Merge pull request #109 from matsim-org/develop

Develop

.editorconfig

@@ -10,6 +10,7 @@ charset = utf-8
 indent_style = tab
 insert_final_newline = true
 trim_trailing_whitespace = true
+max_line_length = 150
 
 [Makefile]
 indent_style = tab

pom.xml

@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>com.github.matsim-org</groupId>
     <artifactId>matsim-episim</artifactId>
-    <version>22.6</version>
+    <version>22.12</version>
 
     <name>MATSim Episim</name>
     <description>Epidemic simulation for MATSim</description>

src/main/R/Covid19ScenarioHubSubmission.R

@@ -0,0 +1,98 @@
+
+library(lubridate)
+library(tidyverse)
+library(readr)
+
+
+
+rm(list=ls())
+source("/Users/jakob/git/matsim-episim/src/main/R/masterJR-utils.R", encoding = 'utf-8')
+
+# Global variables
+directory <- "/Users/jakob/git/public-svn/matsim/scenarios/countries/de/episim/battery/jakob/2022-07-27/4-eu-noAgg/"
+
+origin_date <- ymd("2022-07-24") # first day (sunday) of epiweek 30, 2022
+end_date <- ymd("2023-07-29") # last day (saturday) of epiweek 30, 2023 (latest possible value)
+
+
+
+## read & prep infections
+infections_raw <- read_combine_episim_output_zipped(directory,"infections.txt.csv")
+
+infections_incidence <- convert_infections_into_incidence(directory,infections_raw,FALSE) %>%
+  select(-c(infections_week,nShowingSymptomsCumulative, district, incidence))
+
+
+population_cologne <- infections_raw[1, "nSusceptible"]
+
+population_germany <- 83695430 #https://www.destatis.de/EN/Themes/Society-Environment/Population/Current-Population/Tables/liste-current-population.html
+scale_factor <- population_germany / population_cologne # pop germany / pop koelln
+
+infections_ready <- infections_incidence %>%
+  filter(date >= origin_date & date <= end_date) %>%
+  # mutate(weekday = lubridate::wday(date, label = TRUE)) %>%
+  mutate(year = epiyear(date)) %>%
+  mutate(epiweek = epiweek(date)) %>%
+  group_by(seed,vacCamp,vacType,year,epiweek) %>%
+  summarise(value = sum(infections) * scale_factor, target_end_date = last(date) ) %>%
+  mutate(target_variable = "inc infection") %>%
+  select(year, epiweek, target_end_date, target_variable, value, seed, vacCamp, vacType)
+
+
+## read & prep hospitalizations
+hosp_raw <- read_combine_episim_output_zipped(directory,"post.hospital.tsv")
+
+hosp_ready <- hosp_raw %>%
+  filter(date >= origin_date & date <= end_date) %>%
+  mutate(year = year(date)) %>%
+  mutate(wkday = lubridate::wday(date, label = TRUE)) %>%
+  filter(wkday == "Sat") %>%
+  filter(measurement == "intakesHosp") %>%
+  filter(severity == "Omicron") %>%
+  mutate(epiweek = epiweek(date)) %>%
+  rename("target_end_date" = date, value = n) %>%
+  mutate(value = value * population_cologne / 100000 * scale_factor) %>%
+  mutate(target_variable = "inc hosp") %>%
+  select(year, epiweek, target_end_date, target_variable, value, seed, vacCamp, vacType)
+
+# combine two dataframes and modify columns to match specs
+combined <- rbind(infections_ready, hosp_ready)
+# combined <- infections_ready #todo revert
+
+
+
+
+seed <- unique(combined$seed)
+sample <- seq(length(seed))
+map <- data.frame(seed,sample)
+
+final <- combined %>% filter(vacCamp!="off") %>%
+  mutate(scenario_id = paste0(vacCamp,"_",vacType)) %>%
+  mutate(scenario_id = case_when(scenario_id == "60plus_omicronUpdate"~"A-2022-07-24",
+                              scenario_id == "18plus_omicronUpdate"~"B-2022-07-24",
+                              scenario_id == "60plus_mRNA"~"C-2022-07-24",
+                              scenario_id == "18plus_mRNA"~"D-2022-07-24")) %>%
+  merge(map,by ="seed") %>%
+  mutate(horizon =  case_when(year == 2022 ~ epiweek - 29, year == 2023~ (52-29) + epiweek)) %>%
+  mutate("origin_date" = "2022-07-24") %>%
+  mutate("location" = "DE") %>%
+  mutate(value = round(value)) %>%
+  select(origin_date,scenario_id, horizon, target_end_date, location, sample,target_variable, value) %>%
+  arrange(scenario_id,sample,horizon) %>%
+  mutate(horizon = paste0(horizon," wk"))
+
+write.csv(final,"/Users/jakob/git/covid19-scenario-hub-europe/data-processed/MODUS_Covid-Episim/2022-07-24-MODUS_Covid-Episim.csv", row.names = FALSE)
+
+
+
+# xxx <- read.delim("/Users/jakob/antibodies_2022-07-23.tsv",sep = "\t")
+#
+# yyy <- xxx %>% filter(nVaccinations == 0 & nInfections == 0)
+#
+# nrow(yyy)/nrow(xxx)
+
+
+
+
+
+

src/main/R/analyseCases.R

@@ -0,0 +1,89 @@
+library(lubridate)
+library(tidyverse)
+library(readr)
+
+
+
+rm(list=ls())
+source("/Users/jakob/git/matsim-episim/src/main/R/masterJR-utils.R", encoding = 'utf-8')
+
+# directory_snap_old <- "/Users/jakob/git/public-svn/matsim/scenarios/countries/de/episim/battery/jakob/2022-11-05/2-imm-snap/"
+directory_base <- "/Users/jakob/git/public-svn/matsim/scenarios/countries/de/episim/battery/jakob/2022-11-24/1-makeImmHist/"
+directory_imm <- "/Users/jakob/git/public-svn/matsim/scenarios/countries/de/episim/battery/jakob/2022-11-24/3-imm-20seeds/"
+# file_root<- "antibodies.tsv"
+
+#infections
+file_root_inf<- "infections.txt.csv"
+snap_inf_raw <- read_combine_episim_output_zipped(directory_base, file_root_inf )
+# snap_inf_raw_old <- read_combine_episim_output_zipped(directory_snap, file_root_inf )
+imm_inf_raw <- read_combine_episim_output_zipped(directory_imm, file_root_inf)
+
+unique(snap_inf_raw$seed)
+
+
+start_date <- ymd("2022-04-01")
+end_date <- ymd("2022-09-01")
+snap_inf <- snap_inf_raw %>%
+  filter(date >= start_date) %>%
+  filter(date <= end_date) %>%
+  filter(seed %in% unique(imm_inf_raw$seed))
+  # filter(pHh == 0.0, immuneSigma == 0.0)
+  # mutate(vax = generic + mRNA + vector + ba1Update + ba5Update + natural)
+
+
+imm_inf <- imm_inf_raw %>%
+  filter(date >= start_date) %>%
+  filter(date <= end_date) %>%
+  filter(StrainA == 2.0 & startFromImm =="sepSeeds")
+
+
+  # mutate(vax = generic + mRNA + vector + ba1Update + ba5Update + natural)
+ggplot() + #nShowingSymptoms # SARS_CoV_2
+  geom_line(imm_inf, mapping = aes(date, nShowingSymptoms , group = seed, col = "imm-hist")) +
+  geom_line(snap_inf, mapping = aes(date, nShowingSymptoms , group = seed, col = "snapshot")) +
+  scale_color_manual(name='Regression Model',
+                       breaks=c('snapshot', 'imm-hist'),
+                       values=c('snapshot'='red', 'imm-hist'='blue'))+
+  labs(alt = "hello world") +
+  ggtitle("Infections")
+
+
+
+# antibodies
+file_root_ab<- "antibodies.tsv"
+snap_ab_raw <- read_combine_episim_output_zipped(directory_base, file_root_ab )
+imm_ab_raw <- read_combine_episim_output_zipped(directory_imm, file_root_ab)
+
+
+start_date <- ymd("2021-11-15")
+end_date <- ymd("2029-11-30")
+snap_ab <- snap_ab_raw %>%
+  filter(date >= start_date) %>%
+  filter(date <= end_date) %>%
+  filter(pHh == 0.0, immuneSigma == 0.0)
+# mutate(vax = generic + mRNA + vector + ba1Update + ba5Update + natural)
+imm_ab <- imm_ab_raw %>%
+  filter(date >= start_date) %>%
+  filter(date <= end_date) %>%
+  filter(pHh == 0.0, immuneSigma == 0.0)
+# mutate(vax = generic + mRNA + vector + ba1Update + ba5Update + natural)
+ggplot() + #nShowingSymptoms # SARS_CoV_2
+  geom_line(imm_ab, mapping = aes(date, SARS_CoV_2 , group = seed, col = "imm-hist")) +
+  geom_line(snap_ab, mapping = aes(date, SARS_CoV_2 , group = seed, col = "snapshot")) +
+  scale_color_manual(name='Regression Model',
+                     breaks=c('snapshot', 'imm-hist'),
+                     values=c('snapshot'='red', 'imm-hist'='blue'))+
+  ggtitle("Antibodies")
+
+
+
+
+  # scale_colour_manual(name = "scenario", values = c("red"="red", "blue"="blue"), labels = c("snapshot", "immune history")) +
+  # facet_wrap(pHh ~ immuneSigma)
+
+# antibodies are a bit lower for immune history people
+# jump in snapshot on first day is a bit sus... (maybe there is something wrong there..., not with immune history))
+# what happens to Antibodies from June 30 to July 1?? Why do they jump?
+
+# infections: now imm-Hist (blue) run has lower case numbers... too many antibodies or whats going on?
+# but blue also has slightly lower antibodies. How can this be?