Remove header definition; replace with declarations

src/Combined-methods.c

@@ -7,6 +7,389 @@
 
 /* ************************ drawCombined ************************ */
 
+extern SEXP
+  Data_sym,  /* used for .Data slot */
+  iMethodPrior_sym,
+  Z_sym,
+  beta_sym,
+  eta_sym,
+  gamma_sym,
+  lower_sym,
+  tau_sym,
+  tauMax_sym,
+  upper_sym,
+  order_sym,
+  iteratorBeta_sym,
+  iWithin_sym,
+  nWithin_sym,
+  iBetween_sym,
+  nBetween_sym,
+  incrementBetween_sym,
+  indices_sym,
+  initial_sym,
+  dimIterators_sym,
+  strideLengths_sym,
+  nStrides_sym,
+  dimBefore_sym,
+  dimAfter_sym,
+  posDim_sym,
+  lengthDim_sym,
+  iMethodModel_sym,
+  meansBetas_sym,
+  variancesBetas_sym,
+  betaEqualsMean_sym,
+  acceptBeta_sym,
+  priorsBetas_sym,
+  logPostPriorsBetas_sym,
+  logPostBetas_sym,
+  logPostSigma_sym,
+  logPostTheta_sym,
+  logPostVarsigma_sym,
+  theta_sym,
+  thetaTransformed_sym,
+  cellInLik_sym,
+  mu_sym,
+  sigma_sym,
+  sigmaMax_sym,
+  ASigma_sym,
+  nuSigma_sym,
+  varsigma_sym,
+  varsigmaMax_sym,
+  varsigmaSetToZero_sym,
+  AVarsigma_sym,
+  nuVarsigma_sym,
+  w_sym,
+  scaleTheta_sym,
+  scaleThetaMultiplier_sym,
+  nAcceptTheta_sym,
+  betas_sym,
+  priors_sym,
+  iteratorBetas_sym,
+  dims_sym,
+  prob_sym,
+  ADelta0_sym,
+  meanDelta0_sym,
+
+  mean_sym,
+  sd_sym,
+
+  tolerance_sym,
+  betaIsPredicted_sym,
+  nFailedPropTheta_sym,
+  nFailedPropYStar_sym,
+  maxAttempt_sym,
+  valueAg_sym,
+  weightAg_sym,
+  transformAg_sym,
+  meanAg_sym,
+  sdAg_sym,
+  scaleAg_sym,
+  nAcceptAg_sym,
+  nFailedPropValueAg_sym,
+  funAg_sym,
+  xArgsAg_sym,
+  weightsArgsAg_sym,
+  mxAg_sym,
+  axAg_sym,
+  nxAg_sym,
+  nAgeAg_sym,
+  transformThetaToMxAg_sym,
+  subtotals_sym,
+  transformSubtotals_sym,
+  subtotalsNet_sym,
+  slotsToExtract_sym,
+  iMethodCombined_sym,
+  model_sym,
+  exposure_sym,
+  y_sym,
+  dataModels_sym,
+  datasets_sym,
+  transforms_sym,
+  seriesIndices_sym,
+  updateComponent_sym,
+  updateDataModel_sym,
+  updateSystemModel_sym,
+
+  J_sym,
+
+  UC_sym,
+  DC_sym,
+  UR_sym,
+  DCInv_sym,
+  DRInv_sym,
+  CC_sym,
+  a_sym,
+  R_sym,
+  priorsW_sym,
+  v_sym,
+  forward_sym,
+  offsetsBetas_sym,
+  offsetsPriorsBetas_sym,
+  offsetsSigma_sym,
+  offsetsVarsigma_sym,
+  m0_sym,
+  C0_sym,
+  phi_sym,
+  w_sym,
+  iteratorGamma_sym,
+  iteratorV_sym,
+  delta_sym,
+  phiKnown_sym,
+  /* description */
+  nTime_sym,
+  stepTime_sym,
+  hasAge_sym,
+  hasSex_sym,
+  iSexDominant_sym,
+  stepSexCurrent_sym,
+  stepSexTarget_sym,
+  nAge_sym,
+  stepAge_sym,
+  length_sym,
+  stepTriangle_sym,
+  stepDirection_sym,
+  nBetweenVec_sym,
+  stepBetweenVec_sym,
+  nWithinVec_sym,
+  stepWithinVec_sym,
+  /* cohort iterators */
+  i_sym,
+  iTime_sym,
+  iAge_sym,
+  iTriangle_sym,
+  finished_sym,
+  iVec_sym,
+  lengthVec_sym,
+  increment_sym,
+  lastAgeGroupOpen_sym,
+  /* mappings */
+  hasParCh_sym,
+  isOneToOne_sym,
+  nSharedVec_sym,
+  stepSharedCurrentVec_sym,
+  stepSharedCurrentExposureVec_sym,
+  stepSharedTargetVec_sym,
+  nTimeCurrent_sym,
+  stepTimeCurrent_sym,
+  stepTimeTarget_sym,
+  nAgeCurrent_sym,
+  nAgeTarget_sym,
+  stepAgeCurrent_sym,
+  stepAgeTarget_sym,
+  stepTriangleCurrent_sym,
+  stepTriangleTarget_sym,
+  nOrigDestVec_sym,
+  stepOrigCurrentVec_sym,
+  stepDestCurrentVec_sym,
+  stepOrigDestTargetVec_sym,
+  iMinAge_sym,
+
+  /*new priors*/
+  ATau_sym,
+  nuTau_sym,
+  hasAlphaDLM_sym,
+  hasAlphaICAR_sym,
+  hasAlphaMix_sym,
+  hasCovariates_sym,
+  hasAlphaKnown_sym,
+  hasMean_sym,
+  hasSeason_sym,
+  isKnownUncertain_sym,
+  isNorm_sym,
+  isRobust_sym,
+  isZeroVar_sym,
+  alphaDLM_sym,
+  alphaICAR_sym,
+  alphaMix_sym,
+  iteratorState_sym,
+  iteratorStateOld_sym,
+  K_sym,
+  L_sym,
+  s_sym,
+  UBeta_sym,
+  nuBeta_sym,
+  isSaturated_sym,
+  allStrucZero_sym,
+  alongAllStrucZero_sym,
+  strucZeroArray_sym,
+  mNoTrend_sym,
+  m0NoTrend_sym,
+  CNoTrend_sym,
+  aNoTrend_sym,
+  RNoTrend_sym,
+  GWithTrend_sym,
+  mWithTrend_sym,
+  m0WithTrend_sym,
+  CWithTrend_sym,
+  aWithTrend_sym,
+  hasLevel_sym,
+  omegaAlpha_sym,
+  omegaAlphaMax_sym,
+  AAlpha_sym,
+  nuAlpha_sym,
+  deltaDLM_sym,
+  omegaDelta_sym,
+  omegaDeltaMax_sym,
+  nuDelta_sym,
+  ADelta_sym,
+  minPhi_sym,
+  maxPhi_sym,
+  shape1Phi_sym,
+  shape2Phi_sym,
+  WSqrt_sym,
+  WSqrtInvG_sym,
+  exposureAg_sym,
+  P_sym,
+  AEtaIntercept_sym,
+  AEtaCoef_sym,
+  nuEtaCoef_sym,
+  meanEtaCoef_sym,
+  UEtaCoef_sym,
+  nSeason_sym,
+  ASeason_sym,
+  omegaSeason_sym,
+  omegaSeasonMax_sym,
+  nuSeason_sym,
+  mSeason_sym,
+  m0Season_sym,
+  CSeason_sym,
+  aSeason_sym,
+  RSeason_sym,
+  JOld_sym,
+  /* new priors Jan 2017 */
+  sumsWeightsMix_sym,
+  weightMix_sym,
+  latentWeightMix_sym,
+  foundIndexClassMaxPossibleMix_sym,
+  indexClassMaxPossibleMix_sym,
+  indexClassProbMix_sym,
+  componentWeightMix_sym,
+  latentComponentWeightMix_sym,
+  levelComponentWeightMix_sym,
+  levelComponentWeightOldMix_sym,
+  meanLevelComponentWeightMix_sym,
+  indexClassMix_sym,
+  indexClassMaxMix_sym,
+  indexClassMaxUsedMix_sym,
+  omegaComponentWeightMix_sym,
+  omegaComponentWeightMaxMix_sym,
+  omegaLevelComponentWeightMix_sym,
+  omegaLevelComponentWeightMaxMix_sym,
+  iteratorsDimsMix_sym,
+  iAlong_sym,
+  dimBeta_sym,
+  dimBetaOld_sym,
+  phiMix_sym,
+  mMix_sym,
+  CMix_sym,
+  aMix_sym,
+  RMix_sym,
+  prodVectorsMix_sym,
+  posProdVectors1Mix_sym,
+  posProdVectors2Mix_sym,
+  nBetaNoAlongMix_sym,
+  vectorsMix_sym,
+  omegaVectorsMix_sym,
+  iteratorProdVectorMix_sym,
+  yXMix_sym,
+  XXMix_sym,
+  priorMeanLevelComponentWeightMix_sym,
+  priorSDLevelComponentWeightMix_sym,
+  AComponentWeightMix_sym,
+  nuComponentWeightMix_sym,
+  omegaVectorsMix_sym,
+  omegaVectorsMaxMix_sym,
+  AVectorsMix_sym,
+  nuVectorsMix_sym,
+  minLevelComponentWeight_sym,
+  maxLevelComponentWeight_sym,
+  updateSeriesDLM_sym,
+  ALevelComponentWeightMix_sym,
+  nuLevelComponentWeightMix_sym,
+
+  nuCMP_sym,
+  sdLogNuCMP_sym,
+  sdLogNuMaxCMP_sym,
+  meanMeanLogNuCMP_sym,
+  sdMeanLogNuCMP_sym,
+  meanLogNuCMP_sym,
+  ASDLogNuCMP_sym,
+  nuSDLogNuCMP_sym,
+  nu_sym,
+
+  alphaKnown_sym,
+  AKnownVec_sym,
+
+  /* skeleton */
+  first_sym,
+  last_sym,
+
+  /* Box-Cox */
+  boxCoxParam_sym,
+
+  /* accounts  and combined accounts*/
+  account_sym,
+  population_sym,
+  accession_sym,
+  components_sym,
+  descriptions_sym,
+  iteratorPopn_sym,
+  iteratorAcc_sym,
+  iteratorExposure_sym,
+  transformsExpToComp_sym,
+  transformExpToBirths_sym,
+  iCell_sym,
+  iCellOther_sym,
+  iComp_sym,
+  iPopnNext_sym,
+  iPopnNextOther_sym,
+  iAccNext_sym,
+  iAccNextOther_sym,
+  iOrigDest_sym,
+  iPool_sym,
+  iIntNet_sym,
+  iBirths_sym,
+  iParCh_sym,
+  diffProp_sym,
+  isIncrement_sym,
+  isNet_sym,
+  scaleNoise_sym,
+  usePriorPopn_sym,
+  systemModels_sym,
+  modelUsesExposure_sym,
+  mappingsFromExp_sym,
+  mappingsToExp_sym,
+  mappingsToPopn_sym,
+  mappingsToAcc_sym,
+  iExpFirst_sym,
+  iExpFirstOther_sym,
+  ageTimeStep_sym,
+  iteratorsComp_sym,
+  expectedExposure_sym,
+  iExposure_sym,
+  iExposureOther_sym,
+  isLowerTriangle_sym,
+  isOldestAgeGroup_sym,
+  generatedNewProposal_sym,
+  probSmallUpdate_sym,
+  isSmallUpdate_sym,
+  isSmallUpdateFinal_sym,
+  probPopn_sym,
+  cumProbComp_sym,
+  nCellAccount_sym,
+  /* LN@ */
+  alphaLN2_sym,
+  transformLN2_sym,
+  constraintLN2_sym,
+  nCellBeforeLN2_sym;
+
+
+extern SEXP (*dembase_Collapse_R)(SEXP ,SEXP);
+extern SEXP (*dembase_Extend_R)(SEXP ,SEXP);
+extern int (*dembase_getIAfter)(int, SEXP);
+extern SEXP (*dembase_getIBefore)(int, SEXP);
+extern SEXP (*dembase_getIShared)(int, SEXP);
+
 
 void
 drawCombined_CombinedModelBinomial(SEXP object_R, int nUpdate)