read.rep: Read report-file from an IRATE run

Description Usage Arguments Value Author(s) See Also

View source: R/read.rep.r

Description

Reads in the report-file from an IRATE run

Usage

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

Arguments

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.

Value

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

Author(s)

Robert K. Bauer

See Also

read.par


IRATER documentation built on May 1, 2019, 7:32 p.m.