! no method for `age_breaks()` defined for object of class <setting_contact_model/list> yet

njtierney commented 1 month ago

When trying to fit to a different population data, e.g., Germany, the following error appears.

library(conmat)

extrapolate_polymod
#> function(population,
#>                                 age_breaks = c(seq(0, 75, by = 5), Inf),
#>                                 per_capita_household_size = NULL) {
#>   contact_model_pred <- predict_setting_contacts(
#>     population = population,
#>     # using already fit polymod_setting_models object
#>     # from `create-polymod-model.R`
#>     contact_model = polymod_setting_models,
#>     age_breaks = age_breaks,
#>     per_capita_household_size = per_capita_household_size
#>   )
#> 
#>   contact_model_pred
#> }
#> <bytecode: 0x1211b0978>
#> <environment: namespace:conmat>

germany_polymod_setting_data <- get_polymod_setting_data(countries = "Germany")
germany_polymod_population <- get_polymod_population(countries = "Germany")

germany_contact_setting_model <- fit_setting_contacts(
  contact_data_list = germany_polymod_setting_data,
  population = germany_polymod_population,
)
#> Warning in bgam.fit(G, mf, chunk.size, gp, scale, gamma, method = method, :
#> fitted rates numerically 0 occurred

germany_contact_setting_model
#> Error in `age_breaks()` at conmat/R/utils.R:123:3:
#> ! no method for `age_breaks()` defined for object of class
#>   <setting_contact_model/list> yet

germany_contact_setting_contacts <- predict_setting_contacts(
  population = germany_polymod_population,
  contact_model = germany_contact_setting_model
)
#> Error in predict_setting_contacts(population = germany_polymod_population, : argument "age_breaks" is missing, with no default

^{Created on 2024-05-14 with reprex v2.1.0}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.3 (2024-02-29) #> os macOS Sonoma 14.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Brisbane #> date 2024-05-14 #> pandoc 3.1.13 @ /opt/homebrew/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) #> codetools 0.2-20 2024-03-31 [2] CRAN (R 4.3.1) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0) #> conmat * 0.0.2.9000 2024-01-11 [2] local #> countrycode 1.6.0 2024-03-22 [1] CRAN (R 4.3.1) #> curl 5.2.1 2024-03-01 [1] CRAN (R 4.3.1) #> data.table 1.15.4 2024-03-30 [1] CRAN (R 4.3.1) #> digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1) #> dotCall64 1.1-1 2023-11-28 [2] CRAN (R 4.3.1) #> dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.1) #> evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1) #> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) #> fields 15.2 2023-08-17 [2] CRAN (R 4.3.0) #> fs 1.6.4 2024-04-25 [1] CRAN (R 4.3.1) #> furrr 0.3.1 2022-08-15 [2] CRAN (R 4.3.0) #> future 1.33.2 2024-03-26 [1] CRAN (R 4.3.1) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) #> ggplot2 3.5.0 2024-02-23 [1] CRAN (R 4.3.1) #> globals 0.16.3 2024-03-08 [1] CRAN (R 4.3.1) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) #> gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0) #> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1) #> httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0) #> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1) #> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1) #> lattice 0.22-6 2024-03-20 [1] CRAN (R 4.3.1) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) #> listenv 0.9.1 2024-01-29 [2] CRAN (R 4.3.1) #> lubridate 1.9.3 2023-09-27 [1] CRAN (R 4.3.1) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) #> maps 3.4.2 2023-12-15 [2] CRAN (R 4.3.1) #> Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.1) #> mgcv 1.9-1 2023-12-21 [1] CRAN (R 4.3.1) #> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.3.1) #> nlme 3.1-164 2023-11-27 [1] CRAN (R 4.3.1) #> oai 0.4.0 2022-11-10 [2] CRAN (R 4.3.0) #> parallelly 1.37.1 2024-02-29 [1] CRAN (R 4.3.1) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) #> plyr 1.8.9 2023-10-02 [1] CRAN (R 4.3.1) #> purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) #> R.cache 0.16.0 2022-07-21 [2] CRAN (R 4.3.0) #> R.methodsS3 1.8.2 2022-06-13 [2] CRAN (R 4.3.0) #> R.oo 1.26.0 2024-01-24 [2] CRAN (R 4.3.1) #> R.utils 2.12.3 2023-11-18 [2] CRAN (R 4.3.1) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1) #> reprex 2.1.0 2024-01-11 [2] CRAN (R 4.3.1) #> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) #> rmarkdown 2.26 2024-03-05 [1] CRAN (R 4.3.1) #> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.1) #> scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1) #> sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.3.0) #> socialmixr 0.3.2 2024-04-18 [2] CRAN (R 4.3.1) #> spam 2.10-0 2023-10-23 [2] CRAN (R 4.3.1) #> stringi 1.8.4 2024-05-06 [1] CRAN (R 4.3.1) #> stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.1) #> styler 1.10.3 2024-04-07 [2] CRAN (R 4.3.1) #> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) #> tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.1) #> tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.1) #> timechange 0.3.0 2024-01-18 [1] CRAN (R 4.3.1) #> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) #> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) #> viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) #> wpp2017 1.2-3 2020-02-10 [1] CRAN (R 4.3.0) #> xfun 0.43 2024-03-25 [1] CRAN (R 4.3.1) #> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.1) #> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1) #> #> [1] /Users/nick/Library/R/arm64/4.3/library #> [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```

njtierney commented 2 weeks ago

This actually happens whenever printing a setting contact model:

library(conmat)
small_setting_data <- get_polymod_setting_data()
options(tidyverse.quiet = TRUE)
library(tidyverse)
small_setting_data <- small_setting_data |> 
  map(\(x) filter(x, age_to <= 20, age_from <= 20)) |> 
  conmat:::new_setting_data()

small_setting_data
#> 
#> ── Setting Data ────────────────────────────────────────────────────────────────
#> A list of <data.frame>s containing the number of contacts between ages in each
#> setting.
#> There are 20 age breaks, ranging 0-20 years, with a regular 1 year interval
#> • home: a 441x5 <data.frame>
#> • work: a 441x5 <data.frame>
#> • school: a 441x5 <data.frame>
#> • other: a 441x5 <data.frame>
#> ℹ Access each <data.frame> with `x$name`
#> ℹ e.g., `x$home`


contact_model <- fit_setting_contacts(
  contact_data_list = small_setting_data,
  population = get_polymod_population()
)

contact_model
#> Error in `age_breaks()` at conmat/R/utils.R:123:3:
#> ! no method for `age_breaks()` defined for object of class
#>   <setting_contact_model/list> yet

^{Created on 2024-06-19 with reprex v2.1.0}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.4.0 (2024-04-24) #> os macOS Sonoma 14.5 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Hobart #> date 2024-06-19 #> pandoc 3.1.13 @ /opt/homebrew/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0) #> codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.0) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.4.0) #> conmat * 0.0.2.9000 2024-05-31 [1] local #> countrycode 1.6.0 2024-03-22 [1] CRAN (R 4.4.0) #> curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0) #> data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0) #> digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0) #> dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.4.0) #> dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0) #> evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0) #> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0) #> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0) #> fields 15.2 2023-08-17 [1] CRAN (R 4.4.0) #> forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.4.0) #> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0) #> furrr 0.3.1 2022-08-15 [1] CRAN (R 4.4.0) #> future 1.33.2 2024-03-26 [1] CRAN (R 4.4.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0) #> ggplot2 * 3.5.1 2024-04-23 [1] CRAN (R 4.4.0) #> globals 0.16.3 2024-03-08 [1] CRAN (R 4.4.0) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0) #> gtable 0.3.5 2024-04-22 [1] CRAN (R 4.4.0) #> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0) #> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0) #> httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0) #> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0) #> knitr 1.46 2024-04-06 [1] CRAN (R 4.4.0) #> lattice 0.22-6 2024-03-20 [2] CRAN (R 4.4.0) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0) #> listenv 0.9.1 2024-01-29 [1] CRAN (R 4.4.0) #> lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.4.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0) #> maps 3.4.2 2023-12-15 [1] CRAN (R 4.4.0) #> Matrix 1.7-0 2024-03-22 [2] CRAN (R 4.4.0) #> mgcv 1.9-1 2023-12-21 [2] CRAN (R 4.4.0) #> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0) #> nlme 3.1-164 2023-11-27 [2] CRAN (R 4.4.0) #> oai 0.4.0 2022-11-10 [1] CRAN (R 4.4.0) #> parallelly 1.37.1 2024-02-29 [1] CRAN (R 4.4.0) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0) #> plyr 1.8.9 2023-10-02 [1] CRAN (R 4.4.0) #> purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.4.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.4.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.4.0) #> R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.4.0) #> R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.4.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0) #> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0) #> readr * 2.1.5 2024-01-10 [1] CRAN (R 4.4.0) #> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.4.0) #> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0) #> rmarkdown 2.26 2024-03-05 [1] CRAN (R 4.4.0) #> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0) #> scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0) #> socialmixr 0.3.2 2024-04-18 [1] CRAN (R 4.4.0) #> spam 2.10-0 2023-10-23 [1] CRAN (R 4.4.0) #> stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0) #> stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.4.0) #> styler 1.10.3 2024-04-07 [1] CRAN (R 4.4.0) #> tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.4.0) #> tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.4.0) #> tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0) #> tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.4.0) #> timechange 0.3.0 2024-01-18 [1] CRAN (R 4.4.0) #> tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.4.0) #> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0) #> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0) #> viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.4.0) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0) #> wpp2017 1.2-3 2020-02-10 [1] CRAN (R 4.4.0) #> xfun 0.44 2024-05-15 [1] CRAN (R 4.4.0) #> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0) #> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.4.0) #> #> [1] /Users/nick/Library/R/arm64/4.4/library #> [2] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```

So I need to update the print method so it doesn't look for age breaks, or somehow add them in.

njtierney commented 2 weeks ago

Also add a snapshot test for this print method

idem-lab / conmat

! no method for `age_breaks()` defined for object of class <setting_contact_model/list> yet #160