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idem-lab / conmat

Create Contact Matrices from Population Data
https://idem-lab.github.io/conmat/dev/
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How to effectively compare age groups #138

Closed njtierney closed 1 year ago

njtierney commented 1 year ago

Currently within apply_vaccination we just check that certain dimensions match - I think it is better to check that the age breaks are the same, but for this case, I think that these are the same, but I'm not sure what sort of method we would use to compare them - 80+ is the same as c(80, Inf), and is 0-5, 5-10 the same as 0-4, 5-11?

library(conmat)
ngm_nsw <- generate_ngm_oz(
  state_name = "NSW",
  age_breaks = c(seq(0, 80, by = 5), Inf),
  R_target = 1.5
)

age_breaks(ngm_nsw$home)
#>  [1] "[0,5)"    "[5,10)"   "[10,15)"  "[15,20)"  "[20,25)"  "[25,30)" 
#>  [7] "[30,35)"  "[35,40)"  "[40,45)"  "[45,50)"  "[50,55)"  "[55,60)" 
#> [13] "[60,65)"  "[65,70)"  "[70,75)"  "[75,80)"  "[80,Inf)"
vaccination_effect_example_data
#> # A tibble: 17 × 4
#>    age_band coverage acquisition transmission
#>    <chr>       <dbl>       <dbl>        <dbl>
#>  1 0-4         0           0            0    
#>  2 5-11        0.782       0.583        0.254
#>  3 12-15       0.997       0.631        0.295
#>  4 16-19       0.965       0.786        0.469
#>  5 20-24       0.861       0.774        0.453
#>  6 25-29       0.997       0.778        0.458
#>  7 30-34       0.998       0.803        0.493
#>  8 35-39       0.998       0.829        0.533
#>  9 40-44       0.999       0.841        0.551
#> 10 45-49       0.993       0.847        0.562
#> 11 50-54       0.999       0.857        0.579
#> 12 55-59       0.996       0.864        0.591
#> 13 60-64       0.998       0.858        0.581
#> 14 65-69       0.999       0.864        0.591
#> 15 70-74       0.999       0.867        0.597
#> 16 75-79       0.999       0.866        0.595
#> 17 80+         0.999       0.844        0.556

# these two data sources ^^ are used in `apply_vaccination` below:
# Apply vaccination effect to next generation matrices
ngm_nsw_vacc <- apply_vaccination(
  ngm = ngm_nsw,
  data = vaccination_effect_example_data,
  coverage_col = coverage,
  acquisition_col = acquisition,
  transmission_col = transmission
)

Created on 2023-01-17 with reprex v2.0.2

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.1 (2022-06-23) #> os macOS Monterey 12.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Brisbane #> date 2023-01-17 #> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0) #> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.0) #> codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.1) #> colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0) #> conmat * 0.0.1.9000 2023-01-16 [1] local #> countrycode 1.4.0 2022-05-04 [1] CRAN (R 4.2.0) #> curl 4.3.3 2022-10-06 [1] CRAN (R 4.2.0) #> data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.0) #> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0) #> digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.0) #> dotCall64 1.0-2 2022-10-03 [1] CRAN (R 4.2.0) #> dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.2.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.0) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fields 14.1 2022-08-12 [1] CRAN (R 4.2.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) #> furrr 0.3.1 2022-08-15 [1] CRAN (R 4.2.0) #> future 1.29.0 2022-11-06 [1] CRAN (R 4.2.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) #> ggplot2 3.4.0 2022-11-04 [1] CRAN (R 4.2.0) #> globals 0.16.2 2022-11-21 [1] CRAN (R 4.2.1) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0) #> gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) #> hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0) #> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0) #> httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.0) #> jsonlite 1.8.3 2022-10-21 [1] CRAN (R 4.2.0) #> knitr 1.41 2022-11-18 [1] CRAN (R 4.2.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.1) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0) #> listenv 0.8.0 2019-12-05 [1] CRAN (R 4.2.0) #> lubridate 1.9.0 2022-11-06 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> maps 3.4.1 2022-10-30 [1] CRAN (R 4.2.0) #> Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.0) #> mgcv 1.8-41 2022-10-21 [1] CRAN (R 4.2.0) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0) #> nlme 3.1-160 2022-10-10 [1] CRAN (R 4.2.0) #> oai 0.4.0 2022-11-10 [1] CRAN (R 4.2.0) #> parallelly 1.32.1 2022-07-21 [1] CRAN (R 4.2.0) #> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> plyr 1.8.8 2022-11-11 [1] CRAN (R 4.2.0) #> purrr * 0.3.5 2022-10-06 [1] CRAN (R 4.2.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) #> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0) #> readr 2.1.3 2022-10-01 [1] CRAN (R 4.2.0) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0) #> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0) #> rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.0) #> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0) #> scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> socialmixr 0.2.0 2022-10-27 [1] CRAN (R 4.2.0) #> spam 2.9-1 2022-08-07 [1] CRAN (R 4.2.0) #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0) #> stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0) #> styler 1.8.1 2022-11-07 [1] CRAN (R 4.2.0) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) #> tidyr 1.2.1 2022-09-08 [1] CRAN (R 4.2.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0) #> timechange 0.1.1 2022-11-04 [1] CRAN (R 4.2.0) #> tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) #> vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.0) #> viridis 0.6.2 2021-10-13 [1] CRAN (R 4.2.0) #> viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> wpp2017 1.2-3 2020-02-10 [1] CRAN (R 4.2.0) #> xfun 0.35 2022-11-16 [1] CRAN (R 4.2.0) #> xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0) #> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```
njtierney commented 1 year ago

new behaviour

library(conmat)

perth <- abs_age_lga("Perth (C)")
age_breaks_0_75 <- c(seq(0, 75, by = 5), Inf)
age_breaks_0_80 <- c(seq(0, 80, by = 5), Inf)

perth_contact_0_75 <- extrapolate_polymod(
  perth,
  age_breaks = age_breaks_0_75
)

perth_contact_0_75
#> 
#> ── Setting Prediction Matrices ─────────────────────────────────────────────────
#> A list of matrices containing the model predicted contact rate between ages in
#> each setting.
#> There are 16 age breaks, ranging 0-75+ years, with a regular 5 year interval
#> • home: a 16x16 <matrix>
#> • work: a 16x16 <matrix>
#> • school: a 16x16 <matrix>
#> • other: a 16x16 <matrix>
#> • all: a 16x16 <matrix>
#> ℹ Access each <matrix> with `x$name`
#> ℹ e.g., `x$home`

perth_ngm_0_75 <- generate_ngm(perth_contact_0_75,
                               age_breaks = age_breaks_0_75,
                               R_target = 1.5)

# but this doesn't work unless you refit the extrapolated model
perth_ngm_0_80 <- generate_ngm(perth_contact_0_75,
                               age_breaks = age_breaks_0_80,
                               R_target = 1.5)
#> Error in `check_age_breaks()` at conmat/R/generate-ngm.R:130:2:
#> ! Age breaks must be the same, but they are different:
#>          `x[14:17]`: 65 70 75 Inf    
#> `age_breaks[14:18]`: 65 70 75  80 Inf
#> ℹ You can check the age breaks using `age_breaks(<object>)`

#> Backtrace:
#>     ▆
#>  1. ├─conmat::generate_ngm(...)
#>  2. └─conmat:::generate_ngm.conmat_setting_prediction_matrix(...) at conmat/R/generate-ngm.R:101:2
#>  3.   └─conmat:::check_age_breaks(x = age_breaks(x), y = age_breaks, x_arg = "x", y_arg = "age_breaks") at conmat/R/generate-ngm.R:130:2
#>  4.     └─rlang::abort(...) at conmat/R/utils.R:424:4

Created on 2023-03-08 with reprex v2.0.2

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.2 (2022-10-31) #> os macOS Ventura 13.2 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Hobart #> date 2023-03-08 #> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0) #> codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.0) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0) #> conmat * 0.0.2.9000 2023-03-08 [1] local #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0) #> diffobj 0.3.5 2021-10-05 [1] CRAN (R 4.2.0) #> digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0) #> dplyr 1.1.0 2023-01-29 [1] CRAN (R 4.2.1) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0) #> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fs 1.6.1 2023-02-06 [1] CRAN (R 4.2.0) #> furrr 0.3.1 2022-08-15 [1] CRAN (R 4.2.0) #> future 1.31.0 2023-02-01 [1] CRAN (R 4.2.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) #> ggplot2 3.4.1 2023-02-10 [1] CRAN (R 4.2.0) #> globals 0.16.2 2022-11-21 [1] CRAN (R 4.2.1) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0) #> hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0) #> htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.0) #> knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.2) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0) #> listenv 0.9.0 2022-12-16 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.0) #> mgcv 1.8-41 2022-10-21 [1] CRAN (R 4.2.2) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0) #> nlme 3.1-162 2023-01-31 [1] CRAN (R 4.2.0) #> parallelly 1.34.0 2023-01-13 [1] CRAN (R 4.2.0) #> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.2.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) #> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> readr 2.1.3 2022-10-01 [1] CRAN (R 4.2.0) #> rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.2.0) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0) #> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0) #> rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.0) #> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0) #> scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> styler 1.9.0 2023-01-15 [1] CRAN (R 4.2.0) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) #> tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.2.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0) #> tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0) #> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0) #> vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0) #> waldo 0.4.0 2022-03-16 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> xfun 0.37 2023-01-31 [1] CRAN (R 4.2.0) #> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```
njtierney commented 1 year ago

under the hood this uses the internal function check_age_breaks(), which uses waldo::compare()

conmat:::check_age_breaks(
  x = c(1,2,3),
  y = c(1,2,3)
)
conmat:::check_age_breaks(
  x = c(1,2,3,Inf),
  y = c(1,2,3)
)
#> Error in `conmat:::check_age_breaks()`:
#> ! Age breaks must be the same, but they are different:
#> `old`: 1 2 3 Inf
#> `new`: 1 2 3    
#> ℹ You can check the age breaks using `age_breaks(<object>)`

#> Backtrace:
#>     ▆
#>  1. └─conmat:::check_age_breaks(x = c(1, 2, 3, Inf), y = c(1, 2, 3))
#>  2.   └─rlang::abort(...) at conmat/R/utils.R:424:4

Created on 2023-03-08 with reprex v2.0.2

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.2 (2022-10-31) #> os macOS Ventura 13.2 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Hobart #> date 2023-03-08 #> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0) #> conmat 0.0.2.9000 2023-03-08 [1] local #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0) #> diffobj 0.3.5 2021-10-05 [1] CRAN (R 4.2.0) #> digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0) #> dplyr 1.1.0 2023-01-29 [1] CRAN (R 4.2.1) #> evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0) #> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fs 1.6.1 2023-02-06 [1] CRAN (R 4.2.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) #> ggplot2 3.4.1 2023-02-10 [1] CRAN (R 4.2.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0) #> htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.0) #> knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0) #> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) #> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.2.0) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0) #> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0) #> rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.0) #> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0) #> scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> styler 1.9.0 2023-01-15 [1] CRAN (R 4.2.0) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0) #> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0) #> vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0) #> waldo 0.4.0 2022-03-16 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> xfun 0.37 2023-01-31 [1] CRAN (R 4.2.0) #> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```