Generates simulations of expected mortality by simulating the model coefficients.
Source:R/sim.R
sim.RdWith the given fit from fit_attrib the function sim, from package arm, is used to generate 500 simulations of all the coefficients, from there respective posterior distributions. This is then used to compute the expected response for all simulations and rows in the input dataset.
Arguments
- fit
A model fit created by fit_attrib
- data
The data with either observed values or reference values.
- n_sim
Number of simulations
- PI
Returns a draw from the quasipoisson distribution with the calculated mean as mean. If false the exponential of the mean is returned.
Examples
response <- "deaths_n"
fixef <- "ili_isoweekmean7_13_pr100 +
sin(2 * pi * (isoweek - 1) / 52) +
cos(2 * pi * (isoweek - 1) / 52)"
ranef <- " (ili_isoweekmean7_13_pr100| season)"
offset <- "log(pop_jan1_n)"
data <- attrib::data_fake_attrib_nation
fit <- fit_attrib(data = data, response = response, fixef = fixef, ranef = ranef, offset = offset)
#> boundary (singular) fit: see help('isSingular')
n_sim <- 5
sim(fit, data, n_sim)
#> location_code isoyear isoweek isoyearweek season seasonweek pop_jan1_n
#> 1: nation_nor 2009 30 2009-30 2009/2010 1 5367580
#> 2: nation_nor 2009 31 2009-31 2009/2010 2 5367580
#> 3: nation_nor 2009 32 2009-32 2009/2010 3 5367580
#> 4: nation_nor 2009 33 2009-33 2009/2010 4 5367580
#> 5: nation_nor 2009 34 2009-34 2009/2010 5 5367580
#> ---
#> 2866: nation_nor 2020 25 2020-25 2019/2020 48 5367580
#> 2867: nation_nor 2020 26 2020-26 2019/2020 49 5367580
#> 2868: nation_nor 2020 27 2020-27 2019/2020 50 5367580
#> 2869: nation_nor 2020 28 2020-28 2019/2020 51 5367580
#> 2870: nation_nor 2020 29 2020-29 2019/2020 52 5367580
#> ili_isoweekmean0_6_pr100 ili_isoweekmean7_13_pr100 heatwavedays_n
#> 1: 8.989140e-07 0.000000e+00 0.81818182
#> 2: 2.524744e-06 8.989140e-07 0.54545455
#> 3: 6.818846e-06 2.524744e-06 0.36363636
#> 4: 1.771046e-05 6.818846e-06 0.54545455
#> 5: 4.423928e-05 1.771046e-05 0.36363636
#> ---
#> 2866: 2.433569e-03 4.808987e-03 0.00000000
#> 2867: 1.184660e-03 2.433569e-03 0.18181818
#> 2868: 5.547034e-04 1.184660e-03 0.36363636
#> 2869: 2.498084e-04 5.547034e-04 0.09090909
#> 2870: 1.081928e-04 2.498084e-04 0.90909091
#> deaths_n id_row sim_id sim_value
#> 1: 827 1 1 792.2449
#> 2: 751 2 1 793.7380
#> 3: 811 3 1 795.4706
#> 4: 787 4 1 797.4188
#> 5: 828 5 1 799.5561
#> ---
#> 2866: 791 570 5 780.3430
#> 2867: 787 571 5 780.3696
#> 2868: 785 572 5 780.8801
#> 2869: 754 573 5 781.8429
#> 2870: 770 574 5 783.2312