![[Maturing]](figures/lifecycle-maturing.svg)
Used to produce summary output either internally in regional_epinow or
externally.
Usage
regional_summary(
regional_output = NULL,
data,
results_dir = NULL,
summary_dir = NULL,
target_date = NULL,
region_scale = "Region",
all_regions = TRUE,
return_output = is.null(summary_dir),
plot = TRUE,
max_plot = 10,
...
)Arguments
- regional_output
A list of output as produced by
regional_epinow()and stored in theregionallist.- data
A
<data.frame>of disease reports (confirm) by date (date), and region (region).- results_dir
An optional character string indicating the location of the results directory to extract results from.
- summary_dir
A character string giving the directory in which to store summary of results.
- target_date
A character string giving the target date for which to extract results (in the format "yyyy-mm-dd"). Defaults to latest available estimates.
- region_scale
A character string indicating the name to give the regions being summarised.
- all_regions
Logical, defaults to
TRUE. Should summary plots for all regions be returned rather than just regions of interest.- return_output
Logical, defaults to FALSE. Should output be returned, this automatically updates to TRUE if no directory for saving is specified.
- plot
Logical, defaults to
TRUE. Should regional summary plots be produced.- max_plot
Numeric, defaults to 10. A multiplicative upper bound on the\ number of cases shown on the plot. Based on the maximum number of reported cases.
- ...
Additional arguments passed to
report_plots.
Examples
# get example output from regional_epinow model
regional_out <- readRDS(system.file(
package = "EpiNow2", "extdata", "example_regional_epinow.rds"
))
regional_summary(
regional_output = regional_out$regional,
data = regional_out$summary$reported_cases
)
#> INFO [2025-11-27 17:24:03] No summary directory specified so returning summary output
#> $latest_date
#> [1] "2020-04-21"
#>
#> $results
#> $results$estimates
#> $results$estimates$summarised
#> Indices: <variable>, <region>
#> region date variable strat type median
#> <char> <Date> <char> <char> <char> <num>
#> 1: testland 2020-02-22 R <NA> estimate 2.1755546
#> 2: testland 2020-02-23 R <NA> estimate 2.1416454
#> 3: testland 2020-02-24 R <NA> estimate 2.1012037
#> 4: testland 2020-02-25 R <NA> estimate 2.0607501
#> 5: testland 2020-02-26 R <NA> estimate 2.0219041
#> ---
#> 560: realland 2020-04-26 reported_cases <NA> forecast 2744.5000000
#> 561: realland 2020-04-27 reported_cases <NA> forecast 2602.5000000
#> 562: realland 2020-04-28 reported_cases <NA> forecast 2111.0000000
#> 563: realland <NA> reporting_overdispersion <NA> <NA> 0.1679094
#> 564: realland <NA> rho <NA> <NA> 18.3912056
#> mean sd lower_90 lower_50 lower_20
#> <num> <num> <num> <num> <num>
#> 1: 2.1846025 0.10794295 2.0177562 2.1003475 2.1492054
#> 2: 2.1474213 0.09670777 1.9931312 2.0712255 2.1163732
#> 3: 2.1089527 0.08801488 1.9729887 2.0415659 2.0806889
#> 4: 2.0693779 0.08152743 1.9441177 2.0117011 2.0417723
#> 5: 2.0288621 0.07673437 1.9036506 1.9713526 2.0079071
#> ---
#> 560: 2790.1350000 702.42545825 1731.6500000 2362.2500000 2584.2000000
#> 561: 2680.3250000 809.32458308 1577.7000000 2087.7500000 2395.2000000
#> 562: 2230.4000000 712.77557837 1260.7000000 1740.5000000 1961.0000000
#> 563: 0.1682596 0.01932362 0.1370876 0.1558891 0.1633468
#> 564: 19.5438277 6.13393532 11.7078772 15.3024172 17.1811641
#> upper_20 upper_50 upper_90
#> <num> <num> <num>
#> 1: 2.2162031 2.2600171 2.3616361
#> 2: 2.1727190 2.2128760 2.3126088
#> 3: 2.1285358 2.1745113 2.2609432
#> 4: 2.0891854 2.1330387 2.2176273
#> 5: 2.0433392 2.0835454 2.1659812
#> ---
#> 560: 2863.2000000 3125.7500000 3966.6000000
#> 561: 2788.8000000 3096.2500000 4347.3500000
#> 562: 2313.0000000 2578.7500000 3496.3500000
#> 563: 0.1707838 0.1791721 0.2038153
#> 564: 19.8542697 22.9181453 30.3380606
#>
#>
#>
#> $summarised_results
#> $summarised_results$table
#> Region New infections per day Expected change in reports
#> <char> <char> <fctr>
#> 1: realland 1760 (942 -- 3880) Likely decreasing
#> 2: testland 1709 (764 -- 4526) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.89 (0.76 -- 1.1) -0.031 (-0.069 -- 0.021)
#> 2: 0.89 (0.72 -- 1.1) -0.031 (-0.084 -- 0.026)
#> Doubling/halving time (days)
#> <char>
#> 1: -23 (33 -- -10)
#> 2: -23 (27 -- -8.2)
#>
#> $summarised_results$data
#> region estimate median mean sd lower_90 lower_50
#> <fctr> <char> <num> <num> <num> <num> <num>
#> 1: realland 1760 (942 -- 3880) 1760.00 2064.0 1074.00 942.00 1352.00
#> 2: testland 1709 (764 -- 4526) 1709.00 2124.0 1292.00 764.00 1210.00
#> 3: realland 0.89 (0.76 -- 1.1) 0.89 0.9 0.11 0.76 0.83
#> 4: testland 0.89 (0.72 -- 1.1) 0.89 0.9 0.12 0.72 0.81
#> lower_20 upper_20 upper_50 upper_90 metric
#> <num> <num> <num> <num> <fctr>
#> 1: 1587.00 2030.00 2535.00 3880.0 New infections per day
#> 2: 1488.00 2146.00 2749.00 4526.0 New infections per day
#> 3: 0.87 0.92 0.96 1.1 Effective reproduction no.
#> 4: 0.85 0.94 0.98 1.1 Effective reproduction no.
#> Expected change in reports prob_control
#> <fctr> <list>
#> 1: Likely decreasing 0.84
#> 2: Likely decreasing 0.78
#> 3: Likely decreasing 0.84
#> 4: Likely decreasing 0.78
#>
#> $summarised_results$regions_by_inc
#> [1] "realland" "testland"
#>
#>
#> $summary_plot
#>
#> $summarised_measures
#> $summarised_measures$rt
#> region date strat type median mean sd
#> <char> <Date> <char> <char> <num> <num> <num>
#> 1: realland 2020-02-22 <NA> estimate 2.1965091 2.2083670 0.11686624
#> 2: realland 2020-02-23 <NA> estimate 2.1553367 2.1699645 0.10632806
#> 3: realland 2020-02-24 <NA> estimate 2.1204048 2.1304785 0.09860815
#> 4: realland 2020-02-25 <NA> estimate 2.0819848 2.0900056 0.09334381
#> 5: realland 2020-02-26 <NA> estimate 2.0449176 2.0486246 0.08995381
#> ---
#> 130: testland 2020-04-24 <NA> forecast 0.8944846 0.9015978 0.12445024
#> 131: testland 2020-04-25 <NA> forecast 0.8944846 0.9015978 0.12445024
#> 132: testland 2020-04-26 <NA> forecast 0.8944846 0.9015978 0.12445024
#> 133: testland 2020-04-27 <NA> forecast 0.8944846 0.9015978 0.12445024
#> 134: testland 2020-04-28 <NA> forecast 0.8944846 0.9015978 0.12445024
#> lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num> <num>
#> 1: 2.049067 2.1353738 2.1692977 2.2323750 2.2928182 2.387440
#> 2: 2.010039 2.1034287 2.1322803 2.1873761 2.2476014 2.335752
#> 3: 1.980214 2.0631701 2.0952684 2.1495342 2.2013806 2.279709
#> 4: 1.939899 2.0314610 2.0634560 2.1022222 2.1509765 2.243858
#> 5: 1.904171 1.9887547 2.0223399 2.0667743 2.0995346 2.197421
#> ---
#> 130: 0.717204 0.8075987 0.8546392 0.9365739 0.9836182 1.094407
#> 131: 0.717204 0.8075987 0.8546392 0.9365739 0.9836182 1.094407
#> 132: 0.717204 0.8075987 0.8546392 0.9365739 0.9836182 1.094407
#> 133: 0.717204 0.8075987 0.8546392 0.9365739 0.9836182 1.094407
#> 134: 0.717204 0.8075987 0.8546392 0.9365739 0.9836182 1.094407
#>
#> $summarised_measures$growth_rate
#> region date strat type median mean sd
#> <char> <Date> <char> <char> <num> <num> <num>
#> 1: realland 2020-02-23 <NA> estimate 0.24471768 0.24440892 0.011303876
#> 2: realland 2020-02-24 <NA> estimate 0.23787832 0.23724623 0.009858402
#> 3: realland 2020-02-25 <NA> estimate 0.22898804 0.22927240 0.008785085
#> 4: realland 2020-02-26 <NA> estimate 0.22062263 0.22096076 0.008114626
#> 5: realland 2020-02-27 <NA> estimate 0.21207793 0.21237831 0.007753683
#> ---
#> 128: testland 2020-04-24 <NA> forecast -0.03063276 -0.02861478 0.034976116
#> 129: testland 2020-04-25 <NA> forecast -0.03068320 -0.02863692 0.035130344
#> 130: testland 2020-04-26 <NA> forecast -0.03071984 -0.02865644 0.035235880
#> 131: testland 2020-04-27 <NA> forecast -0.03074878 -0.02867318 0.035314372
#> 132: testland 2020-04-28 <NA> forecast -0.03077213 -0.02868717 0.035374656
#> lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num> <num>
#> 1: 0.22341293 0.23720117 0.24224383 0.24800319 0.252048080 0.26096927
#> 2: 0.21765445 0.23156016 0.23561463 0.24014595 0.243968983 0.25185809
#> 3: 0.21416801 0.22422604 0.22782035 0.23197997 0.234968560 0.24346732
#> 4: 0.20854258 0.21668688 0.21961447 0.22304461 0.225938358 0.23435144
#> 5: 0.19965914 0.20749859 0.21085043 0.21423195 0.216761654 0.22544625
#> ---
#> 128: -0.08318073 -0.05491414 -0.04049717 -0.01747933 -0.004585665 0.02535367
#> 129: -0.08358477 -0.05498174 -0.04046760 -0.01745463 -0.004467709 0.02552564
#> 130: -0.08388781 -0.05502790 -0.04043318 -0.01743246 -0.004389319 0.02563856
#> 131: -0.08411816 -0.05506112 -0.04038107 -0.01741971 -0.004332948 0.02571963
#> 132: -0.08428930 -0.05508511 -0.04033417 -0.01742958 -0.004291000 0.02578029
#>
#> $summarised_measures$cases_by_infection
#> region date strat type median mean sd lower_90 lower_50
#> <char> <Date> <char> <char> <num> <num> <num> <num> <num>
#> 1: realland 2020-02-22 <NA> estimate 206.8 206.3 12.0 186.5 198.7
#> 2: realland 2020-02-23 <NA> estimate 264.6 263.3 15.0 238.4 254.2
#> 3: realland 2020-02-24 <NA> estimate 334.6 333.8 18.9 302.4 320.8
#> 4: realland 2020-02-25 <NA> estimate 420.4 419.9 23.7 382.8 403.8
#> 5: realland 2020-02-26 <NA> estimate 523.8 523.7 29.5 477.2 502.8
#> ---
#> 130: testland 2020-04-24 <NA> forecast 1962.1 2225.1 978.2 1055.2 1521.7
#> 131: testland 2020-04-25 <NA> forecast 1890.7 2195.2 1053.7 975.8 1436.5
#> 132: testland 2020-04-26 <NA> forecast 1823.1 2168.4 1131.0 898.1 1357.8
#> 133: testland 2020-04-27 <NA> forecast 1764.3 2144.8 1210.4 830.7 1281.1
#> 134: testland 2020-04-28 <NA> forecast 1709.4 2124.2 1292.2 765.0 1210.1
#> lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num>
#> 1: 203.7 210.1 214.7 225.1
#> 2: 259.6 267.6 273.8 288.1
#> 3: 328.8 339.1 347.5 362.1
#> 4: 413.3 428.0 437.1 453.6
#> 5: 516.0 534.8 543.0 565.0
#> ---
#> 130: 1768.5 2312.9 2770.8 4147.0
#> 131: 1693.4 2269.0 2772.4 4242.9
#> 132: 1618.9 2223.7 2761.0 4335.2
#> 133: 1550.3 2179.5 2752.5 4429.6
#> 134: 1488.6 2146.7 2749.1 4526.2
#>
#> $summarised_measures$cases_by_report
#> region date strat type median mean sd lower_90 lower_50
#> <char> <Date> <char> <char> <num> <num> <num> <num> <num>
#> 1: realland 2020-02-22 <NA> estimate 34.0 35.8 10.2 23.0 29.0
#> 2: realland 2020-02-23 <NA> estimate 54.0 53.5 13.0 33.0 44.0
#> 3: realland 2020-02-24 <NA> estimate 62.0 63.9 14.8 43.0 54.0
#> 4: realland 2020-02-25 <NA> estimate 72.5 73.1 16.0 46.0 63.0
#> 5: realland 2020-02-26 <NA> estimate 83.0 84.0 18.4 56.0 71.8
#> ---
#> 130: testland 2020-04-24 <NA> forecast 2720.0 2844.1 750.0 1861.5 2325.5
#> 131: testland 2020-04-25 <NA> forecast 2411.0 2531.7 662.7 1595.8 2104.8
#> 132: testland 2020-04-26 <NA> forecast 2725.5 2805.1 781.5 1806.8 2248.2
#> 133: testland 2020-04-27 <NA> forecast 2411.5 2558.3 799.1 1563.3 1947.8
#> 134: testland 2020-04-28 <NA> forecast 2025.5 2190.7 735.6 1212.6 1670.0
#> lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num>
#> 1: 32.0 36.4 41.0 54.0
#> 2: 50.6 56.4 62.0 76.0
#> 3: 59.0 66.0 71.2 90.0
#> 4: 70.0 76.0 82.0 99.1
#> 5: 78.0 87.0 95.5 116.0
#> ---
#> 130: 2518.6 2861.0 3262.0 4133.1
#> 131: 2316.4 2589.6 2939.2 3684.5
#> 132: 2521.6 2854.0 3162.2 4254.1
#> 133: 2215.0 2642.2 2999.2 4066.5
#> 134: 1877.2 2294.0 2600.2 3461.8
#>
#>
#> $reported_cases
#> Index: <region>
#> date confirm region
#> <Date> <num> <char>
#> 1: 2020-02-22 14 testland
#> 2: 2020-02-23 62 testland
#> 3: 2020-02-24 53 testland
#> 4: 2020-02-25 97 testland
#> 5: 2020-02-26 93 testland
#> ---
#> 116: 2020-04-17 3786 realland
#> 117: 2020-04-18 3493 realland
#> 118: 2020-04-19 3491 realland
#> 119: 2020-04-20 3047 realland
#> 120: 2020-04-21 2256 realland
#>
#> $high_plots
#> $high_plots$infections
#>
#> $high_plots$reports
#>
#> $high_plots$R
#>
#> $high_plots$growth_rate
#>
#>
#> $plots
#> $plots$infections
#>
#> $plots$reports
#>
#> $plots$R
#>
#> $plots$growth_rate
#>
#>