njtierney
commented
3 years ago wrote some new helper functions, strangely this works...
library(yahtsee)
#> Loading required package: tsibble
#>
#> Attaching package: 'tsibble'
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, union
hts_form <- pr ~ avg_lower_age + hts(who_subregion, country)
bru_form <- build_bru_formula(
formula = hts_form,
.data = malaria_africa_ts,
special_index = month_num
)
bru_form
#> pr ~ avg_lower_age + (who_subregion(month_num, model = "ar1",
#> group = .who_subregion_id, constr = FALSE) + country(month_num,
#> model = "ar1", group = .country_id, constr = FALSE))
#> <environment: 0x7fd707e5b1d8>
data_w_groups <- create_hts_data(
.data = malaria_africa_ts,
formula = hts_form
)
data_w_groups
#> # A tsibble: 1,046 x 17 [1D]
#> # Key: country [46]
#> who_region who_subregion country date month_num positive examined
#> <fct> <fct> <fct> <date> <dbl> <dbl> <int>
#> 1 AFRO AFRO-W Angola 1989-06-01 120 15.8 50
#> 2 AFRO AFRO-W Angola 2005-11-01 372 82 111
#> 3 AFRO AFRO-W Angola 2006-04-01 300 102 197
#> 4 AFRO AFRO-W Angola 2006-11-01 384 41 347
#> 5 AFRO AFRO-W Angola 2006-12-01 396 173 734
#> 6 AFRO AFRO-W Angola 2007-01-01 276 216 828
#> 7 AFRO AFRO-W Angola 2007-02-01 288 42 71
#> 8 AFRO AFRO-W Angola 2007-03-01 300 119 448
#> 9 AFRO AFRO-W Angola 2011-01-01 324 1 239
#> 10 AFRO AFRO-W Angola 2011-02-01 336 148 1132
#> # … with 1,036 more rows, and 10 more variables: pr <dbl>, avg_lower_age <dbl>,
#> # continent_id <fct>, country_id <fct>, year <int>, month <int>,
#> # avg_upper_age <dbl>, species <fct>, .who_subregion_id <int>,
#> # .country_id <int>
bru_model <- inlabru::bru(
bru_form,
family = "gaussian",
data = data_w_groups
)Created on 2021-06-17 by the reprex package (v2.0.0)
Created on 2021-06-17 by the reprex package (v2.0.0)
Session info
``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.1.0 (2021-05-18) #> os macOS Big Sur 10.16 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> ctype en_AU.UTF-8 #> tz Australia/Perth #> date 2021-06-17 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib source #> anytime 0.3.9 2020-08-27 [1] CRAN (R 4.1.0) #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) #> backports 1.2.1 2020-12-09 [1] CRAN (R 4.1.0) #> cli 2.5.0.9000 2021-06-14 [1] Github (r-lib/cli@571fea6) #> colorspace 2.0-1 2021-05-04 [1] CRAN (R 4.1.0) #> crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.0) #> DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0) #> digest 0.6.27 2020-10-24 [1] CRAN (R 4.1.0) #> dplyr 1.0.6 2021-05-05 [1] CRAN (R 4.1.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) #> evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0) #> fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0) #> formula.tools 1.7.1 2018-03-01 [1] CRAN (R 4.1.0) #> fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0) #> generics 0.1.0 2020-10-31 [1] CRAN (R 4.1.0) #> ggplot2 3.3.3 2020-12-30 [1] CRAN (R 4.1.0) #> glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0) #> gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.1.0) #> htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0) #> INLA 21.05.02 2021-05-03 [1] local #> inlabru 2.3.1 2021-03-22 [1] CRAN (R 4.1.0) #> knitr 1.33 2021-04-24 [1] CRAN (R 4.1.0) #> lattice 0.20-44 2021-05-02 [1] CRAN (R 4.1.0) #> lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.1.0) #> lubridate 1.7.10 2021-02-26 [1] CRAN (R 4.1.0) #> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0) #> Matrix 1.3-4 2021-06-01 [1] CRAN (R 4.1.0) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) #> operator.tools 1.6.3 2017-02-28 [1] CRAN (R 4.1.0) #> pillar 1.6.1 2021-05-16 [1] CRAN (R 4.1.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0) #> R6 2.5.0 2020-10-28 [1] CRAN (R 4.1.0) #> Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.1.0) #> reprex 2.0.0 2021-04-02 [1] CRAN (R 4.1.0) #> rlang 0.4.11 2021-04-30 [1] CRAN (R 4.1.0) #> rmarkdown 2.8 2021-05-07 [1] CRAN (R 4.1.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0) #> scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0) #> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0) #> sp 1.4-5 2021-01-10 [1] CRAN (R 4.1.0) #> stringi 1.6.2 2021-05-17 [1] CRAN (R 4.1.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) #> styler 1.4.1 2021-03-30 [1] CRAN (R 4.1.0) #> tibble 3.1.2 2021-05-16 [1] CRAN (R 4.1.0) #> tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0) #> tsibble * 1.0.1 2021-04-12 [1] CRAN (R 4.1.0) #> utf8 1.2.1 2021-03-12 [1] CRAN (R 4.1.0) #> vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0) #> withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0) #> xfun 0.23 2021-05-15 [1] CRAN (R 4.1.0) #> yahtsee * 0.0.0.9000 2021-06-17 [1] local #> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library ```