# 01 Data Preparation

#### 2026-02-20

# Introduction

Epiflows can be constructed from two data frames:

- flows - Each row represents a flow of cases from one location to another This must have at least three columns:
  1. The location from where the flow originates
  2. The location where the flow terminates
  3. The number of cases in the flow (can be an absolute number or estimate)
- locations - Each row represents a different location located in flows with associated metadata. It must have a minimum of one column specifying the location identifier that will match the first two columns of flows.

The metadata in locations such as population size, duration of stay in a given location, date of first and last cases, etc. can be useful in estimating the risk of spread, but not everyone will code their data with identical column names. To facilitate their use in the function `estimate_risk_spread()`, the epiflows object stores a dictionary of variables in a place called `$vars`. You can see what variables are stored by default and add varaibles using the `global_vars()` function:

    library("epiflows")
    #> epiflows is loaded with the following global variables in `global_vars()`:
    #> coordinates, pop_size, duration_stay, first_date, last_date, num_cases
    global_vars()
    #> [1] "coordinates"   "pop_size"      "duration_stay" "first_date"
    #> [5] "last_date"     "num_cases"

When we create our object, we will use these as arguments to tell epiflows which varaibles in our data frame are important.

We have two such data frames containing data from a Yellow Fever outbreak in Brazil (Dorigatti et al., 2017). We will load these examples into our session:

    library("epiflows")
    data("YF_flows")
    data("YF_locations")
    head(YF_flows)
    #>               from    to         n
    #> 1   Espirito Santo Italy  2827.572
    #> 2     Minas Gerais Italy 15714.103
    #> 3   Rio de Janeiro Italy  8163.938
    #> 4        Sao Paulo Italy 34038.681
    #> 5 Southeast Brazil Italy 76281.763
    #> 6   Espirito Santo Spain  3270.500
    YF_locations
    #>               location_code location_population num_cases_time_window
    #> 1            Espirito Santo             3973697                  2600
    #> 2              Minas Gerais            20997560                  4870
    #> 3            Rio de Janeiro            16635996                   170
    #> 4                 Sao Paulo            44749699                   200
    #> 5          Southeast Brazil            86356952                  7840
    #> 6                 Argentina                  NA                    NA
    #> 7                     Chile                  NA                    NA
    #> 8                   Germany                  NA                    NA
    #> 9                     Italy                  NA                    NA
    #> 10                 Paraguay                  NA                    NA
    #> 11                 Portugal                  NA                    NA
    #> 12                    Spain                  NA                    NA
    #> 13           United Kingdom                  NA                    NA
    #> 14 United States of America                  NA                    NA
    #> 15                  Uruguay                  NA                    NA
    #>    first_date_cases last_date_cases length_of_stay
    #> 1        2017-01-04      2017-04-30             NA
    #> 2        2016-12-19      2017-04-20             NA
    #> 3        2017-02-19      2017-05-10             NA
    #> 4        2016-12-17      2017-04-20             NA
    #> 5        2016-12-17      2017-05-10             NA
    #> 6              <NA>            <NA>           10.9
    #> 7              <NA>            <NA>           10.3
    #> 8              <NA>            <NA>           22.3
    #> 9              <NA>            <NA>           30.1
    #> 10             <NA>            <NA>            7.3
    #> 11             <NA>            <NA>           27.2
    #> 12             <NA>            <NA>           27.2
    #> 13             <NA>            <NA>           19.5
    #> 14             <NA>            <NA>           18.5
    #> 15             <NA>            <NA>            8.0

We want to use these data to estimate the risk of spread to other locations. This can be done with the procedure implemented in the `estimate_risk_spread()` function, which can take an epiflows object.

# Construction of the epiflows object from data frames

With these data frames, we can construct the epiflows object using the `make_epiflows()` function. Note that this assumes that the required columns (id, from, to, and n) are in the correct order. If they aren’t we can specify their locations with the options in `make_epiflows()`. Type `help("make_epiflows")` for more details.

    ef <- make_epiflows(flows         = YF_flows,
                        locations     = YF_locations,
                        pop_size      = "location_population",
                        duration_stay = "length_of_stay",
                        num_cases     = "num_cases_time_window",
                        first_date    = "first_date_cases",
                        last_date     = "last_date_cases"
                       )
    print(ef)
    #>
    #> /// Epidemiological Flows //
    #>
    #>   // class: epiflows, epicontacts
    #>   // 15 locations; 100 flows; directed
    #>   // optional variables: pop_size, duration_stay, num_cases, first_date, last_date
    #>
    #>   // locations
    #>
    #> # A tibble: 15 x 6
    #>    id                 location_population num_cases_time_window first_date_cases
    #>    <chr>                            <dbl>                 <dbl> <fct>
    #>  1 Espirito Santo                 3973697                  2600 2017-01-04
    #>  2 Minas Gerais                  20997560                  4870 2016-12-19
    #>  3 Rio de Janeiro                16635996                   170 2017-02-19
    #>  4 Sao Paulo                     44749699                   200 2016-12-17
    #>  5 Southeast Brazil              86356952                  7840 2016-12-17
    #>  6 Argentina                           NA                    NA <NA>
    #>  7 Chile                               NA                    NA <NA>
    #>  8 Germany                             NA                    NA <NA>
    #>  9 Italy                               NA                    NA <NA>
    #> 10 Paraguay                            NA                    NA <NA>
    #> 11 Portugal                            NA                    NA <NA>
    #> 12 Spain                               NA                    NA <NA>
    #> 13 United Kingdom                      NA                    NA <NA>
    #> 14 United States of ~                  NA                    NA <NA>
    #> 15 Uruguay                             NA                    NA <NA>
    #> # i 2 more variables: last_date_cases <fct>, length_of_stay <dbl>
    #>
    #>   // flows
    #>
    #> # A tibble: 100 x 3
    #>    from             to         n
    #>    <chr>            <chr>  <dbl>
    #>  1 Espirito Santo   Italy  2828.
    #>  2 Minas Gerais     Italy 15714.
    #>  3 Rio de Janeiro   Italy  8164.
    #>  4 Sao Paulo        Italy 34039.
    #>  5 Southeast Brazil Italy 76282.
    #>  6 Espirito Santo   Spain  3270.
    #>  7 Minas Gerais     Spain 18176.
    #>  8 Rio de Janeiro   Spain  9443.
    #>  9 Sao Paulo        Spain 39371.
    #> 10 Southeast Brazil Spain 88231.
    #> # i 90 more rows

Now we can use this with `esitmate_risk_spread()`

    incubation <- function(n) {
      rlnorm(n, 1.46, 0.35)
    }

    infectious <- function(n) {
      rnorm(n, 4.5, 1.5/1.96)
    }
    set.seed(2017-07-25)
    res <- estimate_risk_spread(ef,
                                location_code          = "Espirito Santo",
                                r_incubation           = incubation,
                                r_infectious           = infectious,
                                n_sim                  = 1e5)
    #> Exportations done
    #> Importations done
    res
    #>                          mean_cases lower_limit_95CI upper_limit_95CI
    #> Italy                     0.2231010        0.1521863        0.3071570
    #> Spain                     0.2252568        0.1538359        0.3119207
    #> Portugal                  0.2314011        0.1566451        0.3372611
    #> Germany                   0.1861744        0.1260291        0.2713440
    #> United Kingdom            0.1611980        0.1195965        0.2084865
    #> United States of America  0.9241416        0.6255894        1.3469106
    #> Argentina                 1.1268870        0.7628361        1.6424064
    #> Chile                     0.2644830        0.1790425        0.3854833
    #> Uruguay                   0.2405802        0.1628641        0.3506508
    #> Paraguay                  0.1618686        0.1213829        0.1924263

We can use ggplot2 to visualize these data

    library("ggplot2")
    res$location <- factor(rownames(res), rownames(res))
    ggplot(res, aes(x = mean_cases, y = location)) +
      geom_point(size = 2) +
      geom_errorbarh(aes(xmin = lower_limit_95CI, xmax = upper_limit_95CI), height = .25) +
      theme_bw(base_size = 12, base_family = "Helvetica") +
      ggtitle("Yellow Fever Spread from Espirito Santo, Brazil") +
      xlab("Number of cases") +
      xlim(c(0, NA))
    #> Warning: `geom_errorbarh()` was deprecated in ggplot2 4.0.0.
    #> i Please use the `orientation` argument of `geom_errorbar()` instead.
    #> This warning is displayed once per session.
    #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
    #> generated.
    #> `height` was translated to `width`.

By default, `estimate_risk_spread()` returns a summary of the simulations. To obtain the full simulated output, you can set `return_all_simulations = TRUE`:

    set.seed(2017-07-25)
    res <- estimate_risk_spread(ef,
                                location_code          = "Espirito Santo",
                                r_incubation           = incubation,
                                r_infectious           = infectious,
                                n_sim                  = 1e5,
                                return_all_simulations = TRUE)
    #> Exportations done
    #> Importations done
    head(res)
    #>          Italy     Spain  Portugal   Germany United Kingdom
    #> [1,] 0.1881972 0.1902371 0.1937110 0.1558506      0.1454655
    #> [2,] 0.1643659 0.1661475 0.1691815 0.1361153      0.1291680
    #> [3,] 0.2300272 0.2325205 0.2367666 0.1904910      0.1643677
    #> [4,] 0.2479176 0.2506047 0.2551811 0.2053064      0.1724519
    #> [5,] 0.2580284 0.2600902 0.2655881 0.2136794      0.1770208
    #> [6,] 0.2005721 0.2027461 0.2064485 0.1660986      0.1510575
    #>      United States of America Argentina     Chile   Uruguay  Paraguay
    #> [1,]                0.7736187 0.9433412 0.2214082 0.2014016 0.1501050
    #> [2,]                0.6756559 0.8238866 0.1933715 0.1758983 0.1310973
    #> [3,]                0.9455686 1.1530148 0.2706200 0.2461665 0.1665537
    #> [4,]                1.0191100 1.2426903 0.2916674 0.2653121 0.1712946
    #> [5,]                1.0606723 1.2933709 0.3035624 0.2761323 0.1739739
    #> [6,]                0.8244880 1.0053706 0.2359669 0.2146448 0.1587483
    library("ggplot2")
    ggplot(utils::stack(as.data.frame(res)), aes(x = ind, y = values)) +
      geom_boxplot(outlier.alpha = 0.2) +
      theme_bw(base_size = 12, base_family = "Helvetica") +
      ggtitle("Yellow Fever Spread from Espirito Santo, Brazil") +
      ylab("Number of cases") +
      xlab("Location") +
      ylim(c(0, NA)) +
      coord_flip()

# Using `set_vars()` to update variable keys in the object

In some cases, it may be useful to store several vectors that can represent a single variable in the model and switch them out. These vectors can be stored as separate columns in the data frame and you can use the function `set_vars()` to change which column a default variable points to.

## Example: different durations of stay

### data preparation

Such a case may arise if you have several different durations of stay based on the location of origin. For example, let’s imagine that this was the case for the Brazilian data. First, we’ll construct some dummy data.

    data("YF_Brazil")
    set.seed(5000)
    short_stays <- as.data.frame(replicate(5, rpois(10, 5) + round(runif(10), 1)))
    colnames(short_stays) <- c("ES", "MG", "RdJ", "SP", "SB")
    rownames(short_stays) <- names(YF_Brazil$length_of_stay)
    short_stays
    #>                            ES  MG RdJ   SP  SB
    #> Italy                     5.3 6.6 6.8  7.5 8.6
    #> Spain                     5.9 2.2 3.3  6.4 3.6
    #> Portugal                  3.9 4.1 3.3 10.5 9.2
    #> Germany                  10.6 6.5 8.1  7.8 6.8
    #> United Kingdom            1.1 4.1 4.1  3.1 7.1
    #> United States of America  6.6 5.3 3.0  3.4 3.5
    #> Argentina                 7.5 6.4 5.7  5.3 6.6
    #> Chile                     1.2 6.8 0.8  4.5 2.7
    #> Uruguay                   4.9 8.9 5.6  3.5 7.8
    #> Paraguay                  5.2 3.4 5.0  4.9 4.3

Now, we can merge it with our original locations metadata using the `location_code` column to join the two together correctly:

    short_stays$location_code <- rownames(short_stays)
    (locations <- merge(YF_locations, short_stays, by = "location_code", all = TRUE, sort = FALSE))
    #>               location_code location_population num_cases_time_window
    #> 1                 Argentina                  NA                    NA
    #> 2                     Chile                  NA                    NA
    #> 3                   Germany                  NA                    NA
    #> 4                     Italy                  NA                    NA
    #> 5                  Paraguay                  NA                    NA
    #> 6                  Portugal                  NA                    NA
    #> 7                     Spain                  NA                    NA
    #> 8            United Kingdom                  NA                    NA
    #> 9  United States of America                  NA                    NA
    #> 10                  Uruguay                  NA                    NA
    #> 11           Espirito Santo             3973697                  2600
    #> 12             Minas Gerais            20997560                  4870
    #> 13           Rio de Janeiro            16635996                   170
    #> 14                Sao Paulo            44749699                   200
    #> 15         Southeast Brazil            86356952                  7840
    #>    first_date_cases last_date_cases length_of_stay   ES  MG RdJ   SP  SB
    #> 1              <NA>            <NA>           10.9  7.5 6.4 5.7  5.3 6.6
    #> 2              <NA>            <NA>           10.3  1.2 6.8 0.8  4.5 2.7
    #> 3              <NA>            <NA>           22.3 10.6 6.5 8.1  7.8 6.8
    #> 4              <NA>            <NA>           30.1  5.3 6.6 6.8  7.5 8.6
    #> 5              <NA>            <NA>            7.3  5.2 3.4 5.0  4.9 4.3
    #> 6              <NA>            <NA>           27.2  3.9 4.1 3.3 10.5 9.2
    #> 7              <NA>            <NA>           27.2  5.9 2.2 3.3  6.4 3.6
    #> 8              <NA>            <NA>           19.5  1.1 4.1 4.1  3.1 7.1
    #> 9              <NA>            <NA>           18.5  6.6 5.3 3.0  3.4 3.5
    #> 10             <NA>            <NA>            8.0  4.9 8.9 5.6  3.5 7.8
    #> 11       2017-01-04      2017-04-30             NA   NA  NA  NA   NA  NA
    #> 12       2016-12-19      2017-04-20             NA   NA  NA  NA   NA  NA
    #> 13       2017-02-19      2017-05-10             NA   NA  NA  NA   NA  NA
    #> 14       2016-12-17      2017-04-20             NA   NA  NA  NA   NA  NA
    #> 15       2016-12-17      2017-05-10             NA   NA  NA  NA   NA  NA

Now we can create the epiflows object like we did before, but using our added data:

    ef <- make_epiflows(flows         = YF_flows,
                        locations     = locations,
                        pop_size      = "location_population",
                        duration_stay = "length_of_stay",
                        num_cases     = "num_cases_time_window",
                        first_date    = "first_date_cases",
                        last_date     = "last_date_cases"
                       )

### Using `set_vars()`

We can run the model the same, but now we have the option to switch out which columns from our locations data frame we want to use:

    get_vars(ef)$duration_stay
    #> [1] "length_of_stay"
    set_vars(ef, "duration_stay") <- "ES"
    get_vars(ef)$duration_stay
    #> [1] "ES"
    set.seed(2017-07-25)
    incubation <- function(n) {
      rlnorm(n, 1.46, 0.35)
    }

    infectious <- function(n) {
      rnorm(n, 4.5, 1.5/1.96)
    }
    set.seed(2017-07-25)
    res <- estimate_risk_spread(ef,
                                location_code          = "Espirito Santo",
                                r_incubation           = incubation,
                                r_infectious           = infectious,
                                n_sim                  = 1e5)
    #> Exportations done
    #> Importations done
    res$location <- factor(rownames(res), rownames(res))
    ggplot(res, aes(x = mean_cases, y = location)) +
      geom_point(size = 2) +
      geom_errorbarh(aes(xmin = lower_limit_95CI, xmax = upper_limit_95CI), height = .25) +
      theme_bw(base_size = 12, base_family = "Helvetica") +
      ggtitle("Yellow Fever Spread from Espirito Santo, Brazil") +
      xlab("Number of cases") +
      xlim(c(0, NA))
    #> `height` was translated to `width`.

Changing it back is simple:

    set_vars(ef, "duration_stay") <- "length_of_stay"

    set.seed(2017-07-25)
    res <- estimate_risk_spread(ef,
                                location_code          = "Espirito Santo",
                                r_incubation           = incubation,
                                r_infectious           = infectious,
                                n_sim                  = 1e5)
    #> Exportations done
    #> Importations done
    res$location <- factor(rownames(res), rownames(res))
    ggplot(res, aes(x = mean_cases, y = location)) +
      geom_point(size = 2) +
      geom_errorbarh(aes(xmin = lower_limit_95CI, xmax = upper_limit_95CI), height = .25) +
      theme_bw(base_size = 12, base_family = "Helvetica") +
      ggtitle("Yellow Fever Spread from Espirito Santo, Brazil") +
      xlab("Number of cases") +
      xlim(c(0, NA))
    #> `height` was translated to `width`.

### Using a custom argument

Or, you can specify it by adding it as an argument in the function

    set.seed(2017-07-25)
    res <- estimate_risk_spread(ef,
                                location_code          = "Espirito Santo",
                                r_incubation           = incubation,
                                r_infectious           = infectious,
                                n_sim                  = 1e5,
                                avg_length_stay_days   = rep(2, 10))
    #> Exportations done
    #> Importations done
    res$location <- factor(rownames(res), rownames(res))
    ggplot(res, aes(x = mean_cases, y = location)) +
      geom_point(size = 2) +
      geom_errorbarh(aes(xmin = lower_limit_95CI, xmax = upper_limit_95CI), height = .25) +
      theme_bw(base_size = 12, base_family = "Helvetica") +
      ggtitle("Yellow Fever Spread from Espirito Santo, Brazil") +
      xlab("Number of cases") +
      xlim(c(0, NA))
    #> `height` was translated to `width`.

# References

Dorigatti I, Hamlet A, Aguas R, Cattarino L, Cori A, Donnelly CA, Garske T, Imai N, Ferguson NM. International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017. Euro Surveill. 2017;22(28):pii=30572. DOI: 10.2807/1560-7917.ES.2017.22.28.30572