Saves results from an analysis of variance in R data frames (R.W. Payne & Z.Zhang).

### Options

`TERM` = formula |
Treatment term whose means, effects etc. are to be saved; must be set if any of these are to be saved, unless there is only one treatment term |
---|---|

`STRATUM` = formula |
Model term of the lowest stratum to be searched for effects and contrasts; default `*` implies the lowest stratum |

`SUPPRESSHIGHER` = string token |
Whether to suppress the searching of higher strata if a term is not found in `STRATUM` (`yes` , `no` ); default `no` |

`LSDLEVEL` = scalar |
Significance level (%) for least significant differences and multiple comparisons; default 5 |

`EQFACTORS` = factors |
Factors whose levels are to be assumed to be equal within the comparisons between means calculated for effective standard errors of treatment means |

`RMETHOD` = string tokens |
Types of residuals to form (`simple` , `standardized` , `combined` ); default `simp` |

`MCOMPARISON` = string token |
Method to use to make multiple comparisons between the means (`tukey` , `regwmr` , `duncan` , `scheffe` , `fplsd` , `fulsd` , `fpstudentizedlsd` , `fustudentizedlsd` , `bonferroni` , `sidak` ); default `*` i.e. none |

`SAVE` = `ANOVA` save structure |
Specifies the analysis from which to save the results; default `*` i.e. most recent one |

### Parameters

`INFORMATION` = string tokens |
What to save (`aovtable` , `covariates` , `effects` , `cbeffects` , `partialeffects` , `contrasts` , `means` , `semeans` , `sedmeans` , `lsdmeans` , `dfmeans` , `cbmeans` , `secbmeans` , `sedcbmeans` , `replications` , `fittedvalues` , `missingvalues` , `stratumvariances` , `%cv` , `fixedcoefficients` , `randomcoefficients` ); must be set |
---|---|

`OUTFILENAME` = texts |
Name of the R (`.rda` ) file to create for each set of information; must be set |

`COLUMNNAMES` = texts |
Specifies names for the columns in the file; if this is not set, suitable names are chosen automatically |

`EXIT` = scalars |
Records the exit status, 0 if the information was saved successfully, 1 otherwise |

### Description

`A2RDA`

puts results from an analysis of variance into R data frames. By default the results are from the most recent `ANOVA`

, but you use the `SAVE`

option to specify the save structure from some other analysis.

The `INFORMATION`

parameter specifies the information to save, with settings:

`aovtable` |
analysis of variance table; |
---|---|

`covariates` |
estimated covariate regression coefficients and their standard errors (if any covariates in the analysis); |

`effects` |
table of treatment effects; |

`cbeffects` |
table of effects for a treatment term, combining the information from every stratum where it is estimated; |

`partialeffects` |
table of partial effects for a treatment term, adjusted for every other treatment term; |

`contrasts` |
estimated treatment contrasts; |

`means` |
table of predicted means; |

`semeans` |
table of effective standard errors of means; |

`sedmeans` |
symmetric matrix of standard errors of differences of means; |

`lsdmeans` |
symmetric matrix of least significant differences of means; |

`dfmeans` |
symmetric matrix of degrees of freedom for differences of means; |

`cbmeans` |
table of predicted means for a treatment term, combining information from all the strata in which its effects are estimated; |

`secbmeans` |
table of effective standard errors of combined treatment means; |

`sedcbmeans` |
symmetric matrix of standard errors of differences of combined treatment means; |

`replications` |
replication table; |

`fittedvalues` |
y-variate, fitted values and residuals; |

`missingvalues` |
estimates for missing values (if any); |

`stratumvariances` |
estimated variances of the units in each stratum, stratum variance components and effective numbers of degrees of freedom; |

`%cv` |
coefficients of variation, numbers of residual degrees of freedom and standard errors of individual units in each stratum; |

`fixedcoefficients` |
estimated treatment effects and covariate regression coefficients; |

`randomcoefficients` |
residuals (from all the strata). |

The `OUTFILENAME`

parameter specifies the name of the file to save the information. If this does not have a `.rda`

extension, one will be appended to the name automatically.

The `COLUMNNAMES`

parameter allows you to specify a text containing names to use for the columns in the file. Thus may be useful if you want to avoid name clashes when you are saving several sets of output.

The `EXIT`

parameter can save a scalar to record the exit status for each set of information. This contains zero if the information was saved successfully, and one otherwise. (For example, it will not be possible to save missing-value estimates if no responses were missing.)

The `TERM`

option specifies the treatment term whose means, effects etc. are to be saved. This must be set if any of these are to be saved, unless there is only one treatment term. The `EQFACTORS`

option allows you to specify factors within the tables of means whose levels are assumed to be equal for the two means when forming effective standard errors of treatment means (see the `AKEEP`

directive for more details).

In designs where there is partial confounding, and treatment terms are estimated in more than one stratum, options `STRATUM`

and `SUPPRESSHIGHER`

allow you to specify the strata from which effects and contrasts are taken. By default, Genstat searches all the strata, and takes the information from the lowest of the strata where the term is estimated. If you set the `STRATUM`

option, only strata down to the specified stratum are searched. By setting `SUPPRESSHIGHER=yes`

, you can restrict the search to only that stratum.

The `LSDLEVEL`

option specifies the significance level (%) to use in the calculation of least significant differences, or the experiment-wise significance level for multiple comparisons (default 5%).

The `MCOMPARISON`

option specifies the method to use for multiple comparisons. The settings are `Tukey`

, `REGWMR`

(Ryan/Einot-Gabriel/Welsch multiple range test), `Duncan`

, `Scheffe`

, `FPLSD`

(Fisher’s Protected Least Significant Difference), `FULSD`

(Fisher’s Unprotected Least Significant Difference), `FPSTUDENTIZEDLSD`

(Fisher’s Protected Least Significant Difference, using the Studentized Range statistic rather than Student’s t), `FUSTUDENTIZEDLSD`

(Fisher’s Unprotected Least Significant Difference, using the Studentized Range statistic), `Bonferroni`

and `Sidak`

. By default, no multiple comparisons are done. The results are saved in a textual column, with the means. This contains identical letters (a, b etc.) alongside the sets of means that do not differ significantly. For more details see procedure `AMCOMPARISON`

, which is used to do the calculations.

The `RMETHOD`

option selects the types of residual to save with the fitted values, with settings:

`simple` |
ordinary “simple” residuals (labelled `residual` in the data frame), |
---|---|

`standardized` |
residuals standardized according to their variances (labelled `stdresidual` ), and |

`combined` |
residuals that incorporate the variation from all the strata, (labelled `cbresidual` ). |

By default, only simple residuals are saved. You can save more than one type of residual, by specifying a list of settings (and they are included in the data frame in the order with which they occur in the list).

Options: `TERM`

, `STRATUM`

, `SUPPRESSHIGHER`

, `LSDLEVEL`

, `EQFACTORS`

, `RMETHOD`

, `MCOMPARISON`

, `SAVE`

.

Parameters: `INFORMATION`

, `OUTFILENAME`

, `COLUMNNAMES`

, `EXIT`

.

### Action with `RESTRICT`

If the `Y`

variate in the analysis is restricted, that restriction will carry over into the fitted-values spreadsheet.

### See also

Procedure: `RXGENSTAT`

.

Commands for: Analysis of variance and Input and output.

### Example

CAPTION 'A2RDA example'; STYLE=meta SPLOAD '%gendir%/data/canola.gsh' BLOCKS block/plot TREATMENTS N*S ANOVA yield " save the information " A2RDA [TERM=N.S] INFORMATION=\ aovtable,means,sedmeans,replication,fittedvalues; OUTFILENAME=\ 'aovtable.rda','means.rda','sedmeans.rda','replication.rda',\ 'fittedvalues.rda' " show the contents of the file " FOR file='aovtable.rda','means.rda','sedmeans.rda','replication.rda',\ 'fittedvalues.rda' IMPORT file; ISAVE=cols PRINT cols[] DELETE [REDEFINE=yes] cols " tidy up by deleting file (delete the line below if you want to keep it) " FDELETE file ENDFOR