From 31e2773528f3adceaf223233662ea9d2dfe6b3fd Mon Sep 17 00:00:00 2001
From: Amelie Lucker <amelie.lucker@itwm.fraunhofer.de>
Date: Thu, 2 Jun 2022 12:46:36 +0200
Subject: [PATCH] updated event day = 0
---
R/predict_future_infections.R | 6 +++---
vignettes/future_infections.Rmd | 8 ++++----
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/R/predict_future_infections.R b/R/predict_future_infections.R
index 4f22fd1..8bee90f 100644
--- a/R/predict_future_infections.R
+++ b/R/predict_future_infections.R
@@ -6,9 +6,9 @@
#' meanlog and sdlog are the log-normal distribution parameters derived from
#' the incubation period characteristics described in Xin et al. (2021).
#'
-#' @param last_day_reported_infection Number of days the last infection was reported after the event (1 = event day)
-#' @param total_reported_infections Number of reported symptomatic infections so far
-#' @param total_expected_infections Number of expected symptomatic infections in total
+#' @param last_day_reported_infection Number of days the last infection was reported after the event (0 = event day).
+#' @param total_reported_infections Number of reported symptomatic infections so far.
+#' @param total_expected_infections Number of expected symptomatic infections in total.
#' @param meanlog Number, the parameter of mean from the log-normal distribution.
#' @param sdlog Number, the parameter of sd from the log-normal distribution.
#' @return Vector with expected future infections per day after the event.
diff --git a/vignettes/future_infections.Rmd b/vignettes/future_infections.Rmd
index 2837240..b87b125 100644
--- a/vignettes/future_infections.Rmd
+++ b/vignettes/future_infections.Rmd
@@ -119,7 +119,7 @@ When at some point the updated `total_reported_infections` is not smaller than `
### Output
```{r predict_future_infections}
-last_day_reported_infections = 4 # day 1 = event day
+last_day_reported_infections = 3 # day 0 = event day
total_reported_infections = 4
total_expected_infections = get_expected_total_infections(25, "mixed", "high risk")
@@ -137,7 +137,7 @@ The function `predict_future_infections()` creates a vector with values represen
```{r libraries, foldcode = TRUE, message = FALSE}
data <- data.frame("Erkrankungsdatum" = as.Date("2022-03-15") + 0:3,
"Neue_Faelle" = c(0, 0, 1, 3))
-expected <- data.frame("Erkrankungsdatum" = as.Date("2022-03-15") + 0:(length(predicted_daily_infections) - 1),
+expected <- data.frame("Erkrankungsdatum" = as.Date("2022-03-15") + 1:(length(predicted_daily_infections)),
"ErwarteteWeitereFaelle" = predicted_daily_infections)
g <- ggplot(expected) +
geom_bar(
@@ -155,8 +155,8 @@ g <- ggplot(expected) +
),
stat = 'identity'
) +
- geom_vline(xintercept = expected$Erkrankungsdatum[1]) +
- geom_label(aes(x = expected$Erkrankungsdatum[1], y = data$Neue_Faelle[1] + 4, label = "Event"),
+ geom_vline(xintercept = data$Erkrankungsdatum[1]) +
+ geom_label(aes(x = data$Erkrankungsdatum[1], y = data$Neue_Faelle[1] + 4, label = "Event"),
colour = "black", fill = "white", vjust = 1, size = 7) +
scale_y_continuous(breaks = function(x) unique(
floor(pretty(seq(0, (max(x) + 1) * 1.1))))) +
--
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