Generates overview of samples to inform on sample availability in potential cell definitions. Informs on which columns maybe be used as fixed effect covariates, and how grouping of covariates is best done for random effects.
The covariates in landings define the cells. For each cell the covariates defining the cell is reported, before the total landed weight, along with the number of unique occurances of covariates not in landings (including catchId and sampleId). Lastly the number of fish measurements for Age, Weight and Length is reported.
Arguments
- samples
data.table() with samples (as in
prepRECA), each row corresponding to one sampled fish. Contains columns:- catchId
Column identifying the catch that the sample was taken from. Typically a haul or a landing.
- sampleId
Column identifying the sample. If only one sample is taken for each catch. This can be set equal to catchId
- Age
integer() Age of fish.
- Length
numeric() Length of fish. Must be complete (no NAs)
- Weight
numeric() Weight of fish.
- ...
Additional columns which may be used as covariates.
- landings
data.table() with total landings (as in
prepRECA), each row corresponding to one cell. Contains columns:- LiveWeightKG
numeric(). Total landings (Live/Round weight in Kg) for the cell
- ...
Additional columns which may be used as covariates. These will define each cell.
- covariates
character() vector of columns to consider for covariates.
Value
data.table() with columns
- <Covariates in landings>
one column for each. Defines the cells.
- LiveWeightKG
The total weight (kg) in the cell.
- LiveWeightCumFraction
The fraction of landings in this cell AND all the cells with higher total weight than this cell.
- <Count of covariates not in landings>
Count of unique values for covariate. one column for each. Column name is covariate name (from samples) prefixed with N
- Ncatch
The number of unique catches sampled in the cell.
- Nsample
The number of unique catch-samples in the cell.
- Nage
The number of age readings in the cell.
- Nweight
The number of fish weight measurements in the cell.
- Nlength
The number of fish length measurements in the cell.
Examples
data(catchsamples)
catchsamples$catchId <- catchsamples$LEid
catchsamples$sampleId <- catchsamples$SAid
catchsamples$date <- catchsamples$LEdate
catchsamples$Metier5 <- catchsamples$LEmetier5
data(landings)
landings$LiveWeightKG <- landings$OfficialLandingsWeight
landings$Metier5 <- landings$FishingActivityCategoryEuropeanLvl5
rEcaDataReport(catchsamples, landings, c("Metier5", "VDencrCode"))
#> Metier5 LiveWeightKG LiveWeightCumFraction NVDencrCode Ndate Ncatch Nsample
#> 1: OTB_DEF 39822917 0.4175925 1 1 1 1
#> 2: LLS_DEF 26807800 0.6987055 34 16 34 35
#> 3: SSC_DEF 14299890 0.8486575 29 23 29 29
#> 4: LX_DEF 9328848 0.9464820 0 0 0 0
#> 5: GNS_DEF 2754654 0.9753680 17 9 17 17
#> 6: LLD_DEF 2063217 0.9970034 0 0 0 0
#> 7: PTB_DEF 118092 0.9982417 0 0 0 0
#> 8: LHM_DEF 83410 0.9991164 0 0 0 0
#> 9: OTM_DEF 63339 0.9997806 0 0 0 0
#> 10: FPO_DEF 9051 0.9998755 0 0 0 0
#> 11: PS_DEF 5267 0.9999307 0 0 0 0
#> 12: OTT_DEF 5155 0.9999848 0 0 0 0
#> 13: GND_DEF 1202 0.9999974 0 0 0 0
#> 14: MIS_DEF 251 1.0000000 0 0 0 0
#> Nage Nweight Nlength
#> 1: 29 29 29
#> 2: 962 962 962
#> 3: 721 721 721
#> 4: 0 0 0
#> 5: 338 338 338
#> 6: 0 0 0
#> 7: 0 0 0
#> 8: 0 0 0
#> 9: 0 0 0
#> 10: 0 0 0
#> 11: 0 0 0
#> 12: 0 0 0
#> 13: 0 0 0
#> 14: 0 0 0