Introduction

library(samrat)

1. Reading in our parameters

We start by reading in our parameter file that controls most of our modelling. Please see Parameters Vignette for how to set up and format the parameters .xlsx file.

param_file <- system.file(
  "extdata/som_analysis_parameters.xlsx",
  package = "samrat"
)

pars_list <- samrat_read_params(param_file)
names(pars_list)
#> [1] "pars_list" "gen_pars"  "var_pars"  "cf_pars"

We then use this object when reading in our strata and survey metadata:

# read in the strata params
strata_file <- system.file(
  "extdata/som_analysis_strata.xlsx",
  package = "samrat"
)
strata <- samrat_read_strata(strata_file, pars_list)

# read in the survey meta params
surveymeta_file <- system.file(
  "extdata/som_survey_metadata.xlsx",
  package = "samrat"
)
surveys <- samrat_read_surveymeta(surveymeta_file, pars_list)

Similarly when reading in our demography files:

# read in the demog params
demog_file <- system.file(
  "extdata/som_demog_data.xlsx",
  package = "samrat"
)
demog_list <- samrat_read_demography(demog_file, pars_list)
names(demog_list)
#> [1] "demog_pars_list"  "pop_sources_list" "demog_pars"       "pop_sources"     
#> [5] "dictionary"

And lastly when reading in our predictor files:

# read in the predictor params
predictors_file <- system.file(
  "extdata/som_predictor_data.xlsx",
  package = "samrat"
)

pred_list <- samrat_read_predictors(predictors_file, pars_list)

2. Create the timeseries

Having read in the parameters, we can create the timeseries object that details when mortality is to be inferred for.

# create timeseries
tm_list <- samrat_timeseries(pars_list, strata)
names(tm_list)
#> [1] "ts"        "time_list"

This object contains the time series as ts and parameters detailing the start and end of analysis in time_list.