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Fixes encoding error and makes runnable on mybinder.org #4

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Fixes encoding error and makes runnable on mybinder.org #4

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26d3a64
Fix: Object 'S' not found
consideRatio Apr 24, 2020
e5fac07
MyBinder.org support
consideRatio Apr 24, 2020
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6 changes: 6 additions & 0 deletions .binder/install.R
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install.packages("reshape2")
install.packages("openxlsx")
install.packages("RColorBrewer")
install.packages("rootSolve")
install.packages("deSolve")
1 change: 1 addition & 0 deletions .binder/runtime.txt
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r-2020-04-20
2 changes: 2 additions & 0 deletions README.md
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# SEIR-model-Stockholm
Skattning av peakdag och antal infekterade i covid-19-utbrottet i Stockholms län februari-april 2020.

[![Binder](https://mybinder.org/badge_logo.svg)](https://gke.mybinder.org/v2/gh/FohmAnalys/SEIR-model-Stockholm/master?urlpath=%2Frstudio)
10 changes: 5 additions & 5 deletions Script/Estimate_SEIR_for_sharing_new_incidence.R
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Expand Up @@ -19,7 +19,7 @@ heading <- "
# R version: 3.5.2
#
# What the script does: This script estimates the parameters of the infectivity described in the report
# 'Skattning av peakdagen och antal infekterade i covid-19-utbrottet i Stockholms l�n'.
# 'Skattning av peakdagen och antal infekterade i covid-19-utbrottet i Stockholms län'.
# With these we are able to estimate the number of infectious individuals at different time points,
# the cumulative number of infected, and the estimated effective basic reproduction number.
# If you want to reproduce the results obtained, or change anything, first write the
Expand Down Expand Up @@ -119,8 +119,8 @@ load(file.path(data.path, "Sverige_population_2019.Rdata"))
Region_population <- dat_pop_region_totalt
r_name <- levels(Region_population$ARegion)

region_namn <- unlist(strsplit(r_name, split="s l�n"))
region_namn <- unlist(strsplit(region_namn, split=" l�n"))
region_namn <- unlist(strsplit(r_name, split="s län"))
region_namn <- unlist(strsplit(region_namn, split=" län"))
region_namn <- region_namn[-which(region_namn == "Riket")]

Region_population$ARegion <- region_namn
Expand Down Expand Up @@ -186,7 +186,7 @@ Estimate_function_Stockholm_only_local <- function(p_symp = 0.5, p_lower_inf = 0
## The time-dependent infectivity rate
beta_decrease <- function(t, delta, epsilon, theta){

t_b <- as.numeric(as.Date("2020-03-16")) - as.numeric(as.Date("2019-12-31")) # dagen f�r jobba hemma
t_b <- as.numeric(as.Date("2020-03-16")) - as.numeric(as.Date("2019-12-31")) # dagen får jobba hemma

res <- ((1-delta)/(1+exp(epsilon*(-(t-t_b)))) + delta)* theta

Expand Down Expand Up @@ -388,7 +388,7 @@ fit_cum_inf <- N - fit_S



## The mean prevalence same days as the H�lsorapport Stockholmsstudien (27th March to 3rd April)
## The mean prevalence same days as the Hälsorapport Stockholmsstudien (27th March to 3rd April)
Smittsamma <- fit_I_symp + fit_I_asymp #+ fit_E
SmittsammaF <- Smittsamma[40:47]
mean(SmittsammaF/N)
Expand Down