Man pages for predsci/DICE
DICE: Dynamics of Interacting Community Epidemics
| add_ndays | Add Days |
| add_periods_cols | Add a year column as well as the appropriate day/week/month... |
| AvgClim | Climate Data Processing. |
| BuildDateVecs | Build A Date Vector |
| build.mydata | Read incidence data file and Build the DICE data list, mydata |
| CadenceNum2Name | Number to String Cadence Conversion |
| calcCPLRandomProfiles | Calculate Coupled Incidence Disease Profiles |
| calc.epi.null | Calculate the Historic NULL Model |
| calcLLK | Calculate the Likelihood of each Data Point |
| calc.mech.err | Calculate Error in Mechanistic Fit/Forecast |
| calc.null.err | Calculate Error of Historic Null Model |
| calc.plague.err | Calculate the lower/upper 95 percentile for the PLAGUE model... |
| calcRandomProfiles | Calculate Incidence Disease Profiles |
| calc.sqldata.cor | Calculate Pearson Correlation Matrix Between Seasons |
| calc.sqldata.dist | Calculate Euler Distance Matrix Between Seasons |
| calc.stat.err | Calculate Error in SARIMA Fit/Forecast |
| cdc_download | Pull ili mydata from CDC server (make 5 attempts) |
| CDCweek2date | Convert a CDC week and year to Sunday's Date. |
| corTable | Pearson Correlation Table for % ILI |
| create_patch | Create a New Region |
| Date2CadLabel | Add Cadence to Data |
| Date2CDCweek | Convert a Date to CDC Week and Year |
| diceData | The MASTER DICE DATA SET |
| dice-package | DICE: Dynamics of Interacting Community Epidemics |
| distance.matrix | Calculate a Euclidean Distance Matrix |
| fitCholera | Driver Routine - Fitting a Single Cholera Incidence Profile |
| fitMulti | Driver Routine - Coupled Spatial Model |
| fitMultiWHO | Driver Routine Coupled Spatial Model - WHO Data |
| fitOnePatch | Driver Routine - Fitting a Single Incidence Profile |
| fitOnePatchWHO | Driver Routine for a single region - WHO Data |
| fitPlague | Driver Routine - Fitting a Single Plague Incidence Profile |
| fitSARIMA | SARIMA Fitting to Disease Data |
| fitSARIMASD | SARIMA Fitting to San Diego ILI Data |
| fitSARS | Driver Routine - Fitting a Single Plague Incidence Profile |
| fitSingle | Driver Routine - Uncoupled Spatial Model |
| fitSingleWHO | Driver Routine for an Uncoupled Spatial Model - WHO Data |
| fit.user.data | Fit User Provided Incidence |
| flights | Parameters coming from Gaussian fits to posterior... |
| gammaEpi | Calculate the Gamma Function of Disease Number of Cases |
| get.cdc | Retrieve incidence data from CDC server. |
| get.cdc.da | Augment a CDC Time Series |
| get.cdc.data | Load the full 'DICE' dataset and subset by date and region. |
| get.cdc.prior | Retrieve Prior Parameters for a CDC Run |
| get.DICE.data | Retrieve all available data from the DICE database. |
| get_disease_data | Retrieve Incidence and Climate Data |
| get.first.year | Find the First Year for the Data |
| get.FitLevelName | Spatial Name for Fit Level |
| get.future.average.data | Data Augmentation Using the Historic NULL Model |
| get.future.similar.data | Data Augmentation Using the Most Similar Season |
| get.ModelLevelName | Spatial Name for Model Level |
| get.mysql | Retrieve incidence and climate data from MySQL database. |
| get.prior | Find the Most Similar Season |
| get.sd.da | Augment a San Diego Time Series |
| get.sd.future.average.data | Data Augmentation Using the Historic NULL Model |
| get.sd.future.similar.data | Data Augmentation Using the Most Similar Season-San Diego |
| get.sh.nasa | Retrieve specific humidity data from data-server |
| get.sql.da | Data Augmentation for Mechanistic Model |
| makeDir | Create a sub-directory |
| mcmc.multi.write | Write the MCMC History of a Coupled 'DICE' Run |
| mcmc.onepatch.plot | Plot the Posterior Distribution of the Parameters - Single... |
| mcmc.onepatch.write | Write the MCMC History of a Run - Single Region |
| mcmc.single.write | Write the MCMC History of an Uncoupled 'DICE' Run |
| multiplot | Setup a grid for multi-plots on one page using ggplot2 |
| mydata_New2Old | Data Format Conversion |
| OpenCon | Open a Connection to MySQL Database. |
| PadNAs | Pad Time Series wit NA's |
| plotARIMA | Plot SARIMA Results of Fitting/Forecasting the Disease Data |
| plotDisease | Plot The entire Time Series of the Disease Data |
| plotFitCDCPercentILI | Plot the Results of a 'DICE' Run |
| plotFitCDCPercentILI.external | Plot the Results of a 'DICE' Run - Using an External User... |
| plotFitCDCPercentILI.ggplot2 | Plot the results of a 'DICE' Run Using ggplot2 |
| plotFitOnePatch | Plot the Results of a 'DICE' Run - Single Region |
| plotFitOnePatch.external | Plot the Results of a 'DICE' Run - Using an External User... |
| plotFitOnePatch.ggplot2 | Plot the results of a 'DICE' Run - Single Region |
| plotHists | Plot Histograms of Predicted and Observed Peak Value and Week |
| plotHists.external | Plot Histograms of Predicted and Observed Peak Value and Week... |
| plotHists.ggplot2 | Plot Histograms of Predicted and Observed Peak Week and Value |
| plotMCMC | Plot Posterior Distribution from MCMC Procedure |
| plotMECH | Plot Mechanistic Results of Fitting/Forecasting the Disease... |
| plotUserDataMECH | Plot Mechanistic Results of Fitting/Forecasting User... |
| plotUserDisease | Plot The Time Series of the User Provided Incidence |
| pluralize | Pluralize names |
| port1 | #' Gaussian Fit Parameters for Posterior Distributions #' #'... |
| print.error.dice | Print an Error Message |
| priorTable | Pearson Correlation Table for % ILI - New version |
| psi.lnlike | Calculate the Likelihood of a Model |
| psi.lnlike.deldeviance | Calculate the Difference Deviance of Two models |
| psi.lnlike.deviance | Calculate the Deviance of a Model |
| psi.sim.modelA | A Compartmental SIR Model |
| quanci | Calculate the 0.75 confidence interval of an a distribution |
| results.table | Create a List of Tables for Observations and Results |
| runDICE | Main Driver for the 'DICE' package |
| runDICEUserData | Main Driver for using 'DICE' for Fitting User Provided... |
| runSyntheticMulti | Driver Routine Coupled Spatial Model - Synthetic Data |
| runSyntheticSingle | Driver Routine Uncoupled Spatial Model - Synthetic Data |
| sample.from.prior | Sample from a Prior Gaussian Distribution |
| saveARIMA | Save the Results of a SARIMA Fit |
| saveProfiles | Save the profiles for Model region Save the profiles for... |
| saveProfilesOnePatch | Save the profiles for Model region Save the profiles for... |
| saveRData | Save a Binary RData file |
| saveTables | Save Tables with Results of Fitting/Forecasting the Disease... |
| set.cpl.imask | Set a Mask for the Coupling Parameters |
| set.imask | Set a Mask for Parameters |
| set.iseed | Set the seed for the RNG |
| set.opt.list | Create a Logical List with all the 'DICE' model parameters |
| set.param.cpl.list | Create a List of Coupling Parameters that the Code Recognizes |
| set.param.list | Create a List of all Parameters the Code Recognizes |
| set.plague.model | Setup of Parameters for an MCMC SEIR procedure |
| set.run.list | Create a List of Parameters For MCMC Procedure |
| set.sars.model | Setup of Parameters for an MCMC SEIR procedure |
| set.sirb.model | Setup of Parameters for an MCMC sirb procedure |
| setup.coupling.mcmc | Setup For Coupling Parameters |
| setup.fit.mcmc | Setup parameters for MCMC Procedure - Fit Data |
| setup.model.mcmc | Setup Parameters for MCMC Procedure - Model Data |
| setup.single.prior | Obtain Prior parameters for an Uncoupled CDC 'DICE' Run |
| setup.vector.fit.mcmc | Setup Parameters for MCMC Procedure - Fit Dengue Data |
| setup.vector.model.mcmc | Setup Parameters for MCMC Procedure - Model Dengue Data |
| set.user.data.model | Setup of Parameters for an MCMC procedure |
| set.user.data.opt.list | Create a Logical List with TRUE/FALSE values for parameter... |
| set.user.data.param.list | Short Parameter List - Fixed Force of Infection Case |
| subset.sql.mydata | Subsets the Data |
| SummaryByCountry | Disease Summary By Country |
| SummaryBySource | Disease Summary By Source |
| synthetic.compare | Plot Posterior Distributions for a Synthetic Example For each... |
| trimdata.in | Trim an array of raw cases to find the last observed data... |
| writeCSV | Write the Results of a 'DICE' Run - Uncoupled Multiple Region |
| writecsvOnePatch | Write the Results of a 'DICE' Run - Single Region |
