Man pages for gilesjohnr/hmob
Tools for analyzing human mobility data
| calc.decay.stats | Calculate model summary and validation statistics for trip... |
| calc.hpd | Calculate HPD of aggregated waiting time distributions |
| calc.prop.inf | Calculate proportion infected in each district |
| calc.prop.remain | Proportion of individuals remaining for full epidemic... |
| calc.prop.tot.trips | Calculate the cumulative proportion of trips for values of a... |
| calc.prop.vacc | Calculate vaccination coverage given routine vaccination... |
| calc.prop.vacc.SIA | Calculate vaccination coverage given routine vaccination and... |
| calc.route.type | Calculate observed number of trips of each route type |
| calc.samp.size | Get the sample size of a route-level 'mob.data.array' matrix... |
| calc.timing.magnitude | Calculate peak timing of introduction and proportion infected |
| calc.wait.time | Calculate aggregate waiting time distribution |
| check.distance.matrix | Fix off-diagonal zeros in distance matrix |
| decay.func | Exponential decay function |
| fit.gravity | Fit gravity model to movement matrix |
| fit.jags | Fit model using JAGS |
| fit.prob.travel | Estimate probability of travelling outside origin |
| get.admin.level | Find the lowest admin unit |
| get.age.beta | Get Beta parameters for age groups |
| get.beta.params | Get parameters for Beta distribution |
| get.crossdist | Get distance between two points for one observation |
| get.distance.class | Add distance between origin and destination districts to long... |
| get.distance.counts | Get matrix of trip distance counts |
| get.distance.matrix | Build distance matrix from XY coordinates |
| get.district.names.xy | Add district names and coordinates to long form data set |
| get.district.pop | Add district population sizes to long form data set |
| get.duration.counts | Get matrix of trip duration counts |
| get.gamma.params | Get parameters of Gamma distribution |
| get.holidays | Add national holidays and school breaks to long form data set |
| get.legend | Get legend from ggplot object |
| get.names | Get title for any origin and destination |
| get.param.vals | Get posterior parameter estimates from a model object |
| get.pop.vec | Get unique origin and destination names |
| get.route.type | Get route-type |
| get.sparse.mob.matrix | Get sparse mobility matrix |
| get.stay.data | Make data set of travel and stays |
| get.subsamp | Find the subset of districts which have a minumim number of... |
| get.unique.coords | Get unique coordinates |
| get.unique.names | Get unique origin and destination names |
| get.xy.counts | Get counts of any two variables (e.g. distance vs duration) |
| load.obj | Load specific objects in a .Rdata file |
| mob.data.array | Build mobility data array |
| mob.data.array.pop.level | Reduce a mob.data.array object to population-level |
| mob.data.array.route.level | Reduce a mob.data.array object to route-level |
| parse.longform | Parse raw trip duration data |
| rjags.combine | Combine two rjags objects |
| rjags.mcmc.list | Convert rjags object to mcmc.list |
| see | Quick look at matrices |
| sim.combine | Combine two TSIR scenarios |
| sim.combine.dual | Combine TSIR scenarios containing both gravity model types |
| sim.gamma | Calculate the probability of a Gamma distributed random... |
| sim.gravity | Simulate connectivity values using gravity model |
| sim.gravity.duration | Simulate connectivity values using gravity model with trip... |
| sim.lambda | Simulate decay rate (lambda) |
| sim.pi | Simulate connectivity matrix (pi) |
| sim.rho | Simulate proportion remaining for full generation (rho) |
| sim.tau | Simulate probability of leaving origin (tau) |
| sim.TSIR | Simulate stochastic TSIR |
| sim.TSIR.full | Simulate full stochastic TSIR in parallel |
| summarize.hmob | Calculate summary statistics for a model |
| survey.template | Generalized template for travel survey data |
| trip.map | Plot map of origin and destination district(s) |
