New Cases in Italy

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After two years, I finally decided to stop updating this page and evaluation of all code blocks has been disabled. The data was last updated on October 28/2022.

Introduction

This page focuses on new cases in Italy. This page was created on <2020-08-01 Sat> and regularly updated since then.

R Functions

First we read the data from the CSV files of the Civil Protection repository1:

We get it into R: 

# evolution over time, by Region
data = read.csv(file.path(PATH, "dpc-covid19-ita-regioni.csv"))
data$data <- as.Date(data$data)

# evolution over time at the National level
new_national = read.csv(file.path(PATH, "dpc-covid19-ita-andamento-nazionale.csv"))
new_national$data <- as.Date(new_national$data)

# latest regional data
by_region = read.csv(file.path(PATH, "dpc-covid19-ita-regioni-latest.csv"))
by_region$data <- as.Date(by_region$data)

We then output a table of new cases from R, which we then use in Ruby. (The table is not exported to HTML.)

Inferior Ruby shells perform very badly with long input lines. Make sure you don’t pass the variable to a Ruby :session or the evaluation will break, while IRB tries to cope with the declaration of the input variable.

If you need a :session, you should read data directly from the Ruby session, rather than passing it as a variables. 

new_national[, c("data", "nuovi_positivi")]

New Cases in Italy

Line Plot

The shaded area corresponds to the lockdown. The red horizontal line allows to compare the latest data with historical data. 

p = plot(new_national$nuovi_positivi ~ new_national$data, type="l", lwd=6, pch=16, cex=1.6, col=c("#3B3176"))
#text(new_national$nuovi_positivi ~ new_national$data, labels=new_national$nuovi_positivi, pos=2, cex=1.3)
#abline(v = as.Date("2020-10-25"), col="#FF0000", lwd=3)

grid(p, col = "black", lty="dotted")
#rect(as.Date("2020-03-09"), -200, as.Date("2020-05-19"), 7000, border = "#AA0055", col = "#AA0055", density=2)

text(x = as.Date("2020-03-25"), y = 8000, "First Wave", col="#FF0000")
abline(h = new_national[27,]$nuovi_positivi, col="#FF0000", lwd=2)
#abline(v = as.Date("2020-03-01"), col="#FF0000", lwd=2)

abline(h = 41000, col="#FF0000", lwd=2)
text(x = as.Date("2020-11-15"), y = 42000, "Second Wave", col="#FF0000")

text(x = as.Date("2021-03-16"), y = 28000, "Third Wave", col="#FF0000")
abline(h = 27354, col="#FF0000", lwd=2)

p12_newcases.png

Calendar Heatmap

<<EOS
<div id="heatmap-total"></div>
<script>
calendar_heatmap.create({
    data: [
    #{data.map { |x| "{ day: \"%s\", count: %d }" % [x[0], x[1].to_i] }.join(",") }
    ],
    date_var: "day",
    fill_var: "count",
    target: "#heatmap-total"
});
</script>
EOS

New Cases by Region

Tabular Data

The table is built as follows:

  • egrep selects entries in the current month, getting the current month from the date command
  • the first sed gets rid of the “T17:00:00” timestamp in dates
  • the second sed compacts the date, by removing the year and replacing the month number with its name
  • datamash pivots the table by region and date
current_month=$(date +"%b")
current_month_no=$(date +"%m")
year=$(date +"%Y")

egrep ${year}-${current_month_no} ./data/dpc-covid19-ita-regioni.csv | sed -e "s/T1[78]:00:00//g" | sed -e "s/${year}-${current_month_no}-/${current_month} /g" | datamash -t, crosstab 4,1 sum 13
  Oct 01 Oct 02 Oct 03 Oct 04 Oct 05 Oct 06 Oct 07 Oct 08 Oct 09 Oct 10 Oct 11 Oct 12 Oct 13 Oct 14 Oct 15 Oct 16 Oct 17 Oct 18 Oct 19 Oct 20 Oct 21 Oct 22 Oct 23 Oct 24 Oct 25 Oct 26 Oct 27 Oct 28
Abruzzo 1036 861 472 1889 1279 1190 1053 1200 895 427 1683 1189 1148 1035 892 702 424 1332 1080 1004 842 789 634 337 1230 915 821 767
Basilicata 229 165 134 298 193 162 184 173 165 117 281 192 217 180 183 132 107 261 134 165 122 141 109 87 230 142 141 159
Calabria 775 601 368 1390 838 898 933 861 737 430 1384 842 981 857 764 577 326 1261 830 791 722 703 528 283 1018 691 688 619
Campania 2035 1846 768 3377 2178 2281 2173 2325 1935 991 3839 2487 2401 1891 2193 1764 782 3473 2246 2336 2078 1951 1592 812 2992 2009 1918 1763
Emilia-Romagna 2876 2758 1964 2721 4508 3897 4095 4005 3794 2194 3258 4853 4070 3719 3335 3276 2024 2786 4133 3573 3296 2944 2586 1705 2151 3384 2961 2660
Friuli Venezia Giulia 1254 752 336 1986 1689 1415 1401 1471 833 425 1947 1509 1435 1139 1302 740 308 1599 1371 1173 926 941 568 291 1408 1010 947 760
Lazio 2810 2708 1437 4722 3474 3771 3430 3475 3023 1781 5245 3670 3875 3233 3289 2738 1637 4710 3533 3657 3316 2903 2674 1535 4644 3279 2981 2900
Liguria 882 706 358 1590 1163 1155 1093 1130 903 379 1853 1228 1182 1096 1115 771 328 1737 1113 1091 896 857 657 295 1352 936 817 748
Lombardia 5991 4896 1847 12249 8498 9124 8699 8671 6231 2229 14025 9126 8771 7991 7701 5653 1864 12757 8230 7983 6803 6161 4646 1640 9979 6216 6173 5504
Marche 1026 999 447 1864 1188 1353 1384 1134 989 501 2067 1294 1335 1239 1120 1044 409 1533 1058 1020 973 842 689 317 1358 844 858 737
Molise 123 137 102 133 164 142 139 107 140 80 167 161 146 143 143 145 47 138 147 122 138 91 93 50 123 90 94 105
P.A. Bolzano 570 362 187 1305 758 843 788 754 470 221 1399 832 852 807 706 385 198 1159 641 623 470 478 218 124 683 404 358 291
P.A. Trento 639 512 159 1013 760 804 744 726 585 144 1142 881 749 638 636 446 127 789 578 545 477 400 314 119 485 386 301 269
Piemonte 3249 2754 1341 7547 4899 4659 5010 4874 3672 1335 7812 5170 4991 4240 3843 2865 1480 6818 3946 4341 4305 2068 2181 829 4822 3102 2115 1999
Puglia 1271 954 442 2067 1343 1365 1339 1408 1122 510 2366 1644 1601 1441 1486 1137 464 2331 1469 1464 1352 1294 1018 417 2104 1319 1327 1209
Sardegna 352 246 224 922 631 723 650 497 416 383 1215 750 751 756 565 471 325 1200 740 757 568 620 485 235 1114 703 657 618
Sicilia 1188 1058 498 1873 1430 1270 1403 1221 1090 532 1854 1595 1443 1383 1257 1169 535 2071 1608 1520 1408 1282 1281 542 2127 1562 1331 1472
Toscana 1883 1514 524 3637 2504 2649 2345 2547 1809 581 4085 2716 2675 2373 2341 1664 512 3459 2213 2282 1890 2044 1361 612 3485 2381 2192 1918
Umbria 806 776 451 1198 1078 1143 984 963 888 416 1202 1072 1023 883 887 734 304 1015 812 828 764 705 627 306 923 816 679 600
Valle d’Aosta 77 58 42 182 141 128 175 101 89 35 228 142 120 121 107 75 29 187 121 121 93 75 55 30 123 82 91 51
Veneto 4804 3846 1215 8312 6509 5881 6650 6073 4658 1378 8873 6410 5939 5415 5104 3751 1209 7744 5709 5167 4677 4486 3238 1040 6363 4772 4310 3891

Line Plots

# how many rows and columns?
par(mfrow=c(11, 2))
regions <- c("Valle d'Aosta", "Piemonte", "Liguria", "Lombardia", "Veneto",
             "P.A. Trento", "P.A. Bolzano", "Friuli Venezia Giulia",
             "Emilia-Romagna", "Toscana", "Marche", "Umbria",
             "Lazio", "Abruzzo", "Molise", "Campania",
             "Puglia", "Basilicata", "Calabria", "Sicilia",
             "Sardegna")
for (region in regions) {
  my_plot(region,
          data, 
          max=max(data$nuovi_positivi),
          filter=TRUE, 
          textlabels=FALSE,
          variables=c("nuovi_positivi"),
          graphtypes=c("l"),
          colors=c("black"))
}

new_cases_by_region.png

The source code available on the COVID-19 pages is distributed under the MIT License; the content is distributed under a Creative Commons - Attribution 4.0.

Footnotes:

1

The CSV files containing the data are updated by the first code block in index.html.

Author: Adolfo Villafiorita

Published: 2024-07-15 Mon 08:46

Last modified: 2022-10-29 Sat 11:08

Created: 2020-08-01 Sat 00:00