Man pages for tfojo1/jheem
Executes the JHEEM (Johns Hopkins Epidemiological and Economic Model) - a compartmental model of HIV
| access | Read access population or transition arrays generated by... |
| access-set | Write access population or transition arrays generated by... |
| combine.jheem.results | Combine Two JHEEM Results Objects into One by year |
| create.birth.proportions.from.population | Create a Birth Proportions array based on sex distribution by... |
| create.birth.proportions.hiv.negative | Create a valid Birth Proportions array for births to... |
| create.birth.proportions.hiv.positive.to.negative | Create a valid Birth Proportions array for HIV-uninfected... |
| create.birth.proportions.hiv.positive.to.positive | Create a valid Birth Proportions array for HIV-infected... |
| create.contact.array.from.marginals | Create a transmission contact array from one or more marginal... |
| create.susceptibility.array.from.marginals | Makes a susceptibility array by multiplying multiple marginal... |
| create.transmissibility.array.from.marginals | Makes a transmissibility array by multiplying multiple... |
| expand.jheem.results | Expand JHEEM Results to Contain New Dimensions |
| expand.population.to.general | Shoehorn a given population array into an array of the... |
| expand.population.to.hiv.negative | Shoehorn a given population array into an array of the... |
| expand.population.to.hiv.positive | Shoehorn a given population array into an array of the... |
| expand.to.contact.array | Shoehorn a given array into a transmission contact array |
| expand.to.new.infection.proportions | Shoehorn a given population array into an array of the... |
| expand.to.transition.array.hiv.negative | Expands an array into a transition array for the HIV-negative... |
| expand.to.transition.array.hiv.positive | Expands an array into a transition array for the HIV-positive... |
| extract.diagnosed.hiv | Extract the subset of the HIV-positive population which has... |
| extract.hiv.specific.mortality | Extract HIV-specific mortality from JHEEM Results |
| extract.incidence | Extract HIV incidence from JHEEM Results |
| extract.new.diagnoses | Extract new HIV diagnoses from JHEEM Results |
| extract.overall.hiv.mortality | Extract Overall Mortality in HIV-positive from JHEEM Results |
| extract.population.subset | Extract a subset of the population from JHEEM Results |
| extract.prevalence | Extract HIV prevalence from JHEEM Results |
| extract.tracked.transition | Extract a tracked transition from JHEEM Results |
| get.aging.skeleton.hiv.negative | Get a default array of aging rates for the HIV-negative... |
| get.aging.skeleton.hiv.positive | Get a default array of aging rates for the HIV-positive... |
| get.birth.proportions.to.hiv.negative.skeleton | Create a skeleton Birth Proportions for births into the... |
| get.contact.array.skeleton | Get a skeleton contact array |
| get.general.population.skeleton | Get a skeleton for the population characteristics shared by... |
| get.general.transition.array.skeleton | Create a skeleton transition array for a general population... |
| get.hiv.negative.population.skeleton | Get a skeleton HIV-negative population |
| get.hiv.negative.transition.array.skeleton | Create a skeleton transition array for the HIV-negative... |
| get.hiv.positive.population.skeleton | Get a skeleton HIV-positive population |
| get.hiv.positive.transition.array.skeleton | Create a skeleton transition array for the HIV-positive... |
| get.new.infection.proportions.skeleton | Get a skeleton new infection proportions array |
| get.population.skeleton | Get a skeleton for a population with indicated dimensions |
| get.seeded.initial.populations | Get a pair of seeded initial states |
| get.susceptibility.array.skeleton | Get a skeleton susceptibility array |
| get.transition.array.skeleton | Create a skeleton transition array with arbitrary dimensions |
| get.transmissibility.array.skeleton | Get a skeleton transmissibility array |
| get.uniform.new.infection.proportions | Get a new infection proportions array where new infections... |
| hello | Hello, World! |
| initialize.jheem | Initializes a new controller for JHEEM |
| jheem | jheem: A package |
| make.age.strata | Make Age Strata based on cutoffs |
| multiply.contact.array.from | Multiply a transmission contact array by rates for the 'from'... |
| multiply.contact.array.to | Multiply a transmission contact array by rates for the 'to'... |
| rcpp_hello | Hello, Rcpp! |
| run.jheem | Run a JHEEM Model |
| set.aging | Sets aging rates for both the HIV-negative and HIV-positive... |
| set.aging.hiv.negative | Sets aging rates for HIV-negative population |
| set.aging.hiv.positive | Sets aging rates for HIV-positive population |
| set.birth.proportions.hiv.negative | Sets the proportions according to which new births from... |
| set.birth.proportions.hiv.positive | Sets the proportions according to which new births from... |
| set.birth.proportions.no.maternal.transmission | Sets the proportions according to which new births are... |
| set.emigration | Sets emigration rates for both the HIV-negative and... |
| set.emigration.hiv.negative | Set emigration rates for HIV-negative population |
| set.emigration.hiv.positive | Set emigration rates for HIV-positive population |
| set.fertility | Sets fertility rates for both the HIV-negative and... |
| set.fertility.hiv.negative | Sets fertility rates for the HIV-negative population |
| set.fertility.hiv.positive | Sets fertility rates for the HIV-positive population |
| set.fixed.population.size | Set the population to which to fix sizes |
| set.fixed.population.strata | Set which strata to use for fixed size populations |
| set.fixed.size.strata | Sets which dimensions define strata that will have sizes kept... |
| set.general.mortality | Sets mortality rates for both the HIV-negative and... |
| set.general.mortality.hiv.negative | Set mortality rates for HIV-negative population |
| set.general.mortality.hiv.positive | Set general mortality rates for HIV-positive population (not... |
| set.global.transmission.rate | Sets the global HIV transmission rate |
| set.hiv.specific.mortality | Set HIV-specific mortality rates for HIV-positive population |
| set.immigration.proportions | Sets the proportions according to which new births are... |
| set.immigration.rates | Sets immigration rates |
| set.initial.population.hiv.negative | Set the initial HIV-negative population |
| set.initial.population.hiv.positive | Set the initial HIV-positive population |
| set.initial.populations | Set the initial HIV-positive population |
| set.keep.strata.sizes.constant | Sets whether to keep population strata sizes constant for a... |
| set.new.infection.proportions | Sets the proportions into which new infections from strata of... |
| set.susceptibility | Sets susceptibility to infection for the HIV-negative... |
| set.tracked.transition.hiv.negative | Specify an HIV-negative transition to track |
| set.tracked.transition.hiv.positive | Specify an HIV-positive transition to track |
| set.track.hiv.specific.mortality | Set whether the JHEEM should track HIV-specific mortality |
| set.track.incidence.dimensions | Set which dimensions to keep when tracking incidence |
| set.track.mortality | Set whether the JHEEM should track HIV-specific and overall... |
| set.track.overall.mortality | Set whether the JHEEM should track general mortality |
| set.transition.array.hiv.negative | Sets the array of transition rates between states (within... |
| set.transition.array.hiv.positive | Sets the array of transition rates between states (within... |
| set.transmissibility | Sets transmissibility for the HIV-positive population |
| set.transmission.contact.array | Sets the transmission contact array between HIV-negative and... |
| set.use.fixed.population | Sets whether to use fixed population strata for a given time |
| stratify.males.by.orientation | Takes a population and splits males into heterosexual males... |
| stratify.population | Substratify a population |
| subset.jheem.results | Access a Subset of JHEEM Results by Year |
| test.jheem | Test JHEEM code to make sure that it is working correctly |
