Add input and output object names in code to show how they looks like

[avallecam]

About the input:

• This may inform users how to arrange their data in a certain format or why the code follows preliminary operations before using final_size().
• This may also help to explain in a separate chunk the matrix operations mentioned here #126

About the output:

• Showing the dataframe output allows users to identify how it changes when the within susceptibility is added and how it can be used to integrate the output to different external workflows.
• This change could be extended to the rest of the vignettes

These are the following suggestions:

• Add contact_data$matrix and contact_data$demography after https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/finalsize.Rmd#L92-L97

> contact_data$matrix
      contact.age.group
           [0,5)   [5,18)  [18,40)  [40,65)       65+
  [1,] 1.9157895 1.467205 3.278803 1.559611 0.3658614
  [2,] 0.5191021 8.858736 3.421566 2.616146 0.6260247
  [3,] 0.6252718 1.844236 5.440972 3.492124 0.8092367
  [4,] 0.2792593 1.324010 3.278895 4.178218 1.2380907
  [5,] 0.1306272 0.631752 1.515092 2.468756 1.7142857

> contact_data$demography
   age.group population proportion year
1:     [0,5)    3453670 0.05728738 2005
2:    [5,18)    9761554 0.16191873 2005
3:   [18,40)   18110368 0.30040378 2005
4:   [40,65)   19288101 0.31993930 2005
5:       65+    9673058 0.16045081 2005

• Add the output dataframe of the final_size() function: https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/finalsize.Rmd#L184-L190

  > final_size_data
  demo_grp   susc_grp susceptibility p_infected
  1    [0,5) susc_grp_1              1  0.6434899
  2   [5,18) susc_grp_1              1  0.8777478
  3  [18,40) susc_grp_1              1  0.7723371
  4  [40,65) susc_grp_1              1  0.7023265
  5      65+ susc_grp_1              1  0.5131873

[avallecam]

Great! This suggestion could also be extended to these outputs in the other vignettes. They facilitate the comparability of scenarios in final_size_data, as invited in the reading of the text. In the case of final_size_immunised, it is the first output with a susceptibility matrix of two columns, which generates a tidy dataframe (not necessary to mention but is cool to see). The same for final_size_data in the uncertainty vignette.

• suggestion 1:

https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/varying_susceptibility.Rmd#L158-L162

> final_size_data
   demo_grp   susc_grp susceptibility p_infected      scenario
1     [0,5) susc_grp_1            0.2 0.08438181 Heterogeneous
2    [5,18) susc_grp_1            0.5 0.39000734 Heterogeneous
3   [18,40) susc_grp_1            0.6 0.35635678 Heterogeneous
4   [40,65) susc_grp_1            0.9 0.43945122 Heterogeneous
5       65+ susc_grp_1            1.0 0.32834904 Heterogeneous
6     [0,5) susc_grp_1            1.0 0.64348986       Uniform
7    [5,18) susc_grp_1            1.0 0.87774777       Uniform
8   [18,40) susc_grp_1            1.0 0.77233709       Uniform
9   [40,65) susc_grp_1            1.0 0.70232650       Uniform
10      65+ susc_grp_1            1.0 0.51318727       Uniform

• suggestion 2:

https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/varying_susceptibility.Rmd#L272-L281

> final_size_immunised
   demo_grp     susc_grp susceptibility p_infected
1     [0,5) Un-immunised          0.200 0.05090418
2    [5,18) Un-immunised          0.500 0.25527773
3   [18,40) Un-immunised          0.600 0.23095861
4   [40,65) Un-immunised          0.900 0.29266225
5       65+ Un-immunised          1.000 0.21153844
6     [0,5)    Immunised          0.150 0.03842637
7    [5,18)    Immunised          0.375 0.19832977
8   [18,40)    Immunised          0.450 0.17877476
9   [40,65)    Immunised          0.675 0.22870569
10      65+    Immunised          0.750 0.16326990

• suggestion 3:

https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/uncertainty_params.Rmd#L145

> final_size_data
      demo_grp   susc_grp susceptibility p_infected replicate r0_estimate
   1:    [0,5) susc_grp_1              1  0.6182474         1    1.927639
   2:   [5,18) susc_grp_1              1  0.8612644         1    1.927639
   3:  [18,40) susc_grp_1              1  0.7489203         1    1.927639
   4:  [40,65) susc_grp_1              1  0.6768969         1    1.927639
   5:      65+ susc_grp_1              1  0.4880345         1    1.927639
  ---                                                                    
4996:    [0,5) susc_grp_1              1  0.6037438      1000    1.888608
4997:   [5,18) susc_grp_1              1  0.8513187      1000    1.888608
4998:  [18,40) susc_grp_1              1  0.7351487      1000    1.888608
4999:  [40,65) susc_grp_1              1  0.6621470      1000    1.888608
5000:      65+ susc_grp_1              1  0.4738339      1000    1.888608