Add raw counts to CWAC SSM predictions

We only run state-space models for those CWAC sites that have enough data. See ppl_create_data_ssm. For those sites that don't have enough data, we present the raw data. This function is used to bind the output of ppl_summarise_ssm with the raw data from those sites that didn't have enough data to run an analysis.

Usage

addExtraSitesToSummary(counts, preds)

Arguments

counts

A dataframe with CWAC counts. It is preferable that the dataframe containd missing counts as well. See addMissingCwacCounts

preds

A dataframe with estimates from a state-space model fitted to CWAC data. See ppl_summarise_ssm

Value

A dataframe with predictions for sites with good data, together with raw counts for sites with not enough data to run an analysis.

Examples

if (FALSE) {
sp_code <- 87
config <- configPipeline(
    year = 2022,
    dur = 30,
    module = "abu",
    mod_file = "cwac_ssm_two_season_mean_rev_jump.R",
    package = "jagsUI",
    data_dir = NULL,     # this might have to be adapted?
    out_dir = NULL,     # this might have to be adapted?
    server = FALSE
)
counts <- read.csv(setSpOutFilePath("cwac_data_w_miss", config, config$years_ch, sp_code, ".csv"))
preds <- setSpOutFilePath("ssm_pred", config, config$years_ch, sp_code, "_all.csv")
preds_w_raw <- addExtraSitesToSummary(counts, preds)
}