read.rep: Read report-file from an IRATE run
In IRATER: A R Interface for the Instantaneous RATEs (IRATE) Model

Description Usage Arguments Value Author(s) See Also

View source: R/read.rep.r

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 `.rep`-file to be read.
`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