Epi Curve

Using EpiCurve
jp.decorps@epiconcept.fr
2019-09-09
Epiconcept is made up of a team of doctors, epidemiologists, data scientists and digital specialists. For more
than 20 years, Epiconcept has contributed to the improvement of public health by writing software, carrying
out epidemiological studies, research, evaluation and training to better detect, monitor and prevent disease
and to improve treatment.
Epiconcept provides software, services and studies in the following areas:
• Software for managing public health programs,
• Secure cloud solutions for health data collection, reporting and processing,
• Research projects on vaccine preventable diseases, including measuring the effectiveness and impact of
vaccines,
• Services in the field of epidemiology (protocols, analysis, training, etc.),
• Expertise in data analysis,
• Coaching and assistance to professionals in public health,
• Training (in software use and epidemiology: short and longer introductory modules, advanced courses,
training through long-term practice).
To achieve such goals Epiconcept :
• Recognized research organization,
• Certified datacenter for hosting personal health data,
• Training organisation.
Epiconcept relies on :
• Its expertise in epidemiology
• Its IT expertise,
• Ethical values rooted in practice (responsibility and quality of services, data security and confidentiality,
scientific independence, etc.),
• Capabilities to answer and anticipate tomorrow’s challenges (Research - evaluation, e-health, Big Data,
IoT, etc.),
• A desire to build long-term relationships with its clients and partners.
Its current customers and partners include some of the greatest names in the world such as: Santé Publique
France (and many public health organizations around the world), WHO, ECDC, AFD, MSF, World Bank,
etc.
1
Package EpiCurve
Description
EpiCurve allows the user to create epidemic curves from case-based and aggregated data.
Details
The EpiCurve function creates a graph of number of cases by time of illness (for example date of onset).
Each case is represented by a square. EpiCurve allows the time unit for the x-axis to have hourly, daily,
weekly or monthly intervals. The hourly interval can be split into 1, 2, 3, 4, 6, 8 or 12 hour time units.
EpiCurve works on both case-based (one case per line) or aggregated data (where there is a count of cases
for each date). With aggregated data, you need to specify the variable for the count of cases in the “freq”
parameter.
With case-based (non-aggregated data), the date format for EpiCurve can be:
• hourly: YYYY-MM-DD HH:MM or YYYY-mm-DD HH:MM:SS
• daily: YYYY-MM-DD
• monthly: YYYY-MM
If the date format is daily or hourly, you can change and force the period for aggregation on the graph with
the parameter “period” setted with “day”, “week” or “month”.
For aggregated data, the date formats can be as above, but they can also be weekly: YYYY-Wnn. Here, we
need to specify how the data are aggregated in the parameter “period”. If we want to further aggregate the
aggregated data for the epidemic curve (e.g. move from daily aggregated cases to weekly aggregated cases),
we can specify the parameter “to.period”.
When the date format is hourly, the dataset is considered case-based, whether the “freq” parameter of the
EpiCurve function is supplied or not.
The EpiCurve function
EpiCurve (
x,
date = NULL,
freq = NULL,
cutvar = NULL,
period = NULL,
to.period = NULL,
split = 1,
cutorder = NULL,
colors = NULL,
title = NULL,
xlabel = NULL,
ylabel=NULL,
note=NULL
2
Arguments
Parameter Description
x data.frame with at least one column with dates
date character, name of date column
freq character, name of a column with a value to display
cutvar character, name of a column with factors
period character, c(“hour”, “day”,“week”, “month”)
to.period character, Convert date period to another period only for aggregated data. If period is
“day”, to.period can be “week” or “month”. If period is “week”, to.period can be
“month”.
split integer, c(1,2,3,4,6,8,12) value for hourly split
cutorder character vector of factors
colors character, vector of colors
title character, title of the plot
xlabel character, label for x axis
ylabel character, label for y axis
note character, add a note under the graph
Depends
ggplot2, dplyr, ISOweek, scales, timeDate
3
Plot non-aggregated cases
Daily - non-aggregated cases
DF <- read.csv("daily_unaggregated_cases.csv", stringsAsFactors=FALSE)

kable(head(DF, 12))
UTS V1 V2
2016-10-26 7.20 188
2016-11-02 7.03 95
2016-11-03 5.14 160
2016-11-05 9.89 165
2016-11-05 9.69 109
2016-11-05 4.15 154
2016-11-05 4.97 144
2016-11-06 8.97 187
2016-11-06 4.45 120
2016-11-06 6.60 116
2016-11-07 7.68 141
2016-11-07 10.08 126
EpiCurve(DF,
date = "UTS",
period = "day",
color ="#9900ef",
xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)))
4
0
2
4
6
8
10
12
2016−10−26
2016−10−27
2016−10−28
2016−10−29
2016−10−30
2016−10−31
2016−11−01
2016−11−02
2016−11−03
2016−11−04
2016−11−05
2016−11−06
2016−11−07
2016−11−08
2016−11−09
2016−11−10
2016−11−11
2016−11−12
2016−11−13
2016−11−14
2016−11−15
2016−11−16
2016−11−17
2016−11−18
2016−11−19
2016−11−20
2016−11−21
2016−11−22
2016−11−23
5
2016−11−24
2016−11−25
2016−11−26
2016−11−27
2016−11−28
2016−11−29
2016−11−30
2016−12−01
2016−12−02
2016−12−03
From 2016−10−26 to 2016−12−21
2016−12−04
2016−12−05
2016−12−06
2016−12−07
2016−12−08
2016−12−09
2016−12−10
2016−12−11
2016−12−12
2016−12−13
2016−12−14
2016−12−15
2016−12−16
2016−12−17
2016−12−18
2016−12−19
2016−12−20
2016−12−21
Number of cases
0
2
4
6
8
10
12
14
16
18
12 00:00−00:59
12 01:00−01:59
12 02:00−02:59
EpiCurve(DF,
12 03:00−03:59
12 04:00−04:59
12 05:00−05:59
12 06:00−06:59
12 07:00−07:59
split = 1,
kable(head(DF, 12))
12 08:00−08:59
12 09:00−09:59
date = "UTS",
12 10:00−10:59
12 11:00−11:59
period = "hour",
12 12:00−12:59
color ="#339933",
12 13:00−13:59
12 14:00−14:59
12 15:00−15:59
12 16:00−16:59
12 17:00−17:59
ylabel="Number of cases",
Hourly - non-aggregated cases
12 18:00−18:59
12 19:00−19:59
UTS
12 20:00−20:59
12 21:00−21:59
12 22:00−22:59
2017-04-12
2017-04-12
2017-04-12
2017-04-12
2017-04-12
2017-04-12
2017-04-12
2017-04-12
2017-04-12
2017-04-12
2017-04-12
2017-04-12
12 23:00−23:59
13 00:00−00:59
13 01:00−01:59
6
13 02:00−02:59
19:41
19:37
19:24
19:11
19:05
18:43
18:38
18:36
18:06
17:38
17:35
16:31
13 03:00−03:59
13 04:00−04:59
13 05:00−05:59
13 06:00−06:59
6.18
7.80
6.36
4.61
6.39
8.03
7.02
10.92
4.95
6.81
8.69
5.17
X1
13 07:00−07:59
13 08:00−08:59
13 09:00−09:59
13 10:00−10:59
123
112
188
126
102
175
185
189
120
140
101
166
X2
13 11:00−11:59
13 12:00−12:59
13 13:00−13:59
From 2017−04−12 16:31 to 2017−04−13 03:23

13 14:00−14:59
13 15:00−15:59
13 16:00−16:59
13 17:00−17:59
13 18:00−18:59
13 19:00−19:59
DF <- read.csv("hourly_unaggregated_cases.csv", stringsAsFactors=FALSE)
13 20:00−20:59
13 21:00−21:59
13 22:00−22:59
13 23:00−23:59
Hourly - non-aggregated cases with factors
DF <- read.csv("hourly_unaggregated_cases_factors.csv", stringsAsFactors=FALSE)

kable(head(DF, 12))
UTS X1 X2 Confirmed
2017-04-12 16:31 5.17 166 YES
2017-04-12 17:35 8.69 101 YES
2017-04-12 17:38 6.81 140 NO
2017-04-12 18:06 4.95 120 NO
2017-04-12 18:36 10.92 189 NO
2017-04-12 18:38 7.02 185 YES
2017-04-12 18:43 8.03 175 NO
2017-04-12 19:05 6.39 102 NO
2017-04-12 19:11 4.61 126 NO
2017-04-12 19:24 6.36 188 YES
2017-04-12 19:37 7.80 112 NO
2017-04-12 19:41 6.18 123 NO
EpiCurve(DF,
date = "UTS",
period = "hour",
split = 1,
cutvar = "Confirmed",
color = c("#339933","#eebb00"),
18
16
14
12 Confirmed
10 YES
8
NO
6
4
2
0
12 00:00−00:59
12 01:00−01:59
12 02:00−02:59
12 03:00−03:59
12 04:00−04:59
12 05:00−05:59
12 06:00−06:59
12 07:00−07:59
12 08:00−08:59
12 09:00−09:59
12 10:00−10:59
12 11:00−11:59
12 12:00−12:59
12 13:00−13:59
12 14:00−14:59
12 15:00−15:59
12 16:00−16:59
12 17:00−17:59
12 18:00−18:59
12 19:00−19:59
12 20:00−20:59
12 21:00−21:59
12 22:00−22:59
12 23:00−23:59
13 00:00−00:59
13 01:00−01:59
13 02:00−02:59
13 03:00−03:59
13 04:00−04:59
13 05:00−05:59
13 06:00−06:59
13 07:00−07:59
13 08:00−08:59
13 09:00−09:59
13 10:00−10:59
13 11:00−11:59
13 12:00−12:59
13 13:00−13:59
13 14:00−14:59
13 15:00−15:59
13 16:00−16:59
13 17:00−17:59
13 18:00−18:59
13 19:00−19:59
13 20:00−20:59
13 21:00−21:59
13 22:00−22:59
13 23:00−23:59
From 2017−04−12 16:31 to 2017−04−13 03:23
7
Plot aggregated data
Daily
Without factors
date value
2016-03-01 5
2016-03-03 5
2016-03-05 5
2016-03-06 1
2016-03-07 3
2016-03-14 4
2016-03-15 1
2016-03-16 10
2016-03-27 3
2016-03-28 2
2016-03-30 4
2016-03-31 2
2016-04-01 3
2016-04-03 1
2016-04-04 6
2016-04-07 6
2016-04-08 9
2016-04-09 15
2016-04-13 2
2016-04-14 1
2016-04-15 3
2016-04-16 6
2016-04-17 4
2016-04-18 17
2016-04-27 13
2016-04-29 3
2016-04-30 6
8
Number of cases
0
2
4
6
8
10
12
14
16
2016−03−01
2016−03−02
2016−03−03
EpiCurve(DF,
2016−03−04
2016−03−05
2016−03−06
2016−03−07
2016−03−08
2016−03−09
2016−03−10
2016−03−11
date = "date",
2016−03−12
Epidemic Curve
period = "day",
freq = "value",
2016−03−13
2016−03−14
2016−03−15
2016−03−16
2016−03−17
2016−03−18
2016−03−19
title = "Epidemic Curve",
2016−03−20
2016−03−21
2016−03−22
2016−03−23
note = "Daily epidemic curve")
2016−03−24
2016−03−25
2016−03−26
2016−03−27
2016−03−28
9
2016−03−29
2016−03−30
2016−03−31
2016−04−01
2016−04−02
2016−04−03
2016−04−04
2016−04−05
2016−04−06
Daily epidemic curve

2016−04−07
2016−04−08
2016−04−09
2016−04−10
From 2016−03−01 to 2016−04−30

2016−04−11
2016−04−12
2016−04−13
2016−04−14
xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)),
2016−04−15
2016−04−16
2016−04−17
2016−04−18
2016−04−19
2016−04−20
2016−04−21
2016−04−22
2016−04−23
2016−04−24
2016−04−25
2016−04−26
2016−04−27
2016−04−28
2016−04−29
2016−04−30
With factors
date value factor

2016-03-01 3 Validated Case
2016-03-01 2 Unvalidated Case
10
Number of cases
0
2
4
6
8
10
12
14
16
2016−03−01
2016−03−02
2016−03−03
2016−03−04
EpiCurve(DF,
2016−03−05
2016−03−06
2016−03−07
2016−03−08
2016−03−09
2016−03−10
2016−03−11
2016−03−12
2016−03−13
2016−03−14
2016−03−15
date = "date",
2016−03−16
Epidemic Curve
period = "day",
freq = "value",
2016−03−17
2016−03−18
2016−03−19
cutvar = "factor",
2016−03−20
2016−03−21
2016−03−22
2016−03−23
2016−03−24
2016−03−25
2016−03−26
2016−03−27
2016−03−28
2016−03−29
2016−03−30
2016−03−31
2016−04−01
2016−04−02
2016−04−03
2016−04−04
2016−04−05
2016−04−06
2016−04−07
11
2016−04−08

2016−04−09
2016−04−10
2016−04−11
2016−04−12
2016−04−13
2016−04−14
From 2016−03−01 to 2016−04−30

2016−04−15
2016−04−16
2016−04−17
2016−04−18
2016−04−19
2016−04−20
2016−04−21
2016−04−22
2016−04−23
2016−04−24
2016−04−25
2016−04−26
2016−04−27
2016−04−28
2016−04−29
2016−04−30
factor
Validated Case
Unvalidated Case
Weekly
Without factors
date value
2016-W10 3
2016-W11 4
2016-W12 1
2016-W13 5
2016-W14 2
2016-W15 7
2016-W16 1
2016-W17 4
2016-W18 3
EpiCurve(DF,
date = "date",
freq = "value",
period = "week",
color=c("#990000"),
xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)),
title = "Epidemic Curve\n")
Epidemic Curve
7
5
Number of cases
0
2016−W10
2016−W11
2016−W12
2016−W13
2016−W14
2016−W15
2016−W16
2016−W17
2016−W18
Du 2016−W10 au 2016−W18
12
With factors
date value factor

2016-W10 3 Valid
2016-W10 2 Invalid
2016-W11 4 Valid
2016-W12 1 Invalid
2016-W13 5 Valid
2016-W14 2 Valid
2016-W14 1 Invalid
2016-W15 7 Valid
2016-W15 3 Invalid
2016-W17 1 Valid
2016-W17 1 Invalid
2016-W18 4 Valid
2016-W18 2 Invalid
2016-W20 3 Valid
EpiCurve(DF,
date = "date",
freq = "value",
period = "week",
cutvar = "factor",
color=c("Blue", "Red"),
ylabel="Cases",
Epidemic Curve
10
6 factor
Cases
Valid
4 Invalid
0
2016−W10
2016−W11
2016−W12
2016−W13
2016−W14
2016−W15
2016−W16
2016−W17
2016−W18
2016−W19
2016−W20
From 2016−W10 to 2016−W20
13
Monthly
Without factors
date value
2016-02 3
2016-03 4
2016-04 1
2016-05 5
2016-07 2
2016-08 7
2016-10 1
2016-11 4
2016-12 3
EpiCurve(DF,
date = "date",
freq = "value",
period = "month",
Epidemic Curve
7
5
Number of cases
0
2016−02
2016−03
2016−04
2016−05
2016−06
2016−07
2016−08
2016−09
2016−10
2016−11
2016−12
From 2016−02 to 2016−12
14
With factors
date value factor

2016-02 3 Valid
2016-02 2 Invalid
2016-03 4 Valid
2016-04 1 Invalid
2016-05 5 Valid
2016-06 2 Valid
2016-06 1 Invalid
2016-07 7 Valid
2016-07 3 Invalid
2016-09 1 Valid
2016-09 1 Invalid
2016-11 4 Valid
2016-11 2 Invalid
2016-12 3 Valid
EpiCurve(DF,
date = "date",
freq = "value",
cutvar = "factor",
period = "month",
Epidemic Curve
10
8
Number of cases
6 factor
Valid
4 Invalid
0
2016−02
2016−03
2016−04
2016−05
2016−06
2016−07
2016−08
2016−09
2016−10
2016−11
2016−12
From 2016−02 to 2016−12
15
Converted period (aggragated cases)
“day” to “week”
date value
2016-03-01 5
2016-03-03 5
2016-03-05 5
2016-03-06 1
2016-03-07 3
2016-03-14 4
2016-03-15 1
2016-03-16 10
2016-03-27 3
2016-03-28 2
2016-03-30 4
2016-03-31 2
2016-04-01 3
2016-04-03 1
2016-04-04 6
2016-04-07 6
2016-04-08 9
2016-04-09 15
2016-04-13 2
2016-04-14 1
2016-04-15 3
2016-04-16 6
2016-04-17 4
2016-04-18 17
2016-04-27 13
2016-04-29 3
2016-04-30 6
EpiCurve(DF,
date = "date",
freq = "value",
period = "day",
to.period = "week",
16
Number of cases
0
5
10
15
20
25
30
35
2016−W09
2016−W10
2016−W11
17
2016−W12
2016−W13
2016−W14
2016−W15
Epidemic Curve
2016−W16

2016−W17
From 2016−03−01 to 2016−04−30

“day” to “month”
EpiCurve(DF,
date = "date",
freq = "value",
period = "day",
to.period = "month",
xlabel=sprintf("From %s o %s", min(DF$date), max(DF$date)),
18
Epidemic Curve
95
90
85
80
75
70
65
60
Number of cases
55
50
45
40
35
30
25
20
15
10
0
2016−03
2016−04
From 2016−03−01 o 2016−04−30
19
“week” to “month”
date value
2016-W10 3
2016-W11 4
2016-W12 1
2016-W13 5
2016-W14 2
2016-W15 7
2016-W16 1
2016-W17 4
2016-W18 3
EpiCurve(DF,
date = "date",
freq = "value",
period = "week",
color=c("#990000"),
xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)),
Epidemic Curve
14
12
10
Number of cases
0
2016−03
2016−04
2016−05
Du 2016−W10 au 2016−W18
20
“week” to “month” with factors
date value factor

2016-W10 3 Valid
2016-W10 2 Invalid
2016-W11 4 Valid
2016-W12 1 Invalid
2016-W13 5 Valid
2016-W14 2 Valid
2016-W14 1 Invalid
2016-W15 7 Valid
2016-W15 3 Invalid
2016-W17 1 Valid
2016-W17 1 Invalid
2016-W18 4 Valid
2016-W18 2 Invalid
2016-W20 3 Valid
EpiCurve(DF,
date = "date",
freq = "value",
period = "week",
cutvar = "factor",
color=c("Blue", "Red"),
ylabel="Cases",
21
Epidemic Curve
14
12
10
factor
Cases
8
Valid
6 Invalid
0
2016−03
2016−04
2016−05
From 2016−W10 to 2016−W20
22

Epi Curve

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Epi Curve

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Available Formats

Using EpiCurve

The EpiCurve function

ggplot2, dplyr, ISOweek, scales, timeDate

Daily - non-aggregated cases

DF <- read.csv("daily_unaggregated_cases.csv", stringsAsFactors=FALSE)

From 2017−04−12 16:31 to 2017−04−13 03:23

DF <- read.csv("hourly_unaggregated_cases_factors.csv", stringsAsFactors=FALSE)

From 2017−04−12 16:31 to 2017−04−13 03:23

Daily epidemic curve

From 2016−03−01 to 2016−04−30

date value factor

Daily epidemic curve

From 2016−03−01 to 2016−04−30

date value factor

From 2016−W10 to 2016−W20

From 2016−02 to 2016−12

date value factor

From 2016−02 to 2016−12

Daily epidemic curve

From 2016−03−01 to 2016−04−30

From 2016−03−01 o 2016−04−30

Daily epidemic curve

date value factor

From 2016−W10 to 2016−W20

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