# yaImpute: Nearest Neighbor Observation Imputation and Evaluation Tools

Performs nearest neighbor-based imputation using one or more alternative approaches to processing multivariate data. These include methods based on canonical correlation analysis, canonical correspondence analysis, and a multivariate adaptation of the random forest classification and regression techniques of Leo Breiman and Adele Cutler. Additional methods are also offered. The package includes functions for comparing the results from running alternative techniques, detecting imputation targets that are notably distant from reference observations, detecting and correcting for bias, bootstrapping and building ensemble imputations, and mapping results.

- Author
- Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
- Date of publication
- 2015-07-20 18:36:55
- Maintainer
- Nicholas L. Crookston <ncrookston.fs@gmail.com>
- License
- GPL (>= 2)
- Version
- 1.0-26

## Man pages

- ann
- Approximate nearest neighbor search routines
- ann
- Approximate nearest neighbor search routines
- applyMask
- Removes neighbors that share (or not) group membership with...
- applyMask
- Removes neighbors that share (or not) group membership with...
- asciigridimpute
- Imputes/Predicts data for Ascii Grid maps
- asciigridimpute
- Imputes/Predicts data for Ascii Grid maps
- bestVars
- Computes the number of _best_ X-variables
- bestVars
- Computes the number of _best_ X-variables
- buildConsensus
- Finds the consensus imputations among a list of yai objects
- buildConsensus
- Finds the consensus imputations among a list of yai objects
- compare.yai
- Compares different k-NN solutions
- compare.yai
- Compares different k-NN solutions
- correctbias
- Correct bias by selecting different near neighbors
- correctbias
- Correct bias by selecting different near neighbors
- cor.yai
- Correlation between observed and imputed
- cor.yai
- Correlation between observed and imputed
- ensembleImpute
- Computes the mean, median, or mode among a list of impute.yai...
- ensembleImpute
- Computes the mean, median, or mode among a list of impute.yai...
- errorStats
- Compute error components of k-NN imputations
- errorStats
- Compute error components of k-NN imputations
- foruse
- Report a complete imputation
- foruse
- Report a complete imputation
- grmsd
- Generalized Root Mean Square Distance Between Observed and...
- grmsd
- Generalized Root Mean Square Distance Between Observed and...
- impute.yai
- Impute variables from references to targets
- impute.yai
- Impute variables from references to targets
- MoscowMtStJoe
- Moscow Mountain and St. Joe Woodlands (Idaho, USA) Tree and...
- MoscowMtStJoe
- Moscow Mountain and St. Joe Woodlands (Idaho, USA) Tree and...
- mostused
- Tabulate references most often used in imputation
- mostused
- Tabulate references most often used in imputation
- newtargets
- Finds K nearest neighbors for new target observations
- newtargets
- Finds K nearest neighbors for new target observations
- notablydifferent
- Finds obervations with large differences between observed and...
- notablydifferent
- Finds obervations with large differences between observed and...
- notablydistant
- Find notably distant targets
- notablydistant
- Find notably distant targets
- plot.compare.yai
- Plots a compare.yai object
- plot.compare.yai
- Plots a compare.yai object
- plot.notablydifferent
- Plots the scaled root mean square differences between...
- plot.notablydifferent
- Plots the scaled root mean square differences between...
- plot.varSel
- Boxplot of mean Mahalanobis distances from varSelection()
- plot.varSel
- Boxplot of mean Mahalanobis distances from varSelection()
- plot.yai
- Plot observed verses imputed data
- plot.yai
- Plot observed verses imputed data
- predict.yai
- Generic predict function for class yai
- predict.yai
- Generic predict function for class yai
- Print a summary of a yai object
- Print a summary of a yai object
- rmsd.yai
- Root Mean Square Difference between observed and imputed
- rmsd.yai
- Root Mean Square Difference between observed and imputed
- TallyLake
- Tally Lake, Flathead National Forest, Montana, USA
- TallyLake
- Tally Lake, Flathead National Forest, Montana, USA
- unionDataJoin
- Combines data from several sources
- unionDataJoin
- Combines data from several sources
- vars
- List variables in a yai object
- vars
- List variables in a yai object
- varSelection
- Select variables for imputation models
- varSelection
- Select variables for imputation models
- whatsMax
- Find maximum column for each row
- whatsMax
- Find maximum column for each row
- yai
- Find K nearest neighbors
- yai
- Find K nearest neighbors
- yaiRFsummary
- Build Summary Data For Method RandomForest
- yaiRFsummary
- Build Summary Data For Method RandomForest
- yaiVarImp
- Reports or plots importance scores for yai method...
- yaiVarImp
- Reports or plots importance scores for yai method...

## Files in this package

yaImpute |

yaImpute/inst |

yaImpute/inst/CITATION |

yaImpute/inst/COPYRIGHTS |

yaImpute/src |

yaImpute/src/kd_util.cpp |

yaImpute/src/bd_fix_rad_search.cpp |

yaImpute/src/kd_split.cpp |

yaImpute/src/kd_util.h |

yaImpute/src/kd_pr_search.cpp |

yaImpute/src/pr_queue_k.h |

yaImpute/src/ANN |

yaImpute/src/ANN/ANNperf.h |

yaImpute/src/ANN/ANN.h |

yaImpute/src/ANN/ANNx.h |

yaImpute/src/bd_tree.cpp |

yaImpute/src/bd_tree.h |

yaImpute/src/ANN.cpp |

yaImpute/src/kd_pr_search.h |

yaImpute/src/perf.cpp |

yaImpute/src/annImpute.cpp |

yaImpute/src/pr_queue.h |

yaImpute/src/kd_split.h |

yaImpute/src/kd_tree.h |

yaImpute/src/util.h |

yaImpute/src/bd_search.cpp |

yaImpute/src/bd_pr_search.cpp |

yaImpute/src/kd_fix_rad_search.cpp |

yaImpute/src/kd_dump.cpp |

yaImpute/src/util.cpp |

yaImpute/src/rfoneprox.cpp |

yaImpute/src/brute.cpp |

yaImpute/src/kd_fix_rad_search.h |

yaImpute/src/kd_search.cpp |

yaImpute/src/kd_tree.cpp |

yaImpute/src/kd_search.h |

yaImpute/NAMESPACE |

yaImpute/NEWS |

yaImpute/data |

yaImpute/data/TallyLake.RData |

yaImpute/data/MoscowMtStJoe.RData |

yaImpute/R |

yaImpute/R/correctbias.R |

yaImpute/R/plot.yai.R |

yaImpute/R/yaiRFsummary.R |

yaImpute/R/grmsd.R |

yaImpute/R/cor.yai.R |

yaImpute/R/impute.R |

yaImpute/R/errorstats.R |

yaImpute/R/vars.yai.R |

yaImpute/R/buildConsensus.R |

yaImpute/R/uniondatajoin.R |

yaImpute/R/yai.R |

yaImpute/R/ensembleImpute.R |

yaImpute/R/asciigridimpute.R |

yaImpute/R/yaiVarImp.R |

yaImpute/R/applyMask.R |

yaImpute/R/varSelection.R |

yaImpute/R/findFactors.R |

yaImpute/R/rmsd.yai.R |

yaImpute/R/foruse.R |

yaImpute/R/mostused.R |

yaImpute/R/print.yai.R |

yaImpute/R/compare.yai.R |

yaImpute/R/notablydistant.R |

yaImpute/R/notablydifferent.R |

yaImpute/R/whatsMax.R |

yaImpute/R/predict.yai.R |

yaImpute/R/newtargets.R |

yaImpute/R/ann.R |

yaImpute/MD5 |

yaImpute/DESCRIPTION |

yaImpute/man |

yaImpute/man/plot.compare.yai.Rd |

yaImpute/man/MoscowMtStJoe.Rd |

yaImpute/man/plot.notablydifferent.Rd |

yaImpute/man/correctbias.Rd |

yaImpute/man/cor.yai.Rd |

yaImpute/man/impute.yai.Rd |

yaImpute/man/yai.Rd |

yaImpute/man/errorStats.Rd |

yaImpute/man/foruse.Rd |

yaImpute/man/rmsd.yai.Rd |

yaImpute/man/unionDataJoin.Rd |

yaImpute/man/whatsMax.Rd |

yaImpute/man/newtargets.Rd |

yaImpute/man/bestVars.Rd |

yaImpute/man/TallyLake.Rd |

yaImpute/man/predict.yai.Rd |

yaImpute/man/vars.Rd |

yaImpute/man/yaiVarImp.Rd |

yaImpute/man/ensembleImpute.Rd |

yaImpute/man/plot.yai.Rd |

yaImpute/man/mostused.Rd |

yaImpute/man/notablydistant.Rd |

yaImpute/man/notablydifferent.Rd |

yaImpute/man/buildConsensus.Rd |

yaImpute/man/varSelection.Rd |

yaImpute/man/asciigridimpute.Rd |

yaImpute/man/compare.yai.Rd |

yaImpute/man/yaiRFsummary.Rd |

yaImpute/man/print.Rd |

yaImpute/man/grmsd.Rd |

yaImpute/man/applyMask.Rd |

yaImpute/man/ann.Rd |

yaImpute/man/plot.varSel.Rd |