![[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 [2026-01-29 15:37:36] 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 parameter strat type
#> <char> <Date> <char> <char> <int> <char>
#> 1: testland 2020-02-22 R R NA estimate
#> 2: testland 2020-02-23 R R NA estimate
#> 3: testland 2020-02-24 R R NA estimate
#> 4: testland 2020-02-25 R R NA estimate
#> 5: testland 2020-02-26 R R NA estimate
#> ---
#> 560: realland 2020-04-24 reported_cases imputed_reports NA forecast
#> 561: realland 2020-04-25 reported_cases imputed_reports NA forecast
#> 562: realland 2020-04-26 reported_cases imputed_reports NA forecast
#> 563: realland 2020-04-27 reported_cases imputed_reports NA forecast
#> 564: realland 2020-04-28 reported_cases imputed_reports NA forecast
#> median mean sd lower_90 lower_50 lower_20
#> <num> <num> <num> <num> <num> <num>
#> 1: 2.184287 2.189490 0.10658258 2.028976 2.121626 2.163104
#> 2: 2.144420 2.152334 0.09674741 2.002565 2.092390 2.123740
#> 3: 2.106303 2.113817 0.09014187 1.974097 2.053383 2.078273
#> 4: 2.064986 2.074099 0.08602712 1.944435 2.014499 2.044069
#> 5: 2.027879 2.033331 0.08352446 1.913818 1.971920 2.004880
#> ---
#> 560: 2885.000000 2937.105000 767.07727885 1801.650000 2396.500000 2688.400000
#> 561: 2408.000000 2477.175000 660.01500240 1506.950000 1966.250000 2231.800000
#> 562: 2754.500000 2855.470000 901.57105150 1538.900000 2171.000000 2510.600000
#> 563: 2379.000000 2564.695000 786.53940343 1559.500000 1969.000000 2225.800000
#> 564: 2123.000000 2198.985000 733.84611149 1159.200000 1719.500000 1947.000000
#> upper_20 upper_50 upper_90
#> <num> <num> <num>
#> 1: 2.216040 2.263164 2.360740
#> 2: 2.173351 2.219161 2.301823
#> 3: 2.134551 2.177657 2.257131
#> 4: 2.090072 2.137158 2.215881
#> 5: 2.049114 2.091113 2.167830
#> ---
#> 560: 3152.800000 3375.750000 4158.350000
#> 561: 2575.600000 2875.250000 3650.650000
#> 562: 3002.000000 3369.500000 4378.600000
#> 563: 2654.200000 3024.250000 4048.550000
#> 564: 2310.400000 2550.500000 3651.900000
#>
#>
#>
#> $summarised_results
#> $summarised_results$table
#> Region New infections per day Expected change in reports
#> <char> <char> <fctr>
#> 1: realland 1781 (633 -- 4186) Likely decreasing
#> 2: testland 1905 (805 -- 4772) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.89 (0.68 -- 1.1) -0.032 (-0.095 -- 0.02)
#> 2: 0.91 (0.73 -- 1.1) -0.027 (-0.082 -- 0.027)
#> Doubling/halving time (days)
#> <char>
#> 1: -22 (34 -- -7.3)
#> 2: -26 (26 -- -8.4)
#>
#> $summarised_results$data
#> region estimate median mean sd lower_90 lower_50
#> <fctr> <char> <num> <num> <num> <num> <num>
#> 1: testland 1905 (805 -- 4772) 1905.00 2153.00 1241.00 805.00 1380.00
#> 2: realland 1781 (633 -- 4186) 1781.00 2048.00 1117.00 633.00 1311.00
#> 3: testland 0.91 (0.73 -- 1.1) 0.91 0.90 0.12 0.73 0.83
#> 4: realland 0.89 (0.68 -- 1.1) 0.89 0.89 0.12 0.68 0.82
#> lower_20 upper_20 upper_50 upper_90 metric
#> <num> <num> <num> <num> <fctr>
#> 1: 1666.00 2122.00 2590.00 4772.0 New infections per day
#> 2: 1595.00 2090.00 2538.00 4186.0 New infections per day
#> 3: 0.88 0.93 0.97 1.1 Effective reproduction no.
#> 4: 0.86 0.93 0.97 1.1 Effective reproduction no.
#> Expected change in reports prob_control
#> <fctr> <list>
#> 1: Likely decreasing 0.83
#> 2: Likely decreasing 0.8
#> 3: Likely decreasing 0.83
#> 4: Likely decreasing 0.8
#>
#> $summarised_results$regions_by_inc
#> [1] "testland" "realland"
#>
#>
#> $summary_plot
#>
#> $summarised_measures
#> $summarised_measures$rt
#> region date parameter strat type median mean sd
#> <char> <Date> <char> <int> <char> <num> <num> <num>
#> 1: realland 2020-02-22 R NA estimate 2.2049351 2.2138416 0.1295158
#> 2: realland 2020-02-23 R NA estimate 2.1628476 2.1734210 0.1195927
#> 3: realland 2020-02-24 R NA estimate 2.1214420 2.1318778 0.1122113
#> 4: realland 2020-02-25 R NA estimate 2.0797718 2.0893933 0.1068067
#> 5: realland 2020-02-26 R NA estimate 2.0389297 2.0461299 0.1027379
#> ---
#> 130: testland 2020-04-24 R NA forecast 0.9050343 0.9048163 0.1203174
#> 131: testland 2020-04-25 R NA forecast 0.9050343 0.9048163 0.1203174
#> 132: testland 2020-04-26 R NA forecast 0.9050343 0.9048163 0.1203174
#> 133: testland 2020-04-27 R NA forecast 0.9050343 0.9048163 0.1203174
#> 134: testland 2020-04-28 R NA forecast 0.9050343 0.9048163 0.1203174
#> lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num> <num>
#> 1: 2.0292447 2.1252332 2.1745094 2.2389873 2.2855863 2.430352
#> 2: 2.0053999 2.0957583 2.1311870 2.1889461 2.2386155 2.381127
#> 3: 1.9748117 2.0573242 2.0937232 2.1485770 2.1930990 2.332049
#> 4: 1.9352677 2.0176237 2.0573835 2.1056189 2.1434051 2.282499
#> 5: 1.8926357 1.9743047 2.0180830 2.0615800 2.0978918 2.240053
#> ---
#> 130: 0.7276063 0.8305671 0.8847349 0.9272735 0.9721334 1.113391
#> 131: 0.7276063 0.8305671 0.8847349 0.9272735 0.9721334 1.113391
#> 132: 0.7276063 0.8305671 0.8847349 0.9272735 0.9721334 1.113391
#> 133: 0.7276063 0.8305671 0.8847349 0.9272735 0.9721334 1.113391
#> 134: 0.7276063 0.8305671 0.8847349 0.9272735 0.9721334 1.113391
#>
#> $summarised_measures$growth_rate
#> region date parameter strat type median mean
#> <char> <Date> <char> <int> <char> <num> <num>
#> 1: realland 2020-02-23 r NA estimate 0.24642046 0.24567281
#> 2: realland 2020-02-24 r NA estimate 0.23873611 0.23808137
#> 3: realland 2020-02-25 r NA estimate 0.23008418 0.22969389
#> 4: realland 2020-02-26 r NA estimate 0.22123275 0.22101239
#> 5: realland 2020-02-27 r NA estimate 0.21188251 0.21211660
#> ---
#> 128: testland 2020-04-24 r NA forecast -0.02654710 -0.02740693
#> 129: testland 2020-04-25 r NA forecast -0.02654198 -0.02743037
#> 130: testland 2020-04-26 r NA forecast -0.02653824 -0.02745253
#> 131: testland 2020-04-27 r NA forecast -0.02653589 -0.02747235
#> 132: testland 2020-04-28 r NA forecast -0.02653470 -0.02748941
#> sd lower_90 lower_50 lower_20 upper_20 upper_50
#> <num> <num> <num> <num> <num> <num>
#> 1: 0.011553636 0.22766567 0.23627354 0.24296215 0.24927555 0.254815040
#> 2: 0.010423616 0.22085349 0.22994658 0.23459431 0.24205922 0.246119242
#> 3: 0.009674003 0.21274432 0.22261193 0.22725307 0.23287270 0.237237268
#> 4: 0.009216050 0.20531988 0.21508906 0.21885134 0.22334342 0.227937246
#> 5: 0.008904631 0.19562401 0.20604698 0.20978129 0.21483127 0.218880604
#> ---
#> 128: 0.034104299 -0.08085388 -0.04773931 -0.03261762 -0.02048912 -0.007756095
#> 129: 0.034271145 -0.08155502 -0.04781847 -0.03262071 -0.02035925 -0.007681798
#> 130: 0.034391500 -0.08184558 -0.04787422 -0.03260894 -0.02026943 -0.007633468
#> 131: 0.034484877 -0.08199478 -0.04791398 -0.03260046 -0.02022123 -0.007599391
#> 132: 0.034559069 -0.08211174 -0.04794139 -0.03259634 -0.02018291 -0.007574850
#> upper_90
#> <num>
#> 1: 0.26299273
#> 2: 0.25339695
#> 3: 0.24458760
#> 4: 0.23528659
#> 5: 0.22560042
#> ---
#> 128: 0.02642144
#> 129: 0.02671093
#> 130: 0.02690073
#> 131: 0.02703714
#> 132: 0.02714005
#>
#> $summarised_measures$cases_by_infection
#> region date parameter strat type median mean sd
#> <char> <Date> <char> <int> <char> <num> <num> <num>
#> 1: realland 2020-02-22 infections NA estimate 208.3 208.4 13.3
#> 2: realland 2020-02-23 infections NA estimate 266.9 266.4 16.2
#> 3: realland 2020-02-24 infections NA estimate 337.9 338.0 19.8
#> 4: realland 2020-02-25 infections NA estimate 426.3 425.2 24.0
#> 5: realland 2020-02-26 infections NA estimate 532.3 530.4 29.0
#> ---
#> 130: testland 2020-04-24 infections NA forecast 2117.5 2257.1 944.4
#> 131: testland 2020-04-25 infections NA forecast 2061.9 2226.9 1016.1
#> 132: testland 2020-04-26 infections NA forecast 2008.2 2199.7 1089.4
#> 133: testland 2020-04-27 infections NA forecast 1956.1 2175.4 1164.5
#> 134: testland 2020-04-28 infections NA forecast 1905.3 2153.8 1241.7
#> lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num> <num>
#> 1: 187.8 199.0 205.5 212.1 216.3 229.2
#> 2: 242.6 255.2 262.3 271.0 276.6 289.5
#> 3: 307.1 324.0 333.3 342.8 351.3 368.4
#> 4: 386.9 408.3 417.6 431.9 442.6 465.2
#> 5: 480.5 511.6 521.5 538.7 550.7 581.1
#> ---
#> 130: 1120.0 1646.2 1906.7 2270.4 2724.1 4288.7
#> 131: 1037.1 1579.4 1839.3 2235.1 2686.7 4424.2
#> 132: 954.4 1513.4 1779.7 2199.3 2654.1 4543.8
#> 133: 876.8 1447.7 1721.1 2160.2 2621.9 4656.6
#> 134: 805.5 1380.3 1666.5 2122.7 2590.1 4772.4
#>
#> $summarised_measures$cases_by_report
#> region date parameter strat type median mean sd
#> <char> <Date> <char> <int> <char> <num> <num> <num>
#> 1: realland 2020-02-22 imputed_reports NA estimate 34.0 35.5 9.9
#> 2: realland 2020-02-23 imputed_reports NA estimate 52.5 54.0 12.9
#> 3: realland 2020-02-24 imputed_reports NA estimate 65.0 66.8 15.5
#> 4: realland 2020-02-25 imputed_reports NA estimate 73.0 73.1 15.8
#> 5: realland 2020-02-26 imputed_reports NA estimate 84.0 86.1 20.0
#> ---
#> 130: testland 2020-04-24 imputed_reports NA forecast 2854.5 2981.7 750.9
#> 131: testland 2020-04-25 imputed_reports NA forecast 2448.5 2544.1 669.2
#> 132: testland 2020-04-26 imputed_reports NA forecast 2825.0 2950.3 837.8
#> 133: testland 2020-04-27 imputed_reports NA forecast 2485.5 2573.2 742.9
#> 134: testland 2020-04-28 imputed_reports NA forecast 2116.0 2212.1 730.0
#> lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num> <num>
#> 1: 22.0 28.0 31.6 36.0 42.0 53.1
#> 2: 34.0 45.8 50.0 56.0 61.0 78.1
#> 3: 43.0 57.0 61.0 69.4 77.0 93.0
#> 4: 50.0 62.0 69.6 77.4 84.2 99.0
#> 5: 54.0 71.0 79.0 91.0 102.0 117.1
#> ---
#> 130: 1976.8 2425.0 2705.2 3041.4 3458.2 4348.5
#> 131: 1639.6 2048.0 2273.4 2645.4 2987.8 3783.1
#> 132: 1740.7 2461.5 2635.6 3006.2 3388.8 4372.6
#> 133: 1556.6 2079.8 2294.4 2626.2 3037.8 4019.5
#> 134: 1308.9 1721.8 1920.6 2303.4 2542.2 3645.5
#>
#>
#> $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
#>
#>