check issue: checking Rd \usage sections ... WARNING

[appling]

checking Rd \usage sections ... WARNING

• Objects in \usage without \alias in documentation object 'equals.metadata':
  '\S4method{==}{metadata,metadata}'
• Undocumented arguments in documentation object 'estimateMSE.loadComp'
  'method'
• Undocumented arguments in documentation object 'estimateRho'
  'use.log' 'plot.acf' 'timestep.tol' 'irregular.timesteps.ok'
• Undocumented arguments in documentation object 'fluxInfluence'
  'fit.function' 'obs.calib' 'obs.adjust' 'data.to.predict'
  'correction.method' 'replace.negatives' 'aggregation.interval'
  'influence.on'
• Documented arguments not in \usage in documentation object 'fluxInfluence':
  'fit.and.total.function' 'X.calib' 'Y.calib' 'X.est' 'P.est'
• Undocumented arguments in documentation object 'genericDistanceWeightedInterpolation'
  'inv.dist.fun'
• Undocumented arguments in documentation object 'getMetadata.loadReg'
  'fit'
• Documented arguments not in \usage in documentation object 'getMetadata.loadReg':
  'load.model'
• Undocumented arguments in documentation object 'isTimestepRegular'
  'tol'
• Undocumented arguments in documentation object 'loadComp'
  'MSE.method'
• Undocumented arguments in documentation object 'loadLm'
  'fitting_function' 'y.trans.function'
• Undocumented arguments in documentation object 'loadModel'
  'metadata'
• Undocumented arguments in documentation object 'loadReg2'
  '...'
• Undocumented arguments in documentation object 'metadata'
  'metadata'
• Undocumented arguments in documentation object 'plotCM'
  'linear.interpolation' 'dateField'
• Documented arguments not in \usage in documentation object 'plotCM':
  'linear.interpoltation'
• Undocumented arguments in documentation object 'plotResidualsCM'
  'type' 'xObservations' 'xFlow'
• Undocumented arguments in documentation object 'residDurbinWatson'
  'timestep.tol'
• Objects in \usage without \alias in documentation object 'show.loadModel':
  '\S4method{show}{loadModel}'
• Objects in \usage without \alias in documentation object 'show.metadata':
  '\S4method{show}{metadata}'
• Undocumented arguments in documentation object 'simulateSolute'
  '...'
• Undocumented arguments in documentation object 'simulateSolute.loadLm'
  '...'
• Undocumented arguments in documentation object 'simulateSolute.loadModel'
  '...'
• Undocumented arguments in documentation object 'simulateSolute.loadReg2'
  '...'
• Undocumented arguments in documentation object 'validLoadModelInterface'
  'verbose'
• Undocumented arguments in documentation object 'validMetadataUnits'
  'unit.type'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.