv File

How to best organize your directories

Transition Rates Matrix

Initialize offspring states