COVID-19 Number of Tests 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 presents some data about the number of tests and people tested for COVID-19 over time in Italy and compares them with the number of people found positive.

This page was created on <2020-08-20 Thu> and last updated on <2022-10-29 Sat>.

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.

Getting data into R

We first read the data from the Civil Protection repository adding the ratio between positives and tests, computed on the same day and computed with data shifted by two days (on the assumption tests take two days to complete).

In fact data about tests is used with different semantics by different regions. Some regions reports tests with results (and the ratio new positives / tests makes sense). Other reports the number of test performed, in which case the correct ratio is between positives and tests performed some days earlier. We assume two days and report both ratios for all regions. See the following issue on GitHub for an explanation and some more details https://github.com/pcm-dpc/COVID-19/issues/577 (in Italian). 

DIGITS = 4

national = read.csv(file.path(PATH, "dpc-covid19-ita-andamento-nazionale.csv"))
national$data <- as.Date(national$data)

national$nuovi_casi_testati = c(NA, diff(national$casi_testati, 1))
national$p_over_t <- round(national$nuovi_positivi / national$nuovi_casi_testati, digits = DIGITS) * 100

national$nuovi_tamponi = c(NA, diff(national$tamponi, 1))
national$p_tamponi_over_t <- round(national$nuovi_positivi / national$nuovi_tamponi, digits = DIGITS) * 100

# national$nuovi_casi_testati_2 <- c(NA, NA, head(national$nuovi_casi_testati, -2))
# national$p_over_t_2 = round(national$nuovi_positivi / national$nuovi_casi_testati_2, digits = DIGITS) * 100

# national$nuovi_tamponi_2 <- c(NA, NA, head(national$tamponi_2, -2))
# national$p_tamponi_over_t_2 = round(national$nuovi_positivi / national$nuovi_tamponi_2, digits = DIGITS) * 100

Concerning the regional level, computed columns, such as the number of people tested in a day, have to be computed after filtering, or the diif will work on values from different regions. 

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

These are the columns we are interested in and their translation in English: 

cols = c(
  "data",
  "nuovi_positivi",
  "nuovi_tamponi",
  "nuovi_casi_testati",
  "p_tamponi_over_t",
  "p_over_t"
)

We now define a function to ouput the last N rows of the input data frame. The real “challenge”, here, is transposing the data, to get a more natural presentation (with time progressing from left to right). 

table_data <- function(df, cols, rows = 10) {
  # get the last 10 elements and the interesting columns of the dataframe
  f  <- tail(df, rows)
  rf <- f[, cols]

  # the labels in the transposed matrix are the column names of the original data.frame
  row_labels  <- colnames(rf)
  # the columns in the trasposed matrix are the dates
  col_labels  <- c("Label", format(rf$data, "%a, %b %d"))

  rft <- data.frame(row_labels, t(rf))
  colnames(rft) <- col_labels
  return(rft[-1,])
}

People Tested and Cases in Italy

Data of the last ten days

table_data(national, cols)
Label Wed, Oct 19 Thu, Oct 20 Fri, Oct 21 Sat, Oct 22 Sun, Oct 23 Mon, Oct 24 Tue, Oct 25 Wed, Oct 26 Thu, Oct 27 Fri, Oct 28
nuovi_positivi 41712 40563 36116 31775 25554 11606 48714 35043 31760 29040
nuovi_tamponi 233084 229140 213088 195575 161787 80319 297268 216735 205738 182614
nuovi_casi_testati 40696 40632 35965 33864 28465 15254 48906 38124 35350 33215
p_tamponi_over_t 17.9 17.7 16.95 16.25 15.79 14.45 16.39 16.17 15.44 15.9
p_over_t 102.5 99.83 100.42 93.83 89.77 76.08 99.61 91.92 89.84 87.43

New Cases

New cases. 

## add extra space to right margin of plot within frame
par(mar=c(5, 4, 4, 6) + 0.1)

## Allow a second plot on the same graph
# par(new=TRUE)
new_cases_limits = c( min(national[national$data >= "2020-08-01", c("nuovi_positivi")]), max(national[national$data >= "2020-08-01", c("nuovi_positivi")]) )

p = plot(x = national[national$data >= "2020-08-01", c("data")], 
     y = national[national$data >= "2020-08-01", c("nuovi_positivi")], 
     type="l", lwd=6, pch=21, cex=1.5, col=c("#AA0000"),
     axes=FALSE,
     ylim=new_cases_limits,
     ylab="", xlab="")
text(x = tail(national[national$data >= "2020-08-01", c("data")], 5),
     y = tail(national[national$data >= "2020-08-01", c("nuovi_positivi")], 5),
     labels = tail(national[national$data >= "2020-08-01", c("nuovi_positivi")], 5),
     pos = 1, cex = 1, col="#AA0000")
mtext("New Cases", side=4, line=4, col="#AA0000") 
axis(4, ylim=new_cases_limits, las=1)

grid(p, col = "black", lty = "dotted")

# x-axis
dates = national[national$data >= "2020-08-01", c("data")]
axis.Date(1, at=seq(min(dates), max(dates), by="week"), format="%b %d", las=2)
mtext("Day", side=1, line=2.5)

## Add Legend
legend("topleft", legend = c("Tests", "New Cases"),
       text.col = c("#3B3176", "#AA0000"), pch= c(15, 17), col=c("#3B3176", "#AA0000"))

new_cases_italia.png

New Cases Tested

plot(x = national[national$data >= "2020-08-01", c("data")], 
     y = national[national$data >= "2020-08-01", c("nuovi_casi_testati")], 
     type="l", lwd=6, pch=16, cex=2.5, col=c("#3B3176"))
text(x = tail(national[national$data >= "2020-08-01", c("data")], 1),
     y = tail(national[national$data >= "2020-08-01", c("nuovi_casi_testati")], 1),
     labels = tail(national[national$data >= "2020-08-01", c("nuovi_casi_testati")], 1),
     pos = 4, cex = 1.2, col=c("#3B3176"))
 grid(col="black")

tests_italia.png

Number of Tests and New Cases Tested

Plot new cases and tests together. (Solution taken from How can I plot with 2 different y-axes? on Stack Overflow.) 

## add extra space to right margin of plot within frame
par(mar=c(5, 4, 4, 6) + 0.1)

## Plot first set of data and draw its axis
tests_limits = c( min(national[national$data >= "2020-08-01", c("nuovi_casi_testati")]), max(national[national$data >= "2020-08-01", c("nuovi_casi_testati")]) )
plot(x = national[national$data >= "2020-08-01", c("data")], 
     y = national[national$data >= "2020-08-01", c("nuovi_casi_testati")], 
     type="l", lwd=6, pch=11, cex=1.5, col=c("#3B3176"),
     axes=FALSE,
     ylim=tests_limits,
     ylab="", xlab="")
text(x = tail(national[national$data >= "2020-08-01", c("data")], 1),
     y = tail(national[national$data >= "2020-08-01", c("nuovi_casi_testati")], 1),
     labels = tail(national[national$data >= "2020-08-01", c("nuovi_casi_testati")], 1),
     pos = 4, cex = 1, col=c("#3B3176"))
mtext("Number of Tests", side=2, col="#3B3176", line=4) 
axis(2, ylim=tests_limits, col="black", las=1)  
box()

## Allow a second plot on the same graph
par(new=TRUE)
new_cases_limits = c( min(national[national$data >= "2020-08-01", c("nuovi_positivi")]), max(national[national$data >= "2020-08-01", c("nuovi_positivi")]) )

p = plot(x = national[national$data >= "2020-08-01", c("data")], 
     y = national[national$data >= "2020-08-01", c("nuovi_positivi")], 
     type="l", lwd=6, pch=21, cex=1.5, col=c("#AA0000"),
     axes=FALSE,
     ylim=new_cases_limits,
     ylab="", xlab="")
text(x = tail(national[national$data >= "2020-08-01", c("data")], 1),
     y = tail(national[national$data >= "2020-08-01", c("nuovi_positivi")], 1),
     labels = tail(national[national$data >= "2020-08-01", c("nuovi_positivi")], 1),
     pos = 4, cex = 1, col="#AA0000")
mtext("New Cases", side=4, line=4, col="#AA0000") 
axis(4, ylim=new_cases_limits, las=1)

grid(p, col = "black", lty = "dotted")

# x-axis
dates = national[national$data >= "2020-08-01", c("data")]
axis.Date(1, at=seq(min(dates), max(dates), by="week"), format="%b %d", las=2)
mtext("Day", side=1, line=2.5)

## Add Legend
legend("topleft", legend = c("Tests", "New Cases"),
       text.col = c("#3B3176", "#AA0000"), pch= c(15, 17), col=c("#3B3176", "#AA0000"))

tests_and_new_cases_italia.png

Positive/Number of Tests

Here we plot the number of positive people over tests performed. The standard measurement is the ratio between positive and tests performed (shown in blue). The way I understand it is that this number also includes tests performed on people already diagnosed and recovered.

The second graph, in red, shows the ration of positive over new people tested, that is, of all the people not yet diagnosed, how many resulted positive? 

plot(national$p_over_t ~ national$data, type="o", lwd=3, pch=21, col="#ff0000", main="Positive over Tests", xlab="Date", ylab="Percentage")
text(y = tail(national, 1)$p_over_t, x = tail(national, 1)$data, lab = paste(tail(national, 1)$p_over_t, "%", sep=""), pos=4, col="#ff0000", cex=1.3)

# Second plot with Positive over tests
p = lines(national$p_tamponi_over_t ~ national$data, type="o", lwd=3, pch=21, col="#000088", xlab="Date", ylab="Percentage")
text(y = tail(national, 1)$p_tamponi_over_t, x = tail(national, 1)$data, lab = paste(tail(national, 1)$p_tamponi_over_t, "%", sep=""), pos=4, col="#000088", cex=1.3)

## Add Legend
grid(col="black")
legend("bottomleft", legend = c("Positive over new People Tested", "Positive over Tests Performed"),
       text.col = c("#ff0000", "#000088"), pch= c(15, 17), col=c("#AA0000", "#000088"))

positive_over_tests_italia.png

People Tested and Cases in Trentino

region <- subset(data, denominazione_regione == "P.A. Trento")

region$nuovi_casi_testati = c(NA, diff(region$casi_testati, 1))

region$p_over_t <- round(region$nuovi_positivi / region$nuovi_casi_testati, digits = DIGITS) * 100
region$nuovi_casi_testati_2 = c(NA, NA, diff(region$casi_testati, 2))
region$p_over_t_2 = round(region$nuovi_positivi / region$nuovi_casi_testati_2, digits = DIGITS) * 100
region$nuovi_casi_testati_2 <- c(NA, NA, head(region$nuovi_casi_testati, -2))
region$p_over_t_2 = round(region$nuovi_positivi / region$nuovi_casi_testati_2, digits = DIGITS) * 100

region$nuovi_tamponi = c(NA, diff(region$tamponi, 1))
region$p_tamponi_over_t <- round(region$nuovi_positivi / region$nuovi_tamponi, digits = DIGITS) * 100
region$nuovi_tamponi_2 <- c(NA, NA, head(region$tamponi_2, -2))
region$p_tamponi_over_t_2 = round(region$nuovi_positivi / region$nuovi_tamponi_2, digits = DIGITS) * 100

table_data(region, cols)
Label Wed, Oct 19 Thu, Oct 20 Fri, Oct 21 Sat, Oct 22 Sun, Oct 23 Mon, Oct 24 Tue, Oct 25 Wed, Oct 26 Thu, Oct 27 Fri, Oct 28
nuovi_positivi 578 545 477 400 314 119 485 386 301 269
nuovi_tamponi 2772 2798 2404 2197 1952 735 3162 2185 2065 1804
nuovi_casi_testati 279 257 223 204 134 51 214 203 167 156
p_tamponi_over_t 20.85 19.48 19.84 18.21 16.09 16.19 15.34 17.67 14.58 14.91
p_over_t 207.17 212.06 213.9 196.08 234.33 233.33 226.64 190.15 180.24 172.44

People Tested and Cases in Liguria

region <- subset(data, denominazione_regione == "Liguria")

region$nuovi_casi_testati = c(NA, diff(region$casi_testati, 1))

region$p_over_t <- round(region$nuovi_positivi / region$nuovi_casi_testati, digits = DIGITS) * 100
region$nuovi_casi_testati_2 = c(NA, NA, diff(region$casi_testati, 2))

region$nuovi_tamponi = c(NA, diff(region$tamponi, 1))
region$p_tamponi_over_t <- round(region$nuovi_positivi / region$nuovi_tamponi, digits = DIGITS) * 100

table_data(region, cols)
Label Wed, Oct 19 Thu, Oct 20 Fri, Oct 21 Sat, Oct 22 Sun, Oct 23 Mon, Oct 24 Tue, Oct 25 Wed, Oct 26 Thu, Oct 27 Fri, Oct 28
nuovi_positivi 1113 1091 896 857 657 295 1352 936 817 748
nuovi_tamponi 6312 6161 5682 5151 4444 1984 8533 5762 5631 4918
nuovi_casi_testati 816 755 647 581 520 279 1031 677 645 588
p_tamponi_over_t 17.63 17.71 15.77 16.64 14.78 14.87 15.84 16.24 14.51 15.21
p_over_t 136.4 144.5 138.49 147.5 126.35 105.73 131.13 138.26 126.67 127.21

People Tested and Cases in Veneto

region <- subset(data, denominazione_regione == "Veneto")

region$nuovi_casi_testati = c(NA, diff(region$casi_testati, 1))
region$p_over_t <- round(region$nuovi_positivi / region$nuovi_casi_testati, digits = DIGITS) * 100

region$nuovi_tamponi = c(NA, diff(region$tamponi, 1))
region$p_tamponi_over_t <- round(region$nuovi_positivi / region$nuovi_tamponi, digits = DIGITS) * 100

table_data(region, cols)
Label Wed, Oct 19 Thu, Oct 20 Fri, Oct 21 Sat, Oct 22 Sun, Oct 23 Mon, Oct 24 Tue, Oct 25 Wed, Oct 26 Thu, Oct 27 Fri, Oct 28
nuovi_positivi 5709 5167 4677 4486 3238 1040 6363 4772 4310 3891
nuovi_tamponi 39929 34525 32292 30152 21572 7816 48143 37239 33782 30803
nuovi_casi_testati 2216 2131 1706 1719 1159 431 2696 1913 1792 1580
p_tamponi_over_t 14.3 14.97 14.48 14.88 15.01 13.31 13.22 12.81 12.76 12.63
p_over_t 257.63 242.47 274.15 260.97 279.38 241.3 236.02 249.45 240.51 246.27

People Tested and Cases in Lombardia

region <- subset(data, denominazione_regione == "Lombardia")

region$nuovi_casi_testati = c(NA, diff(region$casi_testati, 1))
region$p_over_t <- round(region$nuovi_positivi / region$nuovi_casi_testati, digits = DIGITS) * 100

region$nuovi_tamponi = c(NA, diff(region$tamponi, 1))
region$p_tamponi_over_t <- round(region$nuovi_positivi / region$nuovi_tamponi, digits = DIGITS) * 100

table_data(region, cols)
Label Wed, Oct 19 Thu, Oct 20 Fri, Oct 21 Sat, Oct 22 Sun, Oct 23 Mon, Oct 24 Tue, Oct 25 Wed, Oct 26 Thu, Oct 27 Fri, Oct 28
nuovi_positivi 8230 7983 6803 6161 4646 1640 9979 6216 6173 5504
nuovi_tamponi 43994 42561 36207 35098 30472 12264 57217 38317 36623 32744
nuovi_casi_testati 5011 4646 4050 3792 2894 1373 5840 4235 4033 3551
p_tamponi_over_t 18.71 18.76 18.79 17.55 15.25 13.37 17.44 16.22 16.86 16.81
p_over_t 164.24 171.83 167.98 162.47 160.54 119.45 170.87 146.78 153.06 155.0

Author: Adolfo Villafiorita

Published: 2024-07-15 Mon 08:46

Last modified: 2022-10-29 Sat 11:09

Created: 2020-08-20 Thu 00:00