Data Sources

We provide access to a variety of different data sources in conmat. Most of these are centred around Australian data, as the package was initially created for disease modelling work in Australia. The aim of this vignette is to give a quick tour of the data sources available in conmat.

library(conmat)

World data

We provide functions to clean up world population data from socialmixr.

world_data <- socialmixr::wpp_age()

head(world_data)
#>   country lower.age.limit year population
#> 1  AFRICA               0 1950   38705049
#> 2  AFRICA               0 1955   44304214
#> 3  AFRICA               0 1960   50491493
#> 4  AFRICA               0 1965   57690110
#> 5  AFRICA               0 1970   65452837
#> 6  AFRICA               0 1975   75017430

We can tidy the data up, filtering down to a specified location and year with the age_population function:

nz_2015 <- age_population(
  data = world_data,
  location_col = country,
  location = "New Zealand",
  age_col = lower.age.limit,
  year_col = year,
  year = 2015
)

nz_2015
#> # A tibble: 21 × 5 (conmat_population)
#>  - age: lower.age.limit
#>  - population: population
#>    country      year population lower.age.limit upper.age.limit
#>    <chr>       <int>      <dbl>           <dbl>           <dbl>
#>  1 New Zealand  2015     308681               0               4
#>  2 New Zealand  2015     315632               5               9
#>  3 New Zealand  2015     297247              10              14
#>  4 New Zealand  2015     318932              15              19
#>  5 New Zealand  2015     339362              20              24
#>  6 New Zealand  2015     315914              25              29
#>  7 New Zealand  2015     287537              30              34
#>  8 New Zealand  2015     273539              35              39
#>  9 New Zealand  2015     312245              40              44
#> 10 New Zealand  2015     313312              45              49
#> # ℹ 11 more rows

This returns a conmat_population object, which is a data frame that knows which columns represent age and population information. This is useful for other modelling parts of the conmat package.

Australian Bureau of Statistics (ABS) data

Accessing Functions

We provide two functions to access LGA (Local Government Area), and state level population age data, which are provided in 5 year age bins from 0, 5, up to 85+. These data are conmat_population tibbles, which means that they know which columns represent the age and population information. This means that functions inside of conmat can work a bit smoother as we refer to these columns frequently.

abs_age_lga()

fairfield <- abs_age_lga(lga_name = "Fairfield (C)")
fairfield
#> # A tibble: 18 × 4 (conmat_population)
#>  - age: lower.age.limit
#>  - population: population
#>    lga           lower.age.limit  year population
#>    <chr>                   <dbl> <dbl>      <dbl>
#>  1 Fairfield (C)               0  2020      12261
#>  2 Fairfield (C)               5  2020      13093
#>  3 Fairfield (C)              10  2020      13602
#>  4 Fairfield (C)              15  2020      14323
#>  5 Fairfield (C)              20  2020      15932
#>  6 Fairfield (C)              25  2020      16190
#>  7 Fairfield (C)              30  2020      14134
#>  8 Fairfield (C)              35  2020      13034
#>  9 Fairfield (C)              40  2020      12217
#> 10 Fairfield (C)              45  2020      13449
#> 11 Fairfield (C)              50  2020      13419
#> 12 Fairfield (C)              55  2020      13652
#> 13 Fairfield (C)              60  2020      12907
#> 14 Fairfield (C)              65  2020      10541
#> 15 Fairfield (C)              70  2020       8227
#> 16 Fairfield (C)              75  2020       5598
#> 17 Fairfield (C)              80  2020       4006
#> 18 Fairfield (C)              85  2020       4240

Note that this is a conmat_population object, which prints in red at the top of the data frame. This provides the information on the age and population columns, stating: age: lower.age.limit, and population: population, indicating which columns refer to the appropriate variables.

Also note that abs_age_lga requires you to know the exact name of the LGA, you can see them in the dataset, abs_lga_lookup

abs_lga_lookup
#> # A tibble: 544 × 3
#>    state lga_code lga                  
#>    <chr>    <dbl> <chr>                
#>  1 NSW      10050 Albury (C)           
#>  2 NSW      10180 Armidale Regional (A)
#>  3 NSW      10250 Ballina (A)          
#>  4 NSW      10300 Balranald (A)        
#>  5 NSW      10470 Bathurst Regional (A)
#>  6 NSW      10500 Bayside (A)          
#>  7 NSW      10550 Bega Valley (A)      
#>  8 NSW      10600 Bellingen (A)        
#>  9 NSW      10650 Berrigan (A)         
#> 10 NSW      10750 Blacktown (C)        
#> # ℹ 534 more rows

And if you’re not sure about a particular name of a place, you can use agrep and filter, to match on similar-ish characters, like so:

library(dplyr)
abs_lga_lookup %>%
  filter(agrepl("Sydney", lga))
#> # A tibble: 2 × 3
#>   state lga_code lga             
#>   <chr>    <dbl> <chr>           
#> 1 NSW      15950 North Sydney (A)
#> 2 NSW      17200 Sydney (C)

abs_age_state()

This takes in the abbreviated state names, and is also a conmat_population object.

abs_age_state(state_name = "NSW")
#> # A tibble: 18 × 4 (conmat_population)
#>  - age: lower.age.limit
#>  - population: population
#>     year state lower.age.limit population
#>    <dbl> <chr>           <dbl>      <dbl>
#>  1  2020 NSW                 0     495091
#>  2  2020 NSW                 5     512778
#>  3  2020 NSW                10     500881
#>  4  2020 NSW                15     468550
#>  5  2020 NSW                20     540233
#>  6  2020 NSW                25     607891
#>  7  2020 NSW                30     611590
#>  8  2020 NSW                35     582824
#>  9  2020 NSW                40     512803
#> 10  2020 NSW                45     527098
#> 11  2020 NSW                50     484708
#> 12  2020 NSW                55     495116
#> 13  2020 NSW                60     461329
#> 14  2020 NSW                65     404034
#> 15  2020 NSW                70     355280
#> 16  2020 NSW                75     253241
#> 17  2020 NSW                80     174990
#> 18  2020 NSW                85     179095

You can see these state names with:

unique(abs_lga_lookup$state)
#> [1] "NSW" "VIC" "QLD" "SA"  "WA"  "TAS" "NT"  "ACT" "OT"

Note that “OT” stands for “other territories”

ABS data

We provide other ABS data, listed now. You can read the full details of the data at their respective helpfiles, by writing, for example, ?abs_education_state.

Education by state data for 2006 -2020

abs_education_state
#> # A tibble: 4,194 × 5
#>     year state aboriginal_and_torres_strait_islande…¹   age n_full_and_part_time
#>    <dbl> <chr> <chr>                                  <dbl>                <dbl>
#>  1  2006 ACT   Aboriginal and Torres Strait Islander      4                    5
#>  2  2006 ACT   Non-Indigenous                             4                  109
#>  3  2006 NSW   Aboriginal and Torres Strait Islander      4                  104
#>  4  2006 NSW   Non-Indigenous                             4                 1870
#>  5  2006 NT    Aboriginal and Torres Strait Islander      4                  102
#>  6  2006 NT    Non-Indigenous                             4                   63
#>  7  2006 QLD   Aboriginal and Torres Strait Islander      4                   37
#>  8  2006 QLD   Non-Indigenous                             4                  740
#>  9  2006 SA    Aboriginal and Torres Strait Islander      4                   42
#> 10  2006 SA    Non-Indigenous                             4                 1023
#> # ℹ 4,184 more rows
#> # ℹ abbreviated name: ¹​aboriginal_and_torres_strait_islander_status

Education by state data for 2020

abs_education_state_2020
#> # A tibble: 808 × 6
#>     year state   age population population_interpolated  prop
#>    <dbl> <chr> <dbl>      <dbl>                   <dbl> <dbl>
#>  1  2020 ACT       0          0                   5569. 0    
#>  2  2020 ACT       1          0                   5702. 0    
#>  3  2020 ACT       2          0                   5781. 0    
#>  4  2020 ACT       3          0                   5814. 0    
#>  5  2020 ACT       4          0                   5809. 0    
#>  6  2020 ACT       5       4558                   5772. 0.790
#>  7  2020 ACT       6       6161                   5710. 1.08 
#>  8  2020 ACT       7       6163                   5623. 1.10 
#>  9  2020 ACT       8       5881                   5510. 1.07 
#> 10  2020 ACT       9       5921                   5370. 1.10 
#> # ℹ 798 more rows

Employment by LGA for 2016

abs_employ_age_lga
#> # A tibble: 5,600 × 8
#>     year state lga                   age_group total_employed total_unemployed
#>    <dbl> <chr> <chr>                 <fct>              <dbl>            <dbl>
#>  1  2016 NSW   Albury (C)            15-19               1527              300
#>  2  2016 NSW   Armidale Regional (A) 15-19                838              217
#>  3  2016 NSW   Ballina (A)           15-19               1064              185
#>  4  2016 NSW   Balranald (A)         15-19                 41                9
#>  5  2016 NSW   Bathurst Regional (A) 15-19               1103              241
#>  6  2016 NSW   Bega Valley (A)       15-19                801               97
#>  7  2016 NSW   Bellingen (A)         15-19                241               42
#>  8  2016 NSW   Berrigan (A)          15-19                168               16
#>  9  2016 NSW   Blacktown (C)         15-19               7534             2136
#> 10  2016 NSW   Bland (A)             15-19                124               14
#> # ℹ 5,590 more rows
#> # ℹ 2 more variables: total_labour_force <dbl>, total <dbl>

Number of people in each household by LGA for 2016

abs_household_lga
#> # A tibble: 4,968 × 5
#>     year state lga                   n_persons_usually_resident n_households
#>    <dbl> <chr> <chr>                 <chr>                             <dbl>
#>  1  2016 NSW   Albury (C)            total                             19495
#>  2  2016 NSW   Albury (C)            1                                  6020
#>  3  2016 NSW   Albury (C)            2                                  6738
#>  4  2016 NSW   Albury (C)            3                                  2740
#>  5  2016 NSW   Albury (C)            4                                  2541
#>  6  2016 NSW   Albury (C)            5                                  1041
#>  7  2016 NSW   Albury (C)            6                                   311
#>  8  2016 NSW   Albury (C)            7                                    56
#>  9  2016 NSW   Albury (C)            8+                                   42
#> 10  2016 NSW   Armidale Regional (A) total                             10276
#> # ℹ 4,958 more rows

LGA age population for 2016 for all states and LGAs

abs_pop_age_lga_2016
#> # A tibble: 9,792 × 5
#>     year state lga                age_group population
#>    <dbl> <chr> <chr>              <fct>          <dbl>
#>  1  2016 ACT   Unincorporated ACT 0-4            28054
#>  2  2016 ACT   Unincorporated ACT 5-9            25767
#>  3  2016 ACT   Unincorporated ACT 10-14          22170
#>  4  2016 ACT   Unincorporated ACT 15-19          24906
#>  5  2016 ACT   Unincorporated ACT 20-24          32615
#>  6  2016 ACT   Unincorporated ACT 25-29          34243
#>  7  2016 ACT   Unincorporated ACT 30-34          34574
#>  8  2016 ACT   Unincorporated ACT 35-39          30340
#>  9  2016 ACT   Unincorporated ACT 40-44          28387
#> 10  2016 ACT   Unincorporated ACT 45-49          26431
#> # ℹ 9,782 more rows

LGA age population for 2020 for all states and LGAs

abs_pop_age_lga_2020
#> # A tibble: 9,774 × 5
#>     year state lga                age_group population
#>    <dbl> <chr> <chr>              <fct>          <dbl>
#>  1  2020 ACT   Unincorporated ACT 0-4            27861
#>  2  2020 ACT   Unincorporated ACT 5-9            28871
#>  3  2020 ACT   Unincorporated ACT 10-14          26015
#>  4  2020 ACT   Unincorporated ACT 15-19          23867
#>  5  2020 ACT   Unincorporated ACT 20-24          32626
#>  6  2020 ACT   Unincorporated ACT 25-29          33992
#>  7  2020 ACT   Unincorporated ACT 30-34          35734
#>  8  2020 ACT   Unincorporated ACT 35-39          35354
#>  9  2020 ACT   Unincorporated ACT 40-44          30155
#> 10  2020 ACT   Unincorporated ACT 45-49          29103
#> # ℹ 9,764 more rows

State age population for 2020

abs_state_age
#> # A tibble: 168 × 3
#>    state age_group population
#>    <chr> <fct>          <dbl>
#>  1 NSW   0-4           495060
#>  2 VIC   0-4           401992
#>  3 QLD   0-4           314592
#>  4 SA    0-4            98400
#>  5 WA    0-4           171531
#>  6 TAS   0-4            29258
#>  7 NT    0-4            17766
#>  8 ACT   0-4            27846
#>  9 NSW   5-9           512687
#> 10 VIC   5-9           416633
#> # ℹ 158 more rows

Epidemiology / disease modelling data

Transmission probabilities from Eyre

A dataset containing data digitised from “The impact of SARS-CoV-2 vaccination on Alpha & Delta variant transmission”, by David W Eyre, Donald Taylor, Mark Purver, David Chapman, Tom Fowler, Koen B Pouwels, A Sarah Walker, Tim EA Peto

eyre_transmission_probabilities
#> # A tibble: 40,804 × 6
#>    setting   case_age contact_age case_age_5y contact_age_5y probability
#>    <chr>        <int>       <int> <chr>       <chr>                <dbl>
#>  1 household        0           0 0-4         0-4                  0.195
#>  2 household        0           1 0-4         0-4                  0.195
#>  3 household        0           2 0-4         0-4                  0.195
#>  4 household        0           3 0-4         0-4                  0.195
#>  5 household        0           4 0-4         0-4                  0.195
#>  6 household        0           5 0-4         5-9                  0.196
#>  7 household        0           6 0-4         5-9                  0.198
#>  8 household        0           7 0-4         5-9                  0.198
#>  9 household        0           8 0-4         5-9                  0.199
#> 10 household        0           9 0-4         5-9                  0.201
#> # ℹ 40,794 more rows

We can visualise the data like so:

library(ggplot2)
library(stringr)
library(dplyr)
eyre_transmission_probabilities %>%
  group_by(
    setting,
    case_age_5y,
    contact_age_5y
  ) %>%
  summarise(
    across(
      probability,
      mean
    ),
    .groups = "drop"
  ) %>%
  rename(
    case_age = case_age_5y,
    contact_age = contact_age_5y
  ) %>%
  mutate(
    across(
      ends_with("age"),
      ~ factor(.x,
        levels = str_sort(
          unique(.x),
          numeric = TRUE
        )
      )
    )
  ) %>%
  ggplot(
    aes(
      x = case_age,
      y = contact_age,
      fill = probability
    )
  ) +
  facet_wrap(~setting) +
  geom_tile() +
  scale_fill_viridis_c() +
  coord_fixed() +
  theme_minimal() +
  theme(
    axis.text = element_text(angle = 45, hjust = 1)
  )