tests/testthat/_snaps/matrix.md

In sbfnk/socialmixr: Social Mixing Matrices for Infectious Disease Modelling

contact matrices look as expected

Code
  contacts
Output
  $test1
  $test1$matrix
           contact.age.group
  age.group      [0,5)     [5,10)     [10,15)    [15,20)    [20,25)     [25,30)
    [0,5)   183.997718  91.069386  46.5576553  31.088569  42.865507  75.2263424
    [5,10)   65.701661 682.253071 134.1139995  34.726523  30.789586  67.2116267
    [10,15)  41.989012 110.824190 707.6366749 106.062186  21.923083  45.1172068
    [15,20)  25.041289  76.227897 160.8464231 707.291536  98.255991  77.9876133
    [20,25)  27.186368  36.415092  16.0317672  93.051886 153.702056  75.9322299
    [25,30)  42.979000  44.367504  17.9306992  43.040950  87.000388 108.0798010
    [30,35)  39.751754  57.440637  28.9813815  24.782785  44.596600  58.2730707
    [35,40)  58.273390  97.171971  52.8985813  38.898581  43.902991  50.2292945
    [40,45)  15.099138  56.134187  62.2483455  53.077107  48.478666  46.1301811
    [45,50)  12.016897   9.028162  38.5181829  64.152075  47.943676  47.4843884
    [50,55)  23.502479  20.165840  20.8134295  45.958540  58.020730  58.0829202
    [55,60)  10.643803  11.724234  23.8827996  15.797772  32.986212  46.8713094
    [60,65)  12.835875  33.216645  18.2250856  12.959672  35.000938  44.2063285
    [65,70)   6.958540  12.958540  10.8548896  12.896350  10.020730  20.2902208
    [70,75)   2.980342   3.042125   9.0645910  16.101099   8.632112   8.9410256
    75+       0.000000   1.911419   0.9557096   2.929135   1.017716   0.9557096
           contact.age.group
  age.group    [30,35)    [35,40)    [40,45)    [45,50)   [50,55)   [55,60)
    [0,5)    92.616701  97.731513  52.196820  28.144334 31.213221 28.606361
    [5,10)  108.920564  99.722278 101.814448  54.782310 38.910862 20.947245
    [10,15)  62.765586 129.842424 116.432200  57.967036 41.465164 26.260053
    [15,20)  51.991742 114.086707  99.396374  80.727493 43.152769 35.268378
    [20,25)  52.321908  44.769158  42.655855  56.574319 25.973527 22.834810
    [25,30)  70.122851  55.887649  52.130202  55.056701 49.848798 31.087151
    [30,35) 100.000000  92.223421  49.291689  33.888289 36.173772 41.204803
    [35,40)  62.141104 105.216066  85.594325  56.246933 43.136695 36.933857
    [40,45)  63.515718  81.945925  83.921891  81.697579 44.154215 34.026036
    [45,50)  50.349210  60.270356  70.377372 103.687156 52.383005 28.287254
    [50,55)  61.020730  54.647589  59.601172  40.331681 49.331681 53.440288
    [55,60)  32.551881  37.121796  35.607034  43.232103 57.303342 62.669081
    [60,65)  50.178193  67.573031  62.369516  39.956859 39.250408 56.088159
    [65,70)  16.854890  25.668319  22.020730  16.207301 15.124380 23.352411
    [70,75)   3.994383   3.042125  19.971917  16.101099 10.016850  8.050549
    75+       2.867129   2.929135   3.946852   1.017716  6.937993  1.973426
           contact.age.group
  age.group   [60,65)   [65,70)    [70,75)       75+
    [0,5)   25.324752  9.144334 10.1049704  2.944234
    [5,10)  25.961192 10.919351  5.9672555  8.765331
    [10,15) 19.043953 12.139183  9.7216339 10.868142
    [15,20) 25.041289 20.851360  5.0825779  5.913293
    [20,25) 10.967174 10.904698  3.9142285  9.816809
    [25,30) 19.902349 12.970600  6.0388505  4.005250
    [30,35) 24.198597  8.148948  4.9689692  3.888289
    [35,40) 26.739839 21.154333 15.0132285 13.691334
    [40,45) 28.930904 13.893852 13.1231714 18.032045
    [45,50) 30.197135  7.056324 11.8310273 26.836660
    [50,55) 27.248761 14.103650 18.2487607 16.854890
    [55,60) 42.089624 14.841435  9.8736074 31.135585
    [60,65) 43.004689 24.135051 13.0215707 18.101289
    [65,70) 22.730509 18.771969  8.8134295 11.041460
    [70,75) 12.044933 18.067399 13.1825397 19.143223
    75+      4.902561  0.000000  0.9557096  6.044290

  $test1$participants
      age.group participants  proportion
         <char>        <int>       <num>
   1:     [0,5)           95 0.093966370
   2:    [5,10)          102 0.100890208
   3:   [10,15)          102 0.100890208
   4:   [15,20)          105 0.103857567
   5:   [20,25)           59 0.058358061
   6:   [25,30)           59 0.058358061
   7:   [30,35)           60 0.059347181
   8:   [35,40)           70 0.069238378
   9:   [40,45)           62 0.061325420
  10:   [45,50)           55 0.054401583
  11:   [50,55)           66 0.065281899
  12:   [55,60)           54 0.053412463
  13:   [60,65)           66 0.065281899
  14:   [65,70)           27 0.026706231
  15:   [70,75)           22 0.021760633
  16:       75+            7 0.006923838


  $test2
  $test2$matrix
           contact.age.group
  age.group     [0,5)        5+
      [0,5) 1.5429448  7.027931
      5+    0.3673316 13.474102

  $test2$demography
     age.group population proportion  year
        <char>      <num>      <num> <int>
  1:     [0,5)   13498647 0.04967121  2005
  2:        5+  258261321 0.95032879  2005

  $test2$participants
     age.group participants proportion
        <char>        <int>      <num>
  1:     [0,5)          654  0.0908712
  2:        5+         6543  0.9091288


  $test3
  $test3$mean.contacts
  [1] 3.887154

  $test3$normalisation
  [1] 1.021165

  $test3$contacts
  [1] 1.0973188 1.4624132 0.9343448

  $test3$matrix
           contact.age.group
  age.group    [0,5)   [5,10)       10+
     [0,5)  1.769367 1.836114 0.8815070
     [5,10) 1.377724 2.468087 0.8621040
     10+    1.035265 1.349344 0.9711241

  $test3$demography
     age.group population proportion  year
        <char>      <num>      <num> <int>
  1:     [0,5)    1271578 0.06282841  2005
  2:    [5,10)    1329536 0.06569210  2005
  3:       10+   17637787 0.87147948  2005

  $test3$participants
     age.group participants proportion
        <char>        <int>      <num>
  1:     [0,5)           95 0.09396637
  2:    [5,10)          102 0.10089021
  3:       10+          814 0.80514342


  $test4
  $test4$matrix
           contact.age.group
  age.group     [0,5)   [5,15)       15+
     [0,5)  0.0000000 2.029545  3.077273
     [5,15) 0.9262205 7.568413 27.364233
     15+    0.1816446 3.539355  7.139665

  $test4$demography
     age.group population proportion  year
        <char>      <num>      <num> <int>
  1:     [0,5)   13498647 0.04967121  2005
  2:    [5,15)   29578398 0.10884016  2005
  3:       15+  228682923 0.84148863  2005

  $test4$participants
     age.group participants proportion
        <char>        <int>      <num>
  1:     [0,5)          660 0.09134948
  2:    [5,15)         1374 0.19017301
  3:       15+         5191 0.71847751

sbfnk/socialmixr documentation built on Feb. 26, 2025, 8:55 p.m.