Description Usage Arguments Value Author(s) See Also

Reads in the report-file from an IRATE run

1 2 | ```
read.rep(fn, skip=0, show.sm=F, short=F)
read.short.rep(fn, skip=0, show.sm=F, short=T)
``` |

`fn` |
Character string indicating the name of the |

`skip` |
Number of lines to skip in report file (default = 0). |

`show.sm` |
Show model report summary while reading the file. |

`short` |
read short report or long report. |

a list containing the model statistics and parameter estimates from an IRATE run:

for `read.short.rep`

or `read.rep(short=T)`

:

`Log_L`

, `AIC`

, `AICc`

, `Effective_Sample_Size`

, `Unpooled_Chi_square`

, `Upooled_df`

, `Unpooled_c_hat`

, `Pooled_Chi_square`

, `Pooled_df`

, `Pooled_c_hat`

othervise the full report file will be returned, containing the following

`rep_info`

report file information

`Log_L`

Log-Likelihood

`K`

Number of parameters

`AIC`

Akaike information criterion

`AICc`

AIC corrected for finite sample sizes

`Effective_Sample_Size`

`Unpooled_Chi_square`

`Upooled_df`

`Unpooled_c_hat`

`Pooled_Chi_square`

`Pooled_df`

`Pooled_c_hat`

`Harvest_Residuals, Harvest_Residuals_of_Age_Class_*`

`Release_Residuals, Release_Residuals_of_Age_Class_*`

`Not_seen_Residuals, Not_seen_Residuals_of_Age_Class_*`

`Obs_Recoveries_of_harvest_fish`

`Obs_Recoveries_of_release_fish`

`Total_Released`

`Total_Recovered_Tags`

`s_matrix`

matrix of survival rates of the tags (Sj,tags)

`S_prob_matrix`

matrix of survival rates used in the calculation of expected cell probabilities

`Exploitation_Rate_of_harvested_fish`

matrix of estimated exploitation rates for harvested fish (Uj,tags(kept))

`Exploitation_Rate_of_released_fish`

matrix of estimated exploitation rates for released fish (Uj,tags(rels))

`Expected_Probability_of_harvested_fish`

matrix of cell expected probabilities for harvested tag returns (Pij)

`Expected_Probability_of_released_fish`

matrix of cell expected probabilities for released tag returns (P'ij)

`Not_Seen_Probability`

matrix of cell expected probabilities for not seen tag returns (P-sum(Pij+P'ij))

`Expected_Number_of_harvested_fish`

matrix of expected number of harvested tag returns (E(Rij)

`Expected_Number_of_released_fish`

matrix of expected number of released tag returns (E(R'ij))

`Expected_Number_of_not_seen`

matrix of expected number of not seen tag returns (N-sum(Rij+R'ij))

`Cell_Likelihoods_of_harvested_fish`

individual cell likelihood values for harvested tag returns

`Cell_Likelihoods_of_released_fish`

individual cell likelihood values for released tag returns

`Cell_Likelihoods_of_not_seen`

individual cell likelihood values for not seen tag returns

`Unpooled_Chi_squares_of_Harvested_Fish`

individual unpooled cell chi-square values for harvested tag returns

`Unpooled_Chi_squares_of_Released_Fish`

individual unpooled cell chi-square values for released tag returns

`Chi_squares_of_Not_Seen`

individual unpooled cell chi-square values for unseen tag returns

`Pooled_Cells_of_Harvested_Fish`

matrix of pooled, observed harvested tag returns

`Pooled_Cells_of_Released_Fish`

matrix of pooled, observed harvested tag returns

`Pooled_Expected_Cells_of_Harvested_Fish`

matrix of pooled expected number of harvested tag returns

`Pooled_Expected_Cells_of_Released_Fish`

matrix of pooled expected number of released tag returns

`Pooled_Chi_squares_of_Harvested_Fish`

matrix of cell chi-square values for harvested tag returns

`Pooled_Chi_squares_of_Released_Fish`

matrix of pooled cell chi-square values for released tag returns

`Pearson_Residuals_for_harvested_fish`

matrix of Pearson residuals for harvested tag returns

`Pearson_Residuals_for_released_fish`

matrix of Pearson residuals for released tag returns

`Pearson_Residuals_for_not_seen`

matrix of Pearson residuals for not seen tag returns

Robert K. Bauer

read.par

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.