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

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njtierney opened this issue May 14, 2024 · 2 comments
Open

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

njtierney opened this issue May 14, 2024 · 2 comments
Milestone
0.1.0

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@njtierney
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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 
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
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Collaborator Author

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 
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
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Also add a snapshot test for this print method

njtierney added a commit that referenced this issue Jun 20, 2024
@njtierney
Working on resolving #160
0ecd8cd 
* exports `new_ngm_setting_matrix()` and `new_setting_data()`
* Exports new `age_breaks()` method for class `setting_contact_model` (used in `fit_setting_contacts()`).
njtierney added a commit that referenced this issue Jun 20, 2024
@njtierney
Merge pull request #165 from idem-lab/fix-age-breaks-160
419c9ba 
Working on resolving #160
@njtierney njtierney added this to the 0.1.0 milestone Jul 2, 2024
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