regional_summary(
regional_output = NULL,
reported_cases,
results_dir = NULL,
summary_dir = NULL,
target_date = NULL,
region_scale = "Region",
all_regions = TRUE,
return_output = FALSE,
max_plot = 10,
...
)
A list of output as produced by regional_epinow
and stored in the
regional
list.
A data frame of confirmed cases (confirm) by date (date), and region (region
).
An optional character string indicating the location of the results directory to extract results from.
A character string giving the directory in which to store summary of results.
A character string giving the target date for which to extract results (in the format "yyyy-mm-dd"). Defaults to latest available estimates.
A character string indicating the name to give the regions being summarised.
Logical, defaults to TRUE
. Should summary plots for all
regions be returned rather than just regions of interest.
Logical, defaults to FALSE. Should output be returned, this automatically updates to TRUE if no directory for saving is specified.
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
.
A list of summary measures and plots
regional_epinow
# \donttest{
# example delays
generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
reporting_delay <- estimate_delay(rlnorm(100, log(6), 1), max_value = 30)
# example case vector from EpiSoon
cases <- example_confirmed[1:30]
cases <- data.table::rbindlist(list(
data.table::copy(cases)[, region := "testland"],
cases[, region := "realland"]
))
# run basic nowcasting pipeline
out <- regional_epinow(
reported_cases = cases,
generation_time = generation_time,
delays = delay_opts(incubation_period, reporting_delay),
output = "region",
rt = NULL
)
#> INFO [2022-03-28 04:11:45] Producing following optional outputs: regions
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpqbXERq/regional-epinow/2020-03-22.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to: /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpqbXERq/epinow/2020-03-22.log
#> INFO [2022-03-28 04:11:45] Reporting estimates using data up to: 2020-03-22
#> INFO [2022-03-28 04:11:45] No target directory specified so returning output
#> INFO [2022-03-28 04:11:45] Producing estimates for: testland, realland
#> INFO [2022-03-28 04:11:45] Regions excluded: none
#> INFO [2022-03-28 04:12:24] Completed estimates for: testland
#> INFO [2022-03-28 04:13:03] Completed estimates for: realland
#> INFO [2022-03-28 04:13:03] Completed regional estimates
#> INFO [2022-03-28 04:13:03] Regions with estimates: 2
#> INFO [2022-03-28 04:13:03] Regions with runtime errors: 0
#> INFO [2022-03-28 04:13:03] No target directory specified so returning timings
regional_summary(
regional_output = out$regional,
reported_cases = cases
)
#> INFO [2022-03-28 04:13:03] No summary directory specified so returning summary output
#> $latest_date
#> [1] "2020-03-22"
#>
#> $results
#> $results$estimates
#> $results$estimates$summarised
#> region date variable strat type median
#> 1: testland 2020-02-22 R <NA> estimate 1.6322468
#> 2: testland 2020-02-23 R <NA> estimate 1.6359159
#> 3: testland 2020-02-24 R <NA> estimate 1.5754194
#> 4: testland 2020-02-25 R <NA> estimate 1.5465078
#> 5: testland 2020-02-26 R <NA> estimate 1.5483517
#> ---
#> 422: realland 2020-03-26 reported_cases <NA> forecast 991.5000000
#> 423: realland 2020-03-27 reported_cases <NA> forecast 1239.5000000
#> 424: realland 2020-03-28 reported_cases <NA> forecast 985.0000000
#> 425: realland 2020-03-29 reported_cases <NA> forecast 1118.5000000
#> 426: realland <NA> reporting_overdispersion <NA> <NA> 0.9963241
#> mean sd lower_90 lower_50 lower_20 upper_20
#> 1: 1.639706 1.119347e-01 1.4638326 1.5687936 1.6079753 1.658615
#> 2: 1.641193 1.058096e-01 1.4750018 1.5740327 1.6129870 1.660551
#> 3: 1.579606 9.872186e-02 1.4237893 1.5164624 1.5525069 1.597319
#> 4: 1.549736 9.252992e-02 1.4037361 1.4895356 1.5245174 1.566864
#> 5: 1.550685 8.904673e-02 1.4111612 1.4926670 1.5262397 1.567475
#> ---
#> 422: 1693.269000 2.136052e+03 54.0000000 393.7500000 716.8000000 1322.800000
#> 423: 1907.321000 2.091694e+03 70.0000000 492.0000000 894.6000000 1638.200000
#> 424: 1607.507000 1.889484e+03 72.0000000 426.7500000 743.0000000 1311.000000
#> 425: 1858.927500 2.144206e+03 71.9500000 477.0000000 859.6000000 1534.400000
#> 426: 1.065823 4.027978e-01 0.5345241 0.7764879 0.9159032 1.087634
#> upper_50 upper_90
#> 1: 1.701449 1.832920
#> 2: 1.701318 1.816132
#> 3: 1.636689 1.748143
#> 4: 1.603731 1.702294
#> 5: 1.601691 1.697571
#> ---
#> 422: 2189.750000 5534.150000
#> 423: 2608.250000 5927.200000
#> 424: 2083.250000 5196.400000
#> 425: 2506.250000 6005.000000
#> 426: 1.274299 1.845573
#>
#>
#>
#> $summarised_results
#> $summarised_results$table
#> Region New confirmed cases by infection date
#> 1: realland 1019 (950 -- 1145)
#> 2: testland 1020 (943 -- 1136)
#> Expected change in daily cases Effective reproduction no.
#> 1: Decreasing 0.79 (0.74 -- 0.84)
#> 2: Decreasing 0.79 (0.75 -- 0.84)
#> Rate of growth Doubling/halving time (days)
#> 1: -0.057 (-0.074 -- -0.049) -12 (-14 -- -9.3)
#> 2: -0.057 (-0.074 -- -0.049) -12 (-14 -- -9.4)
#>
#> $summarised_results$data
#> region estimate median mean sd lower_90 lower_50
#> 1: testland 1020 (943 -- 1136) 1020.00 1029.00 59.000 943.00 1003.00
#> 2: realland 1019 (950 -- 1145) 1019.00 1030.00 64.000 950.00 1004.00
#> 3: realland 0.79 (0.74 -- 0.84) 0.79 0.79 0.030 0.74 0.78
#> 4: testland 0.79 (0.75 -- 0.84) 0.79 0.79 0.029 0.75 0.77
#> lower_20 upper_20 upper_50 upper_90 metric
#> 1: 1015.00 1027.0 1048.00 1136.00 New confirmed cases by infection date
#> 2: 1016.00 1026.0 1046.00 1145.00 New confirmed cases by infection date
#> 3: 0.79 0.8 0.81 0.84 Effective reproduction no.
#> 4: 0.79 0.8 0.81 0.84 Effective reproduction no.
#> Expected change in daily cases prob_control
#> 1: Decreasing 1
#> 2: Decreasing 1
#> 3: Decreasing 1
#> 4: Decreasing 1
#>
#> $summarised_results$regions_by_inc
#> [1] "testland" "realland"
#>
#>
#> $summary_plot
#>
#> $summarised_measures
#> $summarised_measures$rt
#> region date strat type median
#> 1: realland 2020-02-22 <NA> estimate 1.6287134
#> 2: realland 2020-02-23 <NA> estimate 1.6329677
#> 3: realland 2020-02-24 <NA> estimate 1.5726155
#> 4: realland 2020-02-25 <NA> estimate 1.5442543
#> 5: realland 2020-02-26 <NA> estimate 1.5462150
#> 6: realland 2020-02-27 <NA> estimate 1.5490782
#> 7: realland 2020-02-28 <NA> estimate 1.5319744
#> 8: realland 2020-02-29 <NA> estimate 1.3096630
#> 9: realland 2020-03-01 <NA> estimate 1.1617002
#> 10: realland 2020-03-02 <NA> estimate 1.0840952
#> 11: realland 2020-03-03 <NA> estimate 1.0000881
#> 12: realland 2020-03-04 <NA> estimate 0.9316281
#> 13: realland 2020-03-05 <NA> estimate 0.8828817
#> 14: realland 2020-03-06 <NA> estimate 0.8202715
#> 15: realland 2020-03-07 <NA> estimate based on partial data 0.8926061
#> 16: realland 2020-03-08 <NA> estimate based on partial data 0.8674781
#> 17: realland 2020-03-09 <NA> estimate based on partial data 0.8484259
#> 18: realland 2020-03-10 <NA> estimate based on partial data 0.8335932
#> 19: realland 2020-03-11 <NA> estimate based on partial data 0.8220869
#> 20: realland 2020-03-12 <NA> estimate based on partial data 0.8136868
#> 21: realland 2020-03-13 <NA> estimate based on partial data 0.8077592
#> 22: realland 2020-03-14 <NA> estimate based on partial data 0.8034974
#> 23: realland 2020-03-15 <NA> estimate based on partial data 0.8003446
#> 24: realland 2020-03-16 <NA> estimate based on partial data 0.7980612
#> 25: realland 2020-03-17 <NA> estimate based on partial data 0.7968367
#> 26: realland 2020-03-18 <NA> estimate based on partial data 0.7952001
#> 27: realland 2020-03-19 <NA> estimate based on partial data 0.7949698
#> 28: realland 2020-03-20 <NA> estimate based on partial data 0.7936882
#> 29: realland 2020-03-21 <NA> estimate based on partial data 0.7937895
#> 30: realland 2020-03-22 <NA> estimate based on partial data 0.7933397
#> 31: realland 2020-03-23 <NA> forecast 0.7926788
#> 32: realland 2020-03-24 <NA> forecast 0.7923490
#> 33: realland 2020-03-25 <NA> forecast 0.7928867
#> 34: realland 2020-03-26 <NA> forecast 0.7921127
#> 35: realland 2020-03-27 <NA> forecast 0.7918682
#> 36: realland 2020-03-28 <NA> forecast 0.7919460
#> 37: realland 2020-03-29 <NA> forecast 0.7921023
#> 38: testland 2020-02-22 <NA> estimate 1.6322468
#> 39: testland 2020-02-23 <NA> estimate 1.6359159
#> 40: testland 2020-02-24 <NA> estimate 1.5754194
#> 41: testland 2020-02-25 <NA> estimate 1.5465078
#> 42: testland 2020-02-26 <NA> estimate 1.5483517
#> 43: testland 2020-02-27 <NA> estimate 1.5506804
#> 44: testland 2020-02-28 <NA> estimate 1.5330400
#> 45: testland 2020-02-29 <NA> estimate 1.3095249
#> 46: testland 2020-03-01 <NA> estimate 1.1619420
#> 47: testland 2020-03-02 <NA> estimate 1.0838066
#> 48: testland 2020-03-03 <NA> estimate 0.9991528
#> 49: testland 2020-03-04 <NA> estimate 0.9307315
#> 50: testland 2020-03-05 <NA> estimate 0.8817289
#> 51: testland 2020-03-06 <NA> estimate 0.8193897
#> 52: testland 2020-03-07 <NA> estimate based on partial data 0.8916053
#> 53: testland 2020-03-08 <NA> estimate based on partial data 0.8671506
#> 54: testland 2020-03-09 <NA> estimate based on partial data 0.8476947
#> 55: testland 2020-03-10 <NA> estimate based on partial data 0.8326889
#> 56: testland 2020-03-11 <NA> estimate based on partial data 0.8209244
#> 57: testland 2020-03-12 <NA> estimate based on partial data 0.8123660
#> 58: testland 2020-03-13 <NA> estimate based on partial data 0.8062731
#> 59: testland 2020-03-14 <NA> estimate based on partial data 0.8024139
#> 60: testland 2020-03-15 <NA> estimate based on partial data 0.7992736
#> 61: testland 2020-03-16 <NA> estimate based on partial data 0.7969624
#> 62: testland 2020-03-17 <NA> estimate based on partial data 0.7955352
#> 63: testland 2020-03-18 <NA> estimate based on partial data 0.7939984
#> 64: testland 2020-03-19 <NA> estimate based on partial data 0.7935635
#> 65: testland 2020-03-20 <NA> estimate based on partial data 0.7928701
#> 66: testland 2020-03-21 <NA> estimate based on partial data 0.7926409
#> 67: testland 2020-03-22 <NA> estimate based on partial data 0.7918547
#> 68: testland 2020-03-23 <NA> forecast 0.7913393
#> 69: testland 2020-03-24 <NA> forecast 0.7913447
#> 70: testland 2020-03-25 <NA> forecast 0.7922151
#> 71: testland 2020-03-26 <NA> forecast 0.7919235
#> 72: testland 2020-03-27 <NA> forecast 0.7916873
#> 73: testland 2020-03-28 <NA> forecast 0.7914714
#> 74: testland 2020-03-29 <NA> forecast 0.7921955
#> region date strat type median
#> mean sd lower_90 lower_50 lower_20 upper_20 upper_50
#> 1: 1.6380433 0.10731668 1.4747270 1.5690102 1.6060754 1.6545537 1.6985437
#> 2: 1.6399855 0.10164597 1.4822246 1.5754015 1.6117729 1.6574189 1.6976464
#> 3: 1.5788365 0.09501183 1.4319868 1.5174511 1.5523487 1.5957501 1.6336407
#> 4: 1.5493642 0.08924175 1.4101669 1.4912402 1.5248900 1.5656104 1.6016651
#> 5: 1.5506112 0.08600446 1.4174875 1.4942648 1.5268486 1.5667853 1.6009277
#> 6: 1.5539990 0.08459462 1.4231414 1.4983986 1.5300107 1.5697540 1.6028739
#> 7: 1.5367946 0.08325389 1.4088383 1.4824572 1.5122852 1.5505560 1.5858630
#> 8: 1.3131424 0.07044417 1.2044543 1.2676226 1.2923460 1.3242525 1.3551243
#> 9: 1.1633193 0.05538936 1.0760323 1.1281461 1.1481005 1.1745451 1.1968170
#> 10: 1.0860498 0.04581124 1.0124926 1.0562886 1.0743901 1.0951809 1.1144038
#> 11: 1.0018282 0.03796571 0.9422676 0.9783000 0.9918687 1.0084245 1.0243354
#> 12: 0.9337750 0.03228445 0.8865086 0.9129127 0.9250665 0.9380600 0.9511637
#> 13: 0.8846208 0.02889339 0.8424136 0.8673499 0.8769805 0.8883090 0.8985084
#> 14: 0.8213549 0.02623011 0.7823059 0.8066602 0.8153856 0.8248063 0.8329084
#> 15: 0.8927027 0.02984613 0.8473128 0.8759652 0.8866563 0.8973947 0.9066197
#> 16: 0.8693160 0.02698277 0.8307711 0.8548605 0.8628132 0.8722305 0.8814585
#> 17: 0.8503074 0.02622664 0.8136082 0.8356749 0.8436254 0.8530068 0.8630403
#> 18: 0.8350566 0.02617563 0.7977208 0.8202844 0.8285794 0.8386926 0.8492111
#> 19: 0.8233153 0.02660293 0.7835137 0.8077821 0.8166715 0.8276146 0.8376099
#> 20: 0.8143565 0.02725455 0.7725083 0.7981205 0.8078239 0.8194293 0.8295292
#> 21: 0.8082838 0.02791664 0.7634349 0.7914057 0.8020167 0.8136675 0.8247266
#> 22: 0.8037754 0.02840786 0.7569770 0.7865342 0.7972164 0.8095381 0.8212349
#> 23: 0.8006288 0.02867375 0.7547094 0.7830847 0.7939589 0.8070443 0.8185852
#> 24: 0.7982170 0.02890950 0.7507699 0.7806108 0.7916763 0.8048241 0.8158267
#> 25: 0.7965334 0.02913916 0.7480646 0.7789205 0.7896690 0.8032044 0.8143052
#> 26: 0.7950809 0.02932829 0.7474087 0.7775736 0.7884007 0.8021790 0.8130276
#> 27: 0.7944665 0.02957755 0.7472920 0.7768067 0.7876880 0.8016536 0.8130034
#> 28: 0.7933554 0.02983785 0.7452073 0.7757691 0.7867039 0.7999711 0.8119550
#> 29: 0.7933466 0.03015885 0.7437312 0.7758412 0.7868185 0.8002418 0.8122478
#> 30: 0.7928749 0.03047096 0.7431321 0.7752042 0.7862780 0.7997065 0.8120304
#> 31: 0.7926228 0.03051766 0.7430431 0.7742399 0.7860250 0.7993957 0.8114806
#> 32: 0.7922913 0.03045273 0.7416240 0.7738875 0.7857614 0.7986386 0.8109084
#> 33: 0.7929569 0.03031271 0.7430241 0.7743443 0.7863482 0.7991991 0.8115878
#> 34: 0.7927958 0.03002340 0.7430351 0.7743703 0.7860963 0.7986934 0.8113241
#> 35: 0.7930069 0.02969333 0.7439575 0.7747871 0.7859091 0.7990674 0.8116110
#> 36: 0.7926435 0.02934115 0.7436005 0.7749144 0.7853810 0.7986861 0.8111253
#> 37: 0.7930429 0.02907999 0.7448974 0.7754533 0.7856249 0.7989824 0.8111845
#> 38: 1.6397059 0.11193470 1.4638326 1.5687936 1.6079753 1.6586147 1.7014489
#> 39: 1.6411930 0.10580957 1.4750018 1.5740327 1.6129870 1.6605515 1.7013177
#> 40: 1.5796062 0.09872186 1.4237893 1.5164624 1.5525069 1.5973185 1.6366893
#> 41: 1.5497355 0.09252992 1.4037361 1.4895356 1.5245174 1.5668638 1.6037309
#> 42: 1.5506850 0.08904673 1.4111612 1.4926670 1.5262397 1.5674753 1.6016914
#> 43: 1.5538682 0.08765745 1.4188061 1.4966364 1.5290965 1.5704817 1.6034459
#> 44: 1.5366277 0.08655287 1.4051525 1.4803388 1.5115405 1.5528599 1.5842656
#> 45: 1.3129845 0.07347246 1.2020639 1.2651160 1.2912188 1.3256130 1.3539020
#> 46: 1.1627800 0.05731698 1.0733690 1.1258980 1.1481453 1.1736574 1.1971788
#> 47: 1.0849697 0.04692940 1.0078244 1.0558865 1.0739938 1.0948116 1.1134247
#> 48: 1.0004482 0.03896088 0.9393237 0.9765626 0.9914137 1.0081618 1.0223868
#> 49: 0.9323659 0.03310620 0.8835933 0.9117044 0.9245309 0.9380540 0.9499826
#> 50: 0.8832667 0.02947470 0.8422345 0.8659908 0.8763586 0.8876984 0.8977096
#> 51: 0.8201283 0.02647054 0.7824273 0.8056458 0.8143778 0.8243887 0.8321533
#> 52: 0.8914345 0.02968794 0.8465603 0.8748196 0.8855525 0.8968234 0.9058582
#> 53: 0.8682951 0.02593505 0.8310481 0.8540416 0.8622806 0.8713141 0.8802976
#> 54: 0.8496038 0.02452649 0.8146404 0.8352283 0.8431781 0.8519562 0.8622458
#> 55: 0.8345961 0.02419267 0.7989296 0.8197314 0.8276059 0.8376411 0.8475147
#> 56: 0.8229510 0.02456227 0.7863434 0.8074571 0.8156003 0.8265377 0.8366944
#> 57: 0.8141027 0.02536570 0.7766721 0.7973141 0.8064430 0.8184525 0.8288848
#> 58: 0.8081356 0.02629484 0.7683104 0.7908025 0.8005480 0.8133098 0.8235302
#> 59: 0.8037240 0.02710016 0.7624542 0.7857932 0.7962987 0.8090089 0.8200751
#> 60: 0.8006524 0.02766806 0.7580015 0.7825553 0.7930091 0.8061062 0.8175969
#> 61: 0.7982811 0.02812393 0.7547150 0.7799831 0.7908281 0.8038772 0.8156585
#> 62: 0.7966033 0.02845783 0.7530994 0.7781263 0.7894867 0.8023732 0.8137170
#> 63: 0.7951288 0.02863473 0.7523248 0.7767438 0.7881132 0.8007709 0.8127893
#> 64: 0.7944719 0.02877555 0.7515725 0.7763958 0.7873612 0.8005544 0.8123946
#> 65: 0.7933076 0.02887779 0.7493775 0.7754628 0.7859908 0.7993823 0.8114733
#> 66: 0.7932453 0.02905416 0.7487090 0.7752386 0.7859159 0.7990142 0.8117816
#> 67: 0.7927293 0.02929146 0.7479722 0.7746065 0.7852546 0.7985854 0.8113017
#> 68: 0.7924530 0.02938803 0.7479095 0.7743261 0.7850775 0.7985621 0.8103664
#> 69: 0.7921196 0.02951435 0.7470859 0.7737067 0.7846508 0.7980650 0.8105738
#> 70: 0.7928055 0.02970294 0.7478623 0.7747289 0.7850501 0.7988416 0.8110303
#> 71: 0.7926868 0.02984685 0.7486045 0.7743384 0.7849988 0.7987736 0.8106812
#> 72: 0.7929573 0.03000271 0.7482573 0.7746620 0.7852625 0.7992195 0.8112733
#> 73: 0.7926621 0.03012012 0.7484052 0.7741659 0.7846449 0.7987758 0.8115867
#> 74: 0.7931293 0.03024958 0.7480739 0.7741972 0.7851838 0.7992595 0.8122724
#> mean sd lower_90 lower_50 lower_20 upper_20 upper_50
#> upper_90
#> 1: 1.8212265
#> 2: 1.8135475
#> 3: 1.7390201
#> 4: 1.6980564
#> 5: 1.6927822
#> 6: 1.6942818
#> 7: 1.6741462
#> 8: 1.4295287
#> 9: 1.2548865
#> 10: 1.1620916
#> 11: 1.0675546
#> 12: 0.9890602
#> 13: 0.9355675
#> 14: 0.8664468
#> 15: 0.9435970
#> 16: 0.9151955
#> 17: 0.8930346
#> 18: 0.8769624
#> 19: 0.8658018
#> 20: 0.8571191
#> 21: 0.8521743
#> 22: 0.8497203
#> 23: 0.8475227
#> 24: 0.8449439
#> 25: 0.8431614
#> 26: 0.8414513
#> 27: 0.8407910
#> 28: 0.8397064
#> 29: 0.8414035
#> 30: 0.8415769
#> 31: 0.8409005
#> 32: 0.8403171
#> 33: 0.8408514
#> 34: 0.8406670
#> 35: 0.8406123
#> 36: 0.8400169
#> 37: 0.8397399
#> 38: 1.8329196
#> 39: 1.8161321
#> 40: 1.7481430
#> 41: 1.7022939
#> 42: 1.6975710
#> 43: 1.6997360
#> 44: 1.6842825
#> 45: 1.4397871
#> 46: 1.2543140
#> 47: 1.1581395
#> 48: 1.0624003
#> 49: 0.9849970
#> 50: 0.9311381
#> 51: 0.8621833
#> 52: 0.9379101
#> 53: 0.9106242
#> 54: 0.8904856
#> 55: 0.8763264
#> 56: 0.8664992
#> 57: 0.8576175
#> 58: 0.8533785
#> 59: 0.8505473
#> 60: 0.8493344
#> 61: 0.8462909
#> 62: 0.8443542
#> 63: 0.8423259
#> 64: 0.8425316
#> 65: 0.8411789
#> 66: 0.8413629
#> 67: 0.8410591
#> 68: 0.8408014
#> 69: 0.8409095
#> 70: 0.8414818
#> 71: 0.8416032
#> 72: 0.8426234
#> 73: 0.8438992
#> 74: 0.8437577
#> upper_90
#>
#> $summarised_measures$growth_rate
#> region date strat type median
#> 1: realland 2020-02-22 <NA> estimate 1.575462e-01
#> 2: realland 2020-02-23 <NA> estimate 1.588251e-01
#> 3: realland 2020-02-24 <NA> estimate 1.446278e-01
#> 4: realland 2020-02-25 <NA> estimate 1.381169e-01
#> 5: realland 2020-02-26 <NA> estimate 1.383001e-01
#> 6: realland 2020-02-27 <NA> estimate 1.391017e-01
#> 7: realland 2020-02-28 <NA> estimate 1.349743e-01
#> 8: realland 2020-02-29 <NA> estimate 8.064985e-02
#> 9: realland 2020-03-01 <NA> estimate 4.343481e-02
#> 10: realland 2020-03-02 <NA> estimate 2.314296e-02
#> 11: realland 2020-03-03 <NA> estimate 2.001439e-05
#> 12: realland 2020-03-04 <NA> estimate -1.925108e-02
#> 13: realland 2020-03-05 <NA> estimate -3.323086e-02
#> 14: realland 2020-03-06 <NA> estimate -5.136976e-02
#> 15: realland 2020-03-07 <NA> estimate based on partial data -3.132148e-02
#> 16: realland 2020-03-08 <NA> estimate based on partial data -3.760878e-02
#> 17: realland 2020-03-09 <NA> estimate based on partial data -4.237653e-02
#> 18: realland 2020-03-10 <NA> estimate based on partial data -4.644200e-02
#> 19: realland 2020-03-11 <NA> estimate based on partial data -4.967111e-02
#> 20: realland 2020-03-12 <NA> estimate based on partial data -5.201373e-02
#> 21: realland 2020-03-13 <NA> estimate based on partial data -5.370508e-02
#> 22: realland 2020-03-14 <NA> estimate based on partial data -5.485896e-02
#> 23: realland 2020-03-15 <NA> estimate based on partial data -5.565055e-02
#> 24: realland 2020-03-16 <NA> estimate based on partial data -5.630208e-02
#> 25: realland 2020-03-17 <NA> estimate based on partial data -5.662788e-02
#> 26: realland 2020-03-18 <NA> estimate based on partial data -5.704186e-02
#> 27: realland 2020-03-19 <NA> estimate based on partial data -5.713477e-02
#> 28: realland 2020-03-20 <NA> estimate based on partial data -5.737854e-02
#> 29: realland 2020-03-21 <NA> estimate based on partial data -5.738123e-02
#> 30: realland 2020-03-22 <NA> estimate based on partial data -5.749809e-02
#> 31: realland 2020-03-23 <NA> forecast -5.758261e-02
#> 32: realland 2020-03-24 <NA> forecast -5.769667e-02
#> 33: realland 2020-03-25 <NA> forecast -5.751280e-02
#> 34: realland 2020-03-26 <NA> forecast -5.762181e-02
#> 35: realland 2020-03-27 <NA> forecast -5.759345e-02
#> 36: realland 2020-03-28 <NA> forecast -5.780140e-02
#> 37: realland 2020-03-29 <NA> forecast -5.760798e-02
#> 38: testland 2020-02-22 <NA> estimate 1.563979e-01
#> 39: testland 2020-02-23 <NA> estimate 1.575085e-01
#> 40: testland 2020-02-24 <NA> estimate 1.430748e-01
#> 41: testland 2020-02-25 <NA> estimate 1.363474e-01
#> 42: testland 2020-02-26 <NA> estimate 1.367364e-01
#> 43: testland 2020-02-27 <NA> estimate 1.375877e-01
#> 44: testland 2020-02-28 <NA> estimate 1.333328e-01
#> 45: testland 2020-02-29 <NA> estimate 8.016316e-02
#> 46: testland 2020-03-01 <NA> estimate 4.341660e-02
#> 47: testland 2020-03-02 <NA> estimate 2.299287e-02
#> 48: testland 2020-03-03 <NA> estimate -2.095528e-04
#> 49: testland 2020-03-04 <NA> estimate -1.949756e-02
#> 50: testland 2020-03-05 <NA> estimate -3.355912e-02
#> 51: testland 2020-03-06 <NA> estimate -5.165495e-02
#> 52: testland 2020-03-07 <NA> estimate based on partial data -3.148245e-02
#> 53: testland 2020-03-08 <NA> estimate based on partial data -3.769117e-02
#> 54: testland 2020-03-09 <NA> estimate based on partial data -4.242752e-02
#> 55: testland 2020-03-10 <NA> estimate based on partial data -4.649727e-02
#> 56: testland 2020-03-11 <NA> estimate based on partial data -4.956944e-02
#> 57: testland 2020-03-12 <NA> estimate based on partial data -5.192920e-02
#> 58: testland 2020-03-13 <NA> estimate based on partial data -5.348856e-02
#> 59: testland 2020-03-14 <NA> estimate based on partial data -5.456972e-02
#> 60: testland 2020-03-15 <NA> estimate based on partial data -5.537124e-02
#> 61: testland 2020-03-16 <NA> estimate based on partial data -5.606901e-02
#> 62: testland 2020-03-17 <NA> estimate based on partial data -5.640661e-02
#> 63: testland 2020-03-18 <NA> estimate based on partial data -5.678623e-02
#> 64: testland 2020-03-19 <NA> estimate based on partial data -5.682055e-02
#> 65: testland 2020-03-20 <NA> estimate based on partial data -5.718895e-02
#> 66: testland 2020-03-21 <NA> estimate based on partial data -5.709995e-02
#> 67: testland 2020-03-22 <NA> estimate based on partial data -5.723812e-02
#> 68: testland 2020-03-23 <NA> forecast -5.744422e-02
#> 69: testland 2020-03-24 <NA> forecast -5.752912e-02
#> 70: testland 2020-03-25 <NA> forecast -5.739810e-02
#> 71: testland 2020-03-26 <NA> forecast -5.740797e-02
#> 72: testland 2020-03-27 <NA> forecast -5.732514e-02
#> 73: testland 2020-03-28 <NA> forecast -5.742998e-02
#> 74: testland 2020-03-29 <NA> forecast -5.739097e-02
#> region date strat type median
#> mean sd lower_90 lower_50 lower_20
#> 1: 0.1815941092 0.221521149 0.130848310 0.142020409 0.149876628
#> 2: 0.1835819424 0.241156013 0.129254671 0.141418406 0.150206318
#> 3: 0.1646265288 0.174357693 0.118334389 0.129549560 0.137021132
#> 4: 0.1562627687 0.156165277 0.112258922 0.123174444 0.130731612
#> 5: 0.1571776950 0.165489060 0.111771459 0.123162025 0.131103457
#> 6: 0.1583454696 0.173663391 0.112855149 0.123934225 0.131803032
#> 7: 0.1529951540 0.160564588 0.110197003 0.120316485 0.127984441
#> 8: 0.0866982540 0.040453311 0.063635474 0.073963725 0.077764943
#> 9: 0.0449318167 0.018668994 0.023844151 0.036769001 0.040803224
#> 10: 0.0237462338 0.014255120 0.003641038 0.016339768 0.020573899
#> 11: 0.0000182915 0.011249628 -0.017834477 -0.006444107 -0.002201962
#> 12: -0.0192760701 0.010323323 -0.035933431 -0.025543679 -0.021467518
#> 13: -0.0332549539 0.009835409 -0.048377784 -0.039455439 -0.035433484
#> 14: -0.0515511057 0.010231534 -0.067817197 -0.057741205 -0.053606187
#> 15: -0.0302613545 0.007478512 -0.040246097 -0.034501403 -0.032602218
#> 16: -0.0371122360 0.007545292 -0.048436351 -0.040596004 -0.038638590
#> 17: -0.0426250440 0.007848504 -0.055378300 -0.046227082 -0.043736093
#> 18: -0.0470190225 0.007989403 -0.060627786 -0.050809600 -0.047962146
#> 19: -0.0503798137 0.008036011 -0.064215821 -0.054298076 -0.051143313
#> 20: -0.0529331700 0.008072241 -0.067228710 -0.056932795 -0.053583229
#> 21: -0.0546535520 0.008093715 -0.069305234 -0.058545623 -0.055280827
#> 22: -0.0559322761 0.008112906 -0.070945610 -0.059936498 -0.056609145
#> 23: -0.0568281027 0.008108680 -0.071663024 -0.060832384 -0.057517428
#> 24: -0.0575137291 0.008113937 -0.072624059 -0.061567075 -0.058148528
#> 25: -0.0579901282 0.008130125 -0.073215425 -0.062100686 -0.058615692
#> 26: -0.0584050150 0.008162361 -0.073400213 -0.062588218 -0.058882441
#> 27: -0.0585757505 0.008204692 -0.073559745 -0.062957705 -0.059012310
#> 28: -0.0588951500 0.008281319 -0.074262514 -0.063325776 -0.059352455
#> 29: -0.0588903374 0.008347621 -0.074514021 -0.063396491 -0.059232166
#> 30: -0.0590212103 0.008433360 -0.074439545 -0.063495337 -0.059413226
#> 31: -0.0590971178 0.008464202 -0.074755375 -0.063581765 -0.059617683
#> 32: -0.0591962624 0.008459218 -0.074683473 -0.063517759 -0.059947004
#> 33: -0.0590012153 0.008402770 -0.074670605 -0.063210232 -0.059644048
#> 34: -0.0590512849 0.008336777 -0.074326135 -0.063278713 -0.059833202
#> 35: -0.0589915184 0.008242239 -0.074579710 -0.062998068 -0.059650011
#> 36: -0.0591014756 0.008156423 -0.074548981 -0.063068571 -0.059669268
#> 37: -0.0589859573 0.008067291 -0.074305643 -0.062854173 -0.059555471
#> 38: 0.1823859050 0.130673407 0.131087704 0.141265978 0.149524049
#> 39: 0.1841454928 0.137474696 0.129331427 0.140837351 0.149965593
#> 40: 0.1651444321 0.106606351 0.118196670 0.129083034 0.136761632
#> 41: 0.1565933170 0.095816241 0.111770566 0.123030089 0.130092754
#> 42: 0.1572719752 0.096832871 0.111870829 0.122885334 0.130098885
#> 43: 0.1582103395 0.096853636 0.112579829 0.123410900 0.130725140
#> 44: 0.1527548403 0.088451006 0.110097022 0.120014466 0.126896133
#> 45: 0.0866030154 0.030585218 0.062232523 0.073184889 0.077426417
#> 46: 0.0447035804 0.016811013 0.023004849 0.036170905 0.040773508
#> 47: 0.0234060340 0.013770920 0.002559406 0.015823862 0.020524387
#> 48: -0.0003748580 0.011487466 -0.019436896 -0.006900047 -0.002461986
#> 49: -0.0196444633 0.010595564 -0.037255700 -0.026029152 -0.021879100
#> 50: -0.0335747910 0.009992944 -0.049262107 -0.039838100 -0.035882399
#> 51: -0.0517877271 0.010219636 -0.067812045 -0.058243352 -0.054154398
#> 52: -0.0305412243 0.007460018 -0.039791196 -0.034587258 -0.032714464
#> 53: -0.0373058144 0.007213024 -0.047363863 -0.041020220 -0.038621651
#> 54: -0.0427176328 0.007378830 -0.053890350 -0.046496553 -0.043705363
#> 55: -0.0470344601 0.007479408 -0.059049780 -0.050946448 -0.047966010
#> 56: -0.0503597809 0.007503816 -0.063171666 -0.054258568 -0.051169265
#> 57: -0.0528750322 0.007574691 -0.066090123 -0.056761772 -0.053477108
#> 58: -0.0545615072 0.007673324 -0.067673578 -0.058496695 -0.055068207
#> 59: -0.0558107853 0.007794211 -0.069317278 -0.059771415 -0.056213048
#> 60: -0.0566847614 0.007889271 -0.070325684 -0.060542669 -0.056910918
#> 61: -0.0573579268 0.007964122 -0.071728224 -0.061166091 -0.057574893
#> 62: -0.0578307963 0.008006215 -0.072079502 -0.061694359 -0.058076234
#> 63: -0.0582485237 0.008019340 -0.072920184 -0.062212777 -0.058625482
#> 64: -0.0584267917 0.008005156 -0.073025695 -0.062442816 -0.058699399
#> 65: -0.0587543353 0.008003017 -0.073552948 -0.062786335 -0.059085423
#> 66: -0.0587573284 0.007988773 -0.073225081 -0.062701648 -0.059092602
#> 67: -0.0588916208 0.008010594 -0.073646683 -0.062965388 -0.059197067
#> 68: -0.0589654281 0.008007278 -0.073728675 -0.063022489 -0.059294023
#> 69: -0.0590558808 0.008006966 -0.073476136 -0.063176699 -0.059403023
#> 70: -0.0588471206 0.007996884 -0.073467234 -0.062868914 -0.059338556
#> 71: -0.0588766345 0.008009832 -0.073496175 -0.063089304 -0.059392638
#> 72: -0.0587925271 0.008015377 -0.073428768 -0.062925781 -0.059313284
#> 73: -0.0588756627 0.008029071 -0.073374236 -0.062976800 -0.059462222
#> 74: -0.0587350412 0.008023904 -0.073129821 -0.062790899 -0.059362671
#> mean sd lower_90 lower_50 lower_20
#> upper_20 upper_50 upper_90
#> 1: 0.166819361 0.188205236 0.285114215
#> 2: 0.168230544 0.191355588 0.292074092
#> 3: 0.152708753 0.172412822 0.258470821
#> 4: 0.145545094 0.164058860 0.243038799
#> 5: 0.146240243 0.165368485 0.245478888
#> 6: 0.147508235 0.166120250 0.246819201
#> 7: 0.142698906 0.160640937 0.235689848
#> 8: 0.083654544 0.091704200 0.125221152
#> 9: 0.046169933 0.050957188 0.069071426
#> 10: 0.025687991 0.030364694 0.044948886
#> 11: 0.002335683 0.006385167 0.016999844
#> 12: -0.017035365 -0.013106767 -0.002931006
#> 13: -0.031385654 -0.027468206 -0.016950706
#> 14: -0.049303151 -0.045279827 -0.035328771
#> 15: -0.029947681 -0.026954575 -0.017127193
#> 16: -0.036430655 -0.033816638 -0.024901185
#> 17: -0.041293797 -0.039081742 -0.030455374
#> 18: -0.045174108 -0.043183992 -0.035198989
#> 19: -0.048200979 -0.046229781 -0.038673613
#> 20: -0.050490580 -0.048530768 -0.041812328
#> 21: -0.052048351 -0.050113613 -0.043388603
#> 22: -0.053218533 -0.051143658 -0.044895074
#> 23: -0.053928111 -0.051855266 -0.045893797
#> 24: -0.054538039 -0.052431178 -0.046682028
#> 25: -0.054932224 -0.052752276 -0.047439030
#> 26: -0.055338071 -0.053150002 -0.047743160
#> 27: -0.055438044 -0.053281666 -0.047846017
#> 28: -0.055653813 -0.053402789 -0.048168245
#> 29: -0.055612651 -0.053291129 -0.048379141
#> 30: -0.055767036 -0.053329221 -0.048593126
#> 31: -0.055771690 -0.053357224 -0.048536703
#> 32: -0.055898599 -0.053439598 -0.048490801
#> 33: -0.055790201 -0.053346186 -0.048497525
#> 34: -0.055868609 -0.053363021 -0.048588345
#> 35: -0.055855906 -0.053338649 -0.048546373
#> 36: -0.056027348 -0.053511837 -0.048850330
#> 37: -0.055899900 -0.053459750 -0.048878023
#> 38: 0.165950595 0.186371775 0.296950952
#> 39: 0.167298791 0.188966688 0.304381920
#> 40: 0.151529080 0.169940708 0.270677585
#> 41: 0.144236598 0.162260762 0.255829795
#> 42: 0.144623183 0.163231737 0.259049475
#> 43: 0.145293212 0.164419041 0.258991880
#> 44: 0.140657701 0.159044605 0.246529670
#> 45: 0.083351459 0.091198483 0.128872946
#> 46: 0.045958959 0.050708245 0.070090695
#> 47: 0.025608691 0.029863588 0.043667126
#> 48: 0.002154091 0.006020141 0.016136190
#> 49: -0.017195910 -0.013400714 -0.003908225
#> 50: -0.031459527 -0.027719654 -0.018036554
#> 51: -0.049441971 -0.045474089 -0.036129388
#> 52: -0.030162242 -0.027369330 -0.018077355
#> 53: -0.036510115 -0.034335200 -0.025948312
#> 54: -0.041333903 -0.039174880 -0.032030681
#> 55: -0.045258611 -0.043275024 -0.036361106
#> 56: -0.048306514 -0.046163817 -0.039616352
#> 57: -0.050435984 -0.048495616 -0.042575938
#> 58: -0.051854907 -0.049951920 -0.044398069
#> 59: -0.053010065 -0.050986050 -0.045359964
#> 60: -0.053962558 -0.051741129 -0.046458818
#> 61: -0.054570493 -0.052316783 -0.047241985
#> 62: -0.055013052 -0.052724746 -0.047797386
#> 63: -0.055367375 -0.053023907 -0.048202297
#> 64: -0.055526833 -0.053133329 -0.048346377
#> 65: -0.055702187 -0.053349803 -0.048929225
#> 66: -0.055611342 -0.053285255 -0.049098575
#> 67: -0.055745457 -0.053380351 -0.049216964
#> 68: -0.055848031 -0.053456292 -0.049201126
#> 69: -0.055933188 -0.053608283 -0.049207632
#> 70: -0.055707872 -0.053479699 -0.048876367
#> 71: -0.055684648 -0.053612800 -0.048845849
#> 72: -0.055677359 -0.053465005 -0.048774319
#> 73: -0.055775698 -0.053626188 -0.048952880
#> 74: -0.055664848 -0.053455992 -0.048806180
#> upper_20 upper_50 upper_90
#>
#> $summarised_measures$cases_by_infection
#> region date strat type median mean
#> 1: realland 2020-02-22 <NA> estimate 1584.5 1564.8
#> 2: realland 2020-02-23 <NA> estimate 1845.3 1824.5
#> 3: realland 2020-02-24 <NA> estimate 2063.4 2043.5
#> 4: realland 2020-02-25 <NA> estimate 2322.8 2304.7
#> 5: realland 2020-02-26 <NA> estimate 2649.5 2633.2
#> 6: realland 2020-02-27 <NA> estimate 3023.0 3011.0
#> 7: realland 2020-02-28 <NA> estimate 3403.6 3398.5
#> 8: realland 2020-02-29 <NA> estimate 3300.8 3303.4
#> 9: realland 2020-03-01 <NA> estimate 3173.5 3184.6
#> 10: realland 2020-03-02 <NA> estimate 3106.5 3125.2
#> 11: realland 2020-03-03 <NA> estimate 2943.0 2967.0
#> 12: realland 2020-03-04 <NA> estimate 2755.5 2784.0
#> 13: realland 2020-03-05 <NA> estimate 2577.0 2606.2
#> 14: realland 2020-03-06 <NA> estimate 2328.0 2357.5
#> 15: realland 2020-03-07 <NA> estimate based on partial data 2419.7 2453.6
#> 16: realland 2020-03-08 <NA> estimate based on partial data 2285.7 2320.3
#> 17: realland 2020-03-09 <NA> estimate based on partial data 2157.5 2192.9
#> 18: realland 2020-03-10 <NA> estimate based on partial data 2037.4 2071.5
#> 19: realland 2020-03-11 <NA> estimate based on partial data 1923.4 1956.4
#> 20: realland 2020-03-12 <NA> estimate based on partial data 1814.6 1846.8
#> 21: realland 2020-03-13 <NA> estimate based on partial data 1713.7 1743.8
#> 22: realland 2020-03-14 <NA> estimate based on partial data 1618.2 1645.6
#> 23: realland 2020-03-15 <NA> estimate based on partial data 1527.1 1552.3
#> 24: realland 2020-03-16 <NA> estimate based on partial data 1441.5 1464.1
#> 25: realland 2020-03-17 <NA> estimate based on partial data 1360.7 1380.9
#> 26: realland 2020-03-18 <NA> estimate based on partial data 1284.0 1302.0
#> 27: realland 2020-03-19 <NA> estimate based on partial data 1212.6 1228.3
#> 28: realland 2020-03-20 <NA> estimate based on partial data 1144.1 1157.9
#> 29: realland 2020-03-21 <NA> estimate based on partial data 1080.4 1092.7
#> 30: realland 2020-03-22 <NA> estimate based on partial data 1019.6 1030.7
#> 31: realland 2020-03-23 <NA> forecast 962.3 972.0
#> 32: realland 2020-03-24 <NA> forecast 907.8 916.5
#> 33: realland 2020-03-25 <NA> forecast 857.4 865.1
#> 34: realland 2020-03-26 <NA> forecast 809.3 815.9
#> 35: realland 2020-03-27 <NA> forecast 764.6 769.9
#> 36: realland 2020-03-28 <NA> forecast 721.3 725.9
#> 37: realland 2020-03-29 <NA> forecast 680.8 685.0
#> 38: testland 2020-02-22 <NA> estimate 1585.8 1570.2
#> 39: testland 2020-02-23 <NA> estimate 1846.5 1830.2
#> 40: testland 2020-02-24 <NA> estimate 2064.8 2049.0
#> 41: testland 2020-02-25 <NA> estimate 2324.3 2309.8
#> 42: testland 2020-02-26 <NA> estimate 2648.7 2637.8
#> 43: testland 2020-02-27 <NA> estimate 3023.3 3014.6
#> 44: testland 2020-02-28 <NA> estimate 3403.3 3400.8
#> 45: testland 2020-02-29 <NA> estimate 3300.8 3303.9
#> 46: testland 2020-03-01 <NA> estimate 3173.6 3183.5
#> 47: testland 2020-03-02 <NA> estimate 3107.7 3122.8
#> 48: testland 2020-03-03 <NA> estimate 2944.1 2963.5
#> 49: testland 2020-03-04 <NA> estimate 2756.5 2779.7
#> 50: testland 2020-03-05 <NA> estimate 2575.8 2601.5
#> 51: testland 2020-03-06 <NA> estimate 2326.8 2352.7
#> 52: testland 2020-03-07 <NA> estimate based on partial data 2418.4 2448.2
#> 53: testland 2020-03-08 <NA> estimate based on partial data 2284.6 2315.0
#> 54: testland 2020-03-09 <NA> estimate based on partial data 2157.6 2187.7
#> 55: testland 2020-03-10 <NA> estimate based on partial data 2037.8 2066.6
#> 56: testland 2020-03-11 <NA> estimate based on partial data 1925.1 1951.9
#> 57: testland 2020-03-12 <NA> estimate based on partial data 1817.6 1842.6
#> 58: testland 2020-03-13 <NA> estimate based on partial data 1716.4 1740.0
#> 59: testland 2020-03-14 <NA> estimate based on partial data 1620.1 1642.1
#> 60: testland 2020-03-15 <NA> estimate based on partial data 1528.9 1549.2
#> 61: testland 2020-03-16 <NA> estimate based on partial data 1443.0 1461.2
#> 62: testland 2020-03-17 <NA> estimate based on partial data 1361.7 1378.4
#> 63: testland 2020-03-18 <NA> estimate based on partial data 1284.8 1299.7
#> 64: testland 2020-03-19 <NA> estimate based on partial data 1212.8 1226.2
#> 65: testland 2020-03-20 <NA> estimate based on partial data 1144.0 1155.9
#> 66: testland 2020-03-21 <NA> estimate based on partial data 1080.6 1090.9
#> 67: testland 2020-03-22 <NA> estimate based on partial data 1020.2 1029.1
#> 68: testland 2020-03-23 <NA> forecast 962.3 970.5
#> 69: testland 2020-03-24 <NA> forecast 908.1 915.1
#> 70: testland 2020-03-25 <NA> forecast 857.8 863.9
#> 71: testland 2020-03-26 <NA> forecast 809.2 814.8
#> 72: testland 2020-03-27 <NA> forecast 764.1 768.9
#> 73: testland 2020-03-28 <NA> forecast 721.0 725.2
#> 74: testland 2020-03-29 <NA> forecast 680.9 684.5
#> region date strat type median mean
#> sd lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#> 1: 96.8 1386.4 1532.6 1570.1 1592.3 1607.3 1681.7
#> 2: 110.1 1620.8 1789.1 1830.1 1853.8 1871.4 1960.7
#> 3: 119.9 1833.2 2003.9 2048.7 2072.4 2093.3 2198.6
#> 4: 131.3 2074.6 2260.6 2308.5 2332.9 2358.7 2484.6
#> 5: 145.7 2380.6 2580.6 2634.0 2660.0 2687.0 2836.3
#> 6: 162.4 2744.1 2947.9 3006.5 3034.4 3066.9 3253.0
#> 7: 179.8 3108.0 3328.3 3387.9 3416.3 3460.8 3676.3
#> 8: 172.9 3040.2 3235.0 3286.3 3314.3 3359.8 3575.3
#> 9: 166.7 2940.2 3117.1 3163.0 3190.4 3237.6 3458.1
#> 10: 165.4 2888.9 3057.1 3095.6 3125.4 3176.0 3409.1
#> 11: 160.2 2753.2 2899.3 2932.4 2961.5 3014.1 3255.9
#> 12: 154.4 2587.4 2718.1 2746.0 2775.4 2828.2 3068.9
#> 13: 149.0 2420.4 2541.6 2565.7 2594.8 2646.6 2882.5
#> 14: 139.0 2184.1 2296.0 2316.5 2345.3 2391.9 2624.3
#> 15: 149.0 2273.6 2386.1 2407.0 2439.8 2491.4 2740.2
#> 16: 144.7 2151.5 2254.8 2273.0 2304.4 2357.8 2599.2
#> 17: 140.0 2031.6 2127.9 2146.2 2176.8 2229.5 2461.0
#> 18: 134.8 1915.4 2009.4 2026.2 2054.7 2108.6 2324.9
#> 19: 129.4 1805.4 1895.9 1913.0 1939.9 1991.4 2190.0
#> 20: 123.6 1706.2 1790.6 1805.7 1830.8 1881.0 2071.7
#> 21: 117.6 1608.2 1691.3 1705.3 1729.4 1774.9 1957.2
#> 22: 111.4 1514.5 1596.6 1610.1 1632.8 1674.3 1843.2
#> 23: 105.1 1423.9 1507.1 1520.0 1540.2 1578.2 1737.8
#> 24: 98.7 1340.8 1422.5 1435.0 1454.3 1489.0 1642.4
#> 25: 92.4 1268.3 1342.6 1354.7 1372.4 1404.7 1555.8
#> 26: 86.2 1195.0 1266.6 1278.8 1294.2 1323.7 1459.6
#> 27: 80.3 1129.0 1195.9 1207.6 1221.7 1246.8 1373.8
#> 28: 74.7 1066.7 1128.1 1139.6 1152.6 1174.8 1295.1
#> 29: 69.5 1007.3 1065.2 1076.4 1088.5 1108.5 1217.9
#> 30: 64.6 950.9 1004.7 1016.3 1026.9 1046.1 1145.9
#> 31: 60.2 896.5 947.5 958.9 968.7 987.3 1077.0
#> 32: 56.0 845.4 893.0 904.7 913.8 932.6 1014.6
#> 33: 52.2 796.0 843.8 854.4 862.9 880.9 958.2
#> 34: 48.6 749.0 796.1 806.2 814.9 831.2 899.5
#> 35: 45.2 707.8 751.3 761.4 769.5 784.6 847.5
#> 36: 41.9 667.6 708.8 718.3 726.2 739.4 795.9
#> 37: 38.8 630.7 668.9 678.4 685.4 697.7 748.8
#> 38: 87.6 1409.7 1541.7 1572.6 1593.4 1610.3 1684.6
#> 39: 100.4 1647.4 1797.8 1831.7 1854.9 1875.2 1968.1
#> 40: 110.4 1852.3 2012.5 2048.4 2074.2 2096.5 2206.6
#> 41: 122.3 2096.7 2266.5 2307.8 2333.4 2358.9 2487.6
#> 42: 137.3 2401.5 2586.2 2633.5 2660.4 2690.0 2849.0
#> 43: 154.8 2752.4 2955.3 3005.4 3035.2 3071.0 3261.2
#> 44: 173.4 3117.4 3333.1 3386.2 3418.3 3462.0 3686.7
#> 45: 168.4 3049.6 3234.9 3284.6 3315.1 3363.5 3572.7
#> 46: 163.8 2936.2 3114.7 3160.3 3188.8 3237.4 3452.4
#> 47: 163.6 2880.9 3053.1 3094.5 3123.9 3174.6 3392.5
#> 48: 159.3 2741.2 2895.2 2932.1 2962.3 3010.6 3233.3
#> 49: 153.9 2577.2 2712.6 2745.0 2775.6 2823.5 3048.2
#> 50: 148.6 2414.1 2536.4 2564.5 2594.7 2641.5 2867.1
#> 51: 138.3 2179.8 2290.6 2315.3 2344.5 2389.7 2597.6
#> 52: 147.4 2268.5 2382.9 2405.7 2437.7 2486.6 2710.3
#> 53: 141.9 2144.0 2252.7 2271.6 2303.0 2352.1 2572.3
#> 54: 135.6 2024.6 2127.8 2145.3 2175.2 2220.7 2435.8
#> 55: 128.7 1916.3 2008.4 2025.8 2054.4 2098.9 2312.3
#> 56: 121.5 1811.1 1896.5 1912.6 1941.5 1981.1 2183.8
#> 57: 114.3 1712.6 1789.7 1805.6 1832.7 1872.7 2055.9
#> 58: 107.3 1617.4 1690.4 1705.9 1730.2 1767.5 1930.0
#> 59: 100.7 1524.1 1596.4 1610.2 1633.8 1669.0 1820.2
#> 60: 94.4 1437.9 1505.8 1519.9 1542.8 1575.2 1717.6
#> 61: 88.6 1353.6 1419.7 1434.6 1455.8 1484.9 1621.2
#> 62: 83.1 1273.5 1340.5 1354.5 1373.8 1401.1 1530.1
#> 63: 77.9 1197.6 1264.5 1278.5 1295.4 1321.5 1437.1
#> 64: 73.0 1127.5 1194.0 1207.3 1222.4 1246.9 1356.0
#> 65: 68.3 1061.1 1125.7 1139.0 1153.0 1175.4 1278.6
#> 66: 63.9 1000.6 1063.1 1076.0 1089.0 1110.3 1203.3
#> 67: 59.7 944.0 1003.0 1015.6 1027.1 1048.2 1136.9
#> 68: 55.7 893.4 946.1 958.3 969.4 988.9 1071.2
#> 69: 51.9 842.6 893.0 903.9 914.2 932.2 1007.9
#> 70: 48.4 796.6 843.1 853.9 863.9 880.0 951.2
#> 71: 45.0 751.2 795.6 806.1 814.9 829.6 893.6
#> 72: 41.9 709.9 751.5 761.0 769.4 782.8 841.9
#> 73: 39.0 671.0 708.9 718.1 725.9 738.1 790.8
#> 74: 36.3 633.0 669.8 678.3 685.2 696.2 746.4
#> sd lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#>
#> $summarised_measures$cases_by_report
#> region date strat type median mean
#> 1: realland 2020-02-22 <NA> estimate 202.0 325.4
#> 2: realland 2020-02-23 <NA> estimate 295.0 463.2
#> 3: realland 2020-02-24 <NA> estimate 222.5 363.3
#> 4: realland 2020-02-25 <NA> estimate 303.5 471.7
#> 5: realland 2020-02-26 <NA> estimate 314.0 514.2
#> 6: realland 2020-02-27 <NA> estimate 481.5 756.9
#> 7: realland 2020-02-28 <NA> estimate 653.0 996.7
#> 8: realland 2020-02-29 <NA> estimate 666.0 1033.2
#> 9: realland 2020-03-01 <NA> estimate 970.5 1456.2
#> 10: realland 2020-03-02 <NA> estimate 668.0 1046.5
#> 11: realland 2020-03-03 <NA> estimate 809.5 1354.3
#> 12: realland 2020-03-04 <NA> estimate 786.5 1293.0
#> 13: realland 2020-03-05 <NA> estimate 1215.5 1886.7
#> 14: realland 2020-03-06 <NA> estimate 1569.5 2493.4
#> 15: realland 2020-03-07 <NA> estimate based on partial data 1411.5 2348.0
#> 16: realland 2020-03-08 <NA> estimate based on partial data 1955.5 2937.4
#> 17: realland 2020-03-09 <NA> estimate based on partial data 1093.5 1815.8
#> 18: realland 2020-03-10 <NA> estimate based on partial data 1319.0 2145.5
#> 19: realland 2020-03-11 <NA> estimate based on partial data 1159.5 1798.0
#> 20: realland 2020-03-12 <NA> estimate based on partial data 1515.0 2431.7
#> 21: realland 2020-03-13 <NA> estimate based on partial data 1902.0 2931.4
#> 22: realland 2020-03-14 <NA> estimate based on partial data 1578.0 2550.9
#> 23: realland 2020-03-15 <NA> estimate based on partial data 1885.0 2997.7
#> 24: realland 2020-03-16 <NA> estimate based on partial data 1109.5 1839.8
#> 25: realland 2020-03-17 <NA> estimate based on partial data 1232.0 1945.2
#> 26: realland 2020-03-18 <NA> estimate based on partial data 1035.5 1696.2
#> 27: realland 2020-03-19 <NA> estimate based on partial data 1240.5 2094.5
#> 28: realland 2020-03-20 <NA> estimate based on partial data 1546.5 2470.6
#> 29: realland 2020-03-21 <NA> estimate based on partial data 1383.5 2212.1
#> 30: realland 2020-03-22 <NA> estimate based on partial data 1544.5 2478.7
#> 31: realland 2020-03-23 <NA> forecast 895.5 1459.6
#> 32: realland 2020-03-24 <NA> forecast 1042.5 1606.7
#> 33: realland 2020-03-25 <NA> forecast 812.0 1343.5
#> 34: realland 2020-03-26 <NA> forecast 991.5 1693.3
#> 35: realland 2020-03-27 <NA> forecast 1239.5 1907.3
#> 36: realland 2020-03-28 <NA> forecast 985.0 1607.5
#> 37: realland 2020-03-29 <NA> forecast 1118.5 1858.9
#> 38: testland 2020-02-22 <NA> estimate 214.0 331.4
#> 39: testland 2020-02-23 <NA> estimate 309.0 466.4
#> 40: testland 2020-02-24 <NA> estimate 213.0 362.1
#> 41: testland 2020-02-25 <NA> estimate 323.0 493.9
#> 42: testland 2020-02-26 <NA> estimate 291.0 504.2
#> 43: testland 2020-02-27 <NA> estimate 466.5 754.8
#> 44: testland 2020-02-28 <NA> estimate 670.0 1038.0
#> 45: testland 2020-02-29 <NA> estimate 699.0 1108.1
#> 46: testland 2020-03-01 <NA> estimate 976.5 1495.7
#> 47: testland 2020-03-02 <NA> estimate 656.5 1038.8
#> 48: testland 2020-03-03 <NA> estimate 830.5 1390.8
#> 49: testland 2020-03-04 <NA> estimate 839.5 1300.2
#> 50: testland 2020-03-05 <NA> estimate 1178.5 1892.8
#> 51: testland 2020-03-06 <NA> estimate 1566.5 2436.6
#> 52: testland 2020-03-07 <NA> estimate based on partial data 1558.0 2341.3
#> 53: testland 2020-03-08 <NA> estimate based on partial data 1896.5 2950.5
#> 54: testland 2020-03-09 <NA> estimate based on partial data 1153.0 1832.4
#> 55: testland 2020-03-10 <NA> estimate based on partial data 1404.5 2264.2
#> 56: testland 2020-03-11 <NA> estimate based on partial data 1157.0 1879.4
#> 57: testland 2020-03-12 <NA> estimate based on partial data 1499.0 2418.9
#> 58: testland 2020-03-13 <NA> estimate based on partial data 1829.5 2967.5
#> 59: testland 2020-03-14 <NA> estimate based on partial data 1627.5 2632.7
#> 60: testland 2020-03-15 <NA> estimate based on partial data 1947.0 2902.9
#> 61: testland 2020-03-16 <NA> estimate based on partial data 1106.0 1777.2
#> 62: testland 2020-03-17 <NA> estimate based on partial data 1327.5 2124.3
#> 63: testland 2020-03-18 <NA> estimate based on partial data 1081.5 1722.6
#> 64: testland 2020-03-19 <NA> estimate based on partial data 1358.5 2166.3
#> 65: testland 2020-03-20 <NA> estimate based on partial data 1535.0 2503.8
#> 66: testland 2020-03-21 <NA> estimate based on partial data 1384.5 2209.3
#> 67: testland 2020-03-22 <NA> estimate based on partial data 1591.5 2485.0
#> 68: testland 2020-03-23 <NA> forecast 907.0 1484.7
#> 69: testland 2020-03-24 <NA> forecast 1003.5 1574.5
#> 70: testland 2020-03-25 <NA> forecast 879.0 1363.6
#> 71: testland 2020-03-26 <NA> forecast 1071.0 1681.0
#> 72: testland 2020-03-27 <NA> forecast 1199.5 1847.0
#> 73: testland 2020-03-28 <NA> forecast 1048.0 1702.3
#> 74: testland 2020-03-29 <NA> forecast 1201.0 1848.9
#> region date strat type median mean
#> sd lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#> 1: 380.2 14.0 82.8 148.0 278.4 432.0 1014.7
#> 2: 513.7 18.0 123.0 216.6 405.0 628.8 1474.0
#> 3: 456.9 13.0 92.0 161.6 297.4 455.0 1171.4
#> 4: 541.1 20.0 118.0 214.6 409.4 628.5 1487.7
#> 5: 642.7 19.0 119.0 224.0 429.0 662.0 1730.1
#> 6: 870.9 27.0 190.0 349.6 659.8 1021.2 2338.2
#> 7: 1077.0 40.0 271.0 481.6 859.0 1375.0 3191.1
#> 8: 1122.4 43.0 277.8 488.2 879.4 1431.2 3246.1
#> 9: 1670.8 67.0 389.8 700.4 1286.8 1917.2 4339.3
#> 10: 1358.3 38.9 258.0 469.0 868.8 1325.0 3379.2
#> 11: 1702.3 51.0 321.0 579.0 1103.2 1797.0 4292.7
#> 12: 1589.2 53.0 307.0 554.8 1061.4 1693.0 4099.1
#> 13: 2189.7 74.9 494.8 903.6 1607.0 2413.8 5952.3
#> 14: 2884.8 97.9 641.5 1131.8 2082.2 3275.0 8349.2
#> 15: 2702.2 86.9 588.5 1023.8 1952.6 3116.2 7700.6
#> 16: 3321.0 145.8 728.2 1354.8 2572.4 3956.0 9374.6
#> 17: 2137.8 70.9 467.2 800.2 1520.8 2361.5 5926.4
#> 18: 2642.5 98.9 520.2 927.8 1783.4 2752.5 7104.7
#> 19: 1971.8 88.9 468.0 840.0 1572.8 2443.2 5622.2
#> 20: 2747.5 121.9 617.8 1133.8 2053.0 3153.5 8106.9
#> 21: 3230.9 117.9 749.5 1426.6 2485.4 3904.0 9186.1
#> 22: 3071.6 106.9 631.0 1151.6 2121.4 3320.2 8319.2
#> 23: 3422.4 153.0 782.2 1392.8 2567.4 3931.5 9475.2
#> 24: 2205.2 88.0 455.5 828.6 1460.2 2446.0 6162.6
#> 25: 2175.0 78.9 482.0 877.8 1634.0 2661.2 6193.5
#> 26: 2012.6 81.9 425.5 780.6 1381.8 2225.8 5684.3
#> 27: 2616.1 84.0 516.0 932.6 1720.0 2720.5 6532.9
#> 28: 2933.9 85.0 624.5 1132.0 2023.4 3212.2 7958.6
#> 29: 2635.1 79.9 555.2 1023.6 1862.2 2897.5 7008.4
#> 30: 2766.5 90.9 623.8 1126.4 2101.2 3331.2 7905.0
#> 31: 1725.0 71.0 363.8 646.6 1183.2 1931.2 4826.6
#> 32: 1845.0 70.0 393.8 760.6 1376.4 2118.5 5082.6
#> 33: 1649.5 54.0 325.5 610.2 1082.0 1742.2 4376.2
#> 34: 2136.1 54.0 393.8 716.8 1322.8 2189.8 5534.1
#> 35: 2091.7 70.0 492.0 894.6 1638.2 2608.2 5927.2
#> 36: 1889.5 72.0 426.8 743.0 1311.0 2083.2 5196.4
#> 37: 2144.2 71.9 477.0 859.6 1534.4 2506.2 6005.0
#> 38: 374.3 15.0 89.0 156.0 281.0 435.2 1072.2
#> 39: 514.0 18.0 119.0 220.6 412.4 635.0 1417.3
#> 40: 437.7 12.0 89.8 155.0 279.0 467.0 1258.0
#> 41: 538.4 22.9 133.8 240.0 424.8 658.0 1576.1
#> 42: 698.6 20.0 120.0 216.0 381.0 627.0 1637.5
#> 43: 910.0 29.0 180.5 340.0 634.0 996.0 2467.8
#> 44: 1172.6 52.0 265.0 489.6 896.0 1365.2 3364.1
#> 45: 1291.5 49.0 284.5 511.6 922.0 1425.8 3697.1
#> 46: 1573.5 55.9 391.5 749.6 1298.6 2080.5 4552.2
#> 47: 1187.9 42.9 266.8 480.6 871.4 1433.8 3308.5
#> 48: 2008.4 50.8 339.8 590.2 1127.0 1794.0 4573.2
#> 49: 1478.6 54.9 313.8 597.0 1090.8 1735.2 4211.0
#> 50: 2234.5 68.0 434.2 832.6 1574.0 2493.2 6461.0
#> 51: 2932.6 96.0 607.0 1156.8 2076.2 3192.2 7945.1
#> 52: 2580.5 97.9 569.0 1109.8 2026.4 3182.0 7412.3
#> 53: 3340.9 138.9 777.0 1396.6 2499.4 3871.5 9405.8
#> 54: 2287.3 76.9 478.8 873.6 1497.4 2268.2 5719.7
#> 55: 2630.0 102.8 586.0 1045.2 1871.4 2967.2 7310.0
#> 56: 2225.3 90.9 480.8 853.8 1569.2 2489.2 5950.9
#> 57: 2998.1 94.9 597.0 1065.0 1960.2 3133.2 7912.2
#> 58: 3361.2 148.0 795.5 1352.8 2451.6 3839.0 9787.1
#> 59: 3126.1 88.0 641.0 1191.6 2232.2 3506.5 8491.0
#> 60: 3141.2 108.9 749.0 1401.2 2590.8 3899.2 8996.3
#> 61: 2097.5 69.0 436.8 801.6 1486.4 2301.8 5556.9
#> 62: 2747.9 86.0 532.8 941.6 1767.6 2758.0 7134.3
#> 63: 2075.4 59.9 411.5 758.8 1417.8 2197.0 5573.0
#> 64: 2467.8 77.9 548.5 967.6 1880.8 2861.5 7138.1
#> 65: 2879.2 105.9 599.0 1122.4 2091.4 3288.0 8825.1
#> 66: 2688.3 92.0 534.8 963.6 1802.0 2868.8 7000.1
#> 67: 2819.8 73.0 615.2 1139.8 2192.0 3305.5 8063.8
#> 68: 1796.9 58.0 376.0 675.0 1228.4 1884.8 4942.0
#> 69: 1799.6 58.9 391.8 706.0 1324.6 2091.0 5065.1
#> 70: 1502.1 64.9 360.5 637.6 1171.4 1806.0 4376.4
#> 71: 1950.1 56.9 431.8 772.0 1414.4 2215.2 5332.5
#> 72: 2096.6 68.9 447.0 845.6 1614.4 2476.5 5741.6
#> 73: 2121.4 70.0 417.8 756.2 1440.0 2188.8 5553.8
#> 74: 2011.6 77.9 459.0 829.4 1615.8 2500.0 5914.3
#> sd lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
#>
#>
#> $reported_cases
#> date confirm region
#> 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
#> 6: 2020-02-27 78 testland
#> 7: 2020-02-28 250 testland
#> 8: 2020-02-29 238 testland
#> 9: 2020-03-01 240 testland
#> 10: 2020-03-02 561 testland
#> 11: 2020-03-03 347 testland
#> 12: 2020-03-04 466 testland
#> 13: 2020-03-05 587 testland
#> 14: 2020-03-06 769 testland
#> 15: 2020-03-07 778 testland
#> 16: 2020-03-08 1247 testland
#> 17: 2020-03-09 1492 testland
#> 18: 2020-03-10 1797 testland
#> 19: 2020-03-11 977 testland
#> 20: 2020-03-12 2313 testland
#> 21: 2020-03-13 2651 testland
#> 22: 2020-03-14 2547 testland
#> 23: 2020-03-15 3497 testland
#> 24: 2020-03-16 2823 testland
#> 25: 2020-03-17 4000 testland
#> 26: 2020-03-18 3526 testland
#> 27: 2020-03-19 4207 testland
#> 28: 2020-03-20 5322 testland
#> 29: 2020-03-21 5986 testland
#> 30: 2020-03-22 6557 testland
#> 31: 2020-02-22 14 realland
#> 32: 2020-02-23 62 realland
#> 33: 2020-02-24 53 realland
#> 34: 2020-02-25 97 realland
#> 35: 2020-02-26 93 realland
#> 36: 2020-02-27 78 realland
#> 37: 2020-02-28 250 realland
#> 38: 2020-02-29 238 realland
#> 39: 2020-03-01 240 realland
#> 40: 2020-03-02 561 realland
#> 41: 2020-03-03 347 realland
#> 42: 2020-03-04 466 realland
#> 43: 2020-03-05 587 realland
#> 44: 2020-03-06 769 realland
#> 45: 2020-03-07 778 realland
#> 46: 2020-03-08 1247 realland
#> 47: 2020-03-09 1492 realland
#> 48: 2020-03-10 1797 realland
#> 49: 2020-03-11 977 realland
#> 50: 2020-03-12 2313 realland
#> 51: 2020-03-13 2651 realland
#> 52: 2020-03-14 2547 realland
#> 53: 2020-03-15 3497 realland
#> 54: 2020-03-16 2823 realland
#> 55: 2020-03-17 4000 realland
#> 56: 2020-03-18 3526 realland
#> 57: 2020-03-19 4207 realland
#> 58: 2020-03-20 5322 realland
#> 59: 2020-03-21 5986 realland
#> 60: 2020-03-22 6557 realland
#> date confirm region
#>
#> $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
#>
#>
# }