brMask {blindreview} | R Documentation |

Assigns identification randomly to one of the variables of the dataset as chosen by the user, say Treatment, and assigns random number to the observations of the dataset. Then runs the appropriate forward search function on the blinded dataset. A file is created so that the user can identify any outliers identified by the forward search procedure in terms of their original, unchanged values. Output is primarily for plotting by the plotdiag.blind.all function.

```
brMask(data, blinded, analysis,
initial.sample=1000, n.obs.per.level=1, skip.step1=NULL, fixed=NULL,
lme.random=NULL, lme.formula=NULL,
glm.estimate.phi=TRUE, glm.cobs=1, glm.response.cols=NULL,
glm.indep.cols=NULL, glm.formula=NULL, glm.binomialrhs=NULL,
glm.family=NULL, cph.formula.elements=NULL, cph.event.time=NULL,
cph.status=NULL, cph.x=NULL, cph.ties=NULL, cph.redunCorr=0.9,
arguments=FALSE, verbose=TRUE)
```

`data` |
Dataset to be evaluated |

`blinded` |
Character, name of variable to be blinded |

`analysis` |
Character, one of "lme", "lm", "glm", or "cph" |

`initial.sample` |
Number of observations in Step 1 of forward search |

`n.obs.per.level` |
Number of observations per level of (possibly crossed) factor levels |

`skip.step1` |
NULL or a vector of integers for observations to be included in Step 1 |

`fixed` |
Fixed effects formula as described in stats::lm |

`lme.random` |
Random effects formula as described in nlme::lme |

`lme.formula` |
a simplified formula of the form resp ~ cov | group where resp is the response, cov is the primary covariate, and group is the grouping factor, as in nlme::groupedData |

`glm.estimate.phi` |
TRUE causes phi to be estimated; FALSE causes phi to be set = 1 |

`glm.cobs` |
Number of observations to include in each inner subgroup of Step 1 |

`glm.response.cols` |
Vector of column numbers (2) of responses and nonresponses |

`glm.indep.cols` |
Column number(s) of independent variables |

`glm.formula` |
Formula relating response to independent variables. Required except for family=binomial |

`glm.binomialrhs` |
Right-hand side of formula, as text object. Required for family=binomial |

`glm.family` |
Error distribution and link |

`cph.formula.elements` |
Vector of names of independent variables to appear in a formula object |

`cph.event.time` |
Vector of event times, censored or not |

`cph.status` |
Vector indicator of event or censoring: 1 = event, 0 = censored, same length as event.time |

`cph.x` |
Data frame of independent variables, with number of rows = length of event.time, First column is Observation. Factor variables must be defined in advance. Does not include event time or status. |

`cph.ties` |
Character string specifying the method of handling ties in event time, "efron", "breslow" or "exact", . See survival::coxph for definitions. Default is "efron" if specified =NULL |

`cph.redunCorr` |
Level of correlation required before declare variables are redundant |

`arguments` |
Logical. TRUE causes display of arguments of forsearch_xxx function |

`verbose` |
TRUE causes function identifier to display before and after run |

LIST, unnecessary elements for current analysis are NULL

`Analysis` |
"lme", "lm", "glm", or "cph" |

`Unmask` |
Data frame of original and masked values |

`Rows in stage` |
List of (masked) observation numbers in each stage |

`Standardized residuals` |
Matrix of errors at each stage |

`Number of model parameters` |
Rank of model |

`Sigma` |
Estimate of random error at final stage; used to standardize all residuals |

`Fixed parameter estimates` |
Matrix of parameter estimates at each stage |

`s^2` |
Estimate of random error at each stage |

`Leverage` |
Matrix of leverage of each observation at each stage |

`Modified Cook distance` |
Estimate of sum of squared changes in parameter estimates at each stage |

`t statistics` |
t statistics for each fixed parameter |

`Family` |
Family and link |

`Residual deviance` |
Vector of deviances |

`Null deviance` |
Vector of null deviances |

`PhiHat` |
Vector of values of phi parameter |

`Deviance residuals and augments` |
Deviance residuals with indication of whether each is included in fit |

`AIC` |
Vector of AIC values |

`Number of rows included in Step 1` |
Number of observations included in Step 1 |

`Rows by subgroup` |
List of row numbers, by subgroup |

`Random parameter estimates` |
Matrix of parameter estimates at each stage |

`Dims` |
Dims from fit of lme function |

`Fit statistics` |
AIC, BIC, and log likelihood |

`Wald Test` |
Wald test from fit of coxph function |

`LogLikelihood` |
Log likelihood from fit of coxph function |

`Likelihood ratio test` |
Likelihood ratio test from fit of coxph function |

`forsearch Call` |
Call to forsearch function |

`Call` |
Call to this function |

William R. Fairweather

Atkinson, A and M Riani. Robust Diagnostic Regression Analysis, Springer, New York, 2000. Pinheiro, JC and DM Bates. Mixed-Effects Models in S and S-Plus, Springer, New York, 2000. https://CRAN.R-project.org/package=forsearch

[Package *blindreview* version 1.3.0 Index]