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
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