.Rhistory

input.plot <- function(data,
color_scheme = c("#999999","#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7"),
period.labels = c("Negative", 'Neg->Pos', 'Positive', 'Pos-> Neg',"Negative again"),
sampling.times = NULL){
plot.data <- data[,c(1:4)];#only select indicators
#replace all negative numbers for lastObs
data$lastneg[data$lastneg<0 ]<- data$lastObs[data$lastneg<0 ]
data$firstpos[data$firstpos<0 ]<- data$lastObs[data$firstpos<0 ]
data$lastpos[data$lastpos<0 ]<- data$lastObs[data$lastpos<0 ]
data$firstrec[data$firstrec<0 ]<- data$lastObs[data$firstrec<0 ]
#replace infinity for appropriate values
data[is.infinite(data$lastneg),]$lastneg<-data[is.infinite(data$lastneg),]$firstpos
data[is.infinite(data$firstpos),]$firstpos<-data[is.infinite(data$firstpos),]$lastpos
data[is.infinite(data$lastpos),]$lastpos<-data[is.infinite(data$lastpos),]$lastObs
data[is.infinite(data$firstrec),]$firstrec<-data[is.infinite(data$firstrec),]$lastObs
#make sure that lastneg<=firspos<=lastpos<=firstrec
with(data,{
lastneg <- mapply(min,lastneg,firstpos);
firstpos <- mapply(min,firstpos, lastpos);
lastpos <-mapply(min,lastpos,firstneg);
firstrec <-mapply(min,firstneg,lastObs);
})
#replace real time with interval
if(!is.null(sampling.times)){
plot.data$start <-0;
plot.data$neg1 <- data$lastneg-plot.data$start;
plot.data$negpos <- data$firstpos - data$lastneg;
plot.data$pos <-data$lastpos - data$firstpos;
plot.data$posneg2 <- data$firstrec - data$lastpos;
plot.data$neg2 <-  data$lastObs-data$firstrec;}else
{
#take into account the sampling times
plot.data$start <-min(sampling.times);
plot.data$neg1 <- data$lastneg-plot.data$start;
plot.data$negpos <- data$firstpos - data$lastneg;
plot.data$pos <-data$lastpos - data$firstpos;
plot.data$posneg2 <- data$firstrec - data$lastpos;
plot.data$neg2 <-  data$lastObs-data$firstrec;
}
#melt down
plot.data <- melt(plot.data,id = c("host_id","inoculationStatus","group","treatment"))
#create plots per treatment
plots <- list();
for(i in unique(plot.data$treatment)){
y_breaks <- if(is.null(sampling.times)){c(0:max(plot.data$value[!is.infinite(plot.data$value)]))}else{sampling.times}
plots[[length(plots)+1]]<- ggplot(data = plot.data[plot.data$treatment == i,]%>%
arrange(group)%>%
arrange(desc(host_id)))+
geom_bar(aes(y = value, x = as.factor(host_id),
fill = factor(variable,levels = c("neg1","negpos","pos","posneg2","neg2")[c(5,4,3,2,1)])),stat= 'identity')+
coord_flip()+
scale_fill_manual('State',
values = color_scheme,
labels = period.labels[c(5,4,3,2,1)])+ylab("Days post challenge")+
xlab("host ID")+
ggtitle(i)+
scale_y_continuous(breaks = y_breaks )+
scale_x_discrete(limits = rev)+
if(length(unique(plot.data$group))>1){facet_grid(group + inoculationStatus ~. , scales = "free_y")}
}
return(list(plots = plots, data = plot.data))
}
test <- input.plot(transform.data.for.plot(localF$data),sampling.times = seq(0,3,.1))
data
source("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
test <- input.plot(transform.data.for.plot(localF$data),sampling.times = seq(0,3,.1))
data
data$lastpos
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
test <- input.plot(transform.data.for.plot(localF$data),sampling.times = seq(0,3,.1))
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
test <- input.plot(transform.data.for.plot(localF$data),sampling.times = seq(0,3,.1))
in.data
plot.data
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
test <- input.plot(transform.data.for.plot(localF$data),sampling.times = seq(0,3,.1))
in.data
in.data$lastneg
mapply(min,in.data$lastneg,in.data$firstpos)
in.data$firstpos
in.data$lastpos
in.data$firstneg
in.data
#make sure that lastneg<=firspos<=lastpos<=firstrec
in.data$firstpos <- mapply(max,in.data$firstpos, in.data$lastneg);
in.data$lastpos <-mapply(max,in.data$lastpos,in.data$firstpos);
in.data$firstrec <-mapply(max,in.data$firstrec,in.data$lastpos);
in.data
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
source("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
test <- input.plot(transform.data.for.plot(localF$data),sampling.times = seq(0,3,.1))
test
source("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
test <- input.plot(transform.data.for.plot(localF$data),sampling.times = seq(0,3,.1))
test
#output estimation
localF
#output estimation
localF$estimation
install.packages("learnr")
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#load required packages
library("yaml")
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#obtain the information from the configuration file
getwd()
settings <- read_yaml("summerfair_config_example.yaml")
settings <- read_yaml("summerfair_config_example.yaml")
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
settings
path <- "./data/processed/example_project/"
#host.data <- read.csv(paste0(path, "host.csv"))               #static host data
#host.event.data <- read.csv(paste0(path,"host_events.csv"))   #events in the host
#environment.data <- read.csv(paste0(path,"environment.csv"))        #static environment data
#environment.event.data <- read.csv(paste0(path,"environment_events.csv"))  #events in environment
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
data_path <- settings$data_path
host.data <- read.csv(paste0(data_path, "host.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
data_path <- settings$data_path
host.data <- read.csv(paste0(data_path, "host.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
data_path <- settings$data_path
host.data <- read.csv(paste0(settings$data_path, "/host.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
data_path <- settings$data_path
host.data <- read.csv(paste0(settings$data_path, "/host.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
data_path <- settings$data_path
host.data <- read.csv(paste0(settings$data_path, "/hosts.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
data_path <- settings$data_path
host.data <- read.csv(paste0(settings$data_path, "/hosts.csv"))               #static host data
settings$data_path
settings <- read_yaml("summerfair_config_example.yaml")
data_path <- settings$data_path
data_path
rm(settings)
settings <- read_yaml("summerfair_config_example.yaml")
settings
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
data_path <- settings$data_path
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
settings$data_path
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#read in data
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#read in data
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
#read in data
getwd()
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
#read in data
getwd()
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#read in data
getwd()
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#read in data
getwd()
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
#read in data
settings$data_path
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
#read in data
settings$data_path
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#read in data
settings$data_path
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"))               #static host data
host.event.data <- read.csv(paste0(settings$data_path,"host_events.csv"))   #events in the host
environment.data <- read.csv(paste0(settings$data_path,"environment.csv"))        #static environment data
environment.event.data <- read.csv(paste0(settings$data_path,"environment_events.csv"))  #events in environment
host.data
#read in data
settings$data_path
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"), setp =";")               #static host data
#read in data
settings$data_path
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"), sep =";")               #static host data
host.event.data <- read.csv(paste0(settings$data_path,"host_events.csv"))   #events in the host
environment.data <- read.csv(paste0(settings$data_path,"environment.csv"))        #static environment data
environment.event.data <- read.csv(paste0(settings$data_path,"environment_events.csv"))  #events in environment
host.data
#read in data
settings$data_path
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"), sep =";")               #static host data
host.event.data <- read.csv(paste0(settings$data_path,"host_events.csv"), sep =";")   #events in the host
environment.data <- read.csv(paste0(settings$data_path,"environment.csv"), sep =";")        #static environment data
environment.event.data <- read.csv(paste0(settings$data_path,"environment_events.csv"), sep =";")  #events in environment
#read in data - deal with separator issues if needed (sep = ";")
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"), sep =";")               #static host data
host.event.data <- read.csv(paste0(settings$data_path,"host_events.csv"), sep =";")   #events in the host
environment.data <- read.csv(paste0(settings$data_path,"environment.csv"), sep =";")        #static environment data
environment.event.data <- read.csv(paste0(settings$data_path,"environment_events.csv"), sep =";")  #events in environment
host.event.data
input.data.events <- host.event.data%>%filter(measurement_type == "esbl_count")
#load required packages
library("yaml")
library("tidyverse")
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#read in data - deal with separator issues if needed (sep = ";")
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"), sep =";")               #static host data
host.event.data <- read.csv(paste0(settings$data_path,"host_events.csv"), sep =";")   #events in the host
environment.data <- read.csv(paste0(settings$data_path,"environment.csv"), sep =";")        #static environment data
environment.event.data <- read.csv(paste0(settings$data_path,"environment_events.csv"), sep =";")  #events in environment
input.data.events <- host.event.data%>%filter(measurement_type == "esbl_count")
input.data.events
host.data
environment.event.data
environment.data
environment.event.data
left_join(x = input.data.events,
y = host.data)
#load required packages
library("yaml")
library("tidyverse")
#obtain the information from the configuration file
settings <- read_yaml("summerfair_config_example.yaml")
#read in data - deal with separator issues if needed (sep = ";")
host.data <- read.csv(paste0(settings$data_path, "hosts.csv"), sep =";")               #static host data
host.event.data <- read.csv(paste0(settings$data_path,"host_events.csv"), sep =";")   #events in the host
environment.data <- read.csv(paste0(settings$data_path,"environment.csv"), sep =";")        #static environment data
environment.event.data <- read.csv(paste0(settings$data_path,"environment_events.csv"), sep =";")  #events in environment
input.data.events
#filter out only relevant information. Here the count of ESBL producing E.coli
input.data.events <- host.event.data%>%filter(measurement_type == "esbl_count")
#When only using host data for measurements use function join_host_environment
input.data.events <- join_host_environment(input.data.events, environment.event.data)
## function to join host and environmental data such that each host sample is placed in a environment
#join_host_environment <- function(host_event_data,
#                                  environment_event_data){
input.data.events
environment.event.data
## function to join host and environmental data such that each host sample is placed in a environment
#join_host_environment <- function(host_event_data,
#                                  environment_event_data){
#create temporary output object
temp.output <- input.data.events#host_event_data
temp.output
depth(temp.output)
depht(temp.output)
dim(temp.output)
for(i in c(1:dim(temp.output)[1]))
{
print(input.data.events$host_id[i])
}
input.data.events[i]
input.data.events[i,]
environment.event.data
input.data.events[i,c("host_id","event_day","event_time")]
#find last movement of this host
environment_event_data<-environment.event.data
#select host_id, day and time
event_key <- temp.output[i,c("host_id","event_day","event_time")]
event_key$host_id
environment_event_data[,environment_event_data$host_id== event_key$host_id]
environment_event_data[environment_event_data$host_id== event_key$host_id,]
#last movement
last(environment_event_data[environment_event_data$host_id== event_key$host_id & environment_event_data$event_day <= event_key$event_day,])
#last movement
last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day &
environment_event_data$event_time <= event_key$event_time,])
if(!is.na(event_key$event_time)){
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day &
environment_event_data$event_time <= event_key$event_time,"environment_id"])
}else
{
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day,"environment_id"])
}
env.id
#find last movement of this host
environment_event_data<-environment.event.data
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day,"environment_id"])
env.id
#last movement
if(!is.na(event_key$event_time)){
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day &
environment_event_data$event_time <= event_key$event_time,"environment_id"])
}else
#last movement
if(!is.na(event_key$event_time)){
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day &
environment_event_data$event_time <= event_key$event_time,"environment_id"])
}else{
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day,"environment_id"])
}
env.id
if(!is.na(event_key$event_time)){
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day &
environment_event_data$event_time <= event_key$event_time,"environment_id"])
}else{
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day,"environment_id"])
}
env.id
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day,"environment_id"])
env.id
event_key$event_time
is.na(event_key$event_time)
is.null(event_key$event_time)
!is.na(as.numeric(event_key$event_time))
as.numeric(event_key$event_time)
is.na(as.numeric(event_key$event_time))
#last movement
if(!is.na(as.numeric(event_key$event_time))){
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day &
environment_event_data$event_time <= event_key$event_time,"environment_id"])
}else{
env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day,"environment_id"])
}
env.id
temp.output$environment_id <- NULL
temp.output$environment_id
temp.output
#create temporary output object
temp.output <- input.data.events#host_event_data
temp.output$environment_id <- NA;
#iterate over the events of host
for(i in c(1:dim(temp.output)[1]))
{
#select host_id, day and time
event_key <- temp.output[i,c("host_id","event_day","event_time")]
#find last movement of this host
environment_event_data<-environment.event.data
#last movement
if(!is.na(as.numeric(event_key$event_time))){
temp.output$environment_id[i]<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day &
environment_event_data$event_time <= event_key$event_time,"environment_id"])
}else{
temp.output$environment_id[i]<-env.id<-last(environment_event_data[environment_event_data$host_id== event_key$host_id &
environment_event_data$event_day <= event_key$event_day,"environment_id"])
}
}
return(temp.output)
temp.output
#When only using host data for measurements use function join_host_environment
input.data.events <- join_host_environment(input.data.events, environment.event.data)
#source required SUMMERFAIR files
source("LocalAlgorithm.R")
#filter out only relevant information. Here the count of ESBL producing E.coli
input.data.events <- host.event.data%>%filter(measurement_type == "esbl_count")
#When only using host data for measurements use function join_host_environment
input.data.events <- join_host_environment(input.data.events, environment.event.data)
#add additional data of the hosts
input.data.events <- left_join(x = input.data.events,
y = host.data)
#add position of host in the environment based on time
input.data.events
readRDS("dataE.RDS")
dataE
head(input.data.events)
head(dataE)
join_host_environment
head(input.data.events)
settings$rule_name
eval(str2expression(paste0("rule.",settings$rule_name)))
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))))
#load required packages
library("yaml")
library("tidyverse")
#source required SUMMERFAIR files
source("LocalAlgorithm.R")
#load required packages
library("yaml")
library("tidyverse")
#source required SUMMERFAIR files
source("LocalAlgorithm.R")
arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))))
head(input.data.events)
source("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/LocalAlgorithm.R", echo=TRUE)
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))))
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/LocalAlgorithm.R", echo=TRUE)
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))))
data
arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))))
data
#treatment_type is required to have at least a value
input.data.events$treatment_type <- "control"
#treatment_type is required to have at least a value
input.data.events$treatment_type <- "control"
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))))
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))),
var.id = NULL)
input.data.events
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))),
var.id = host_groupNumber)
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))),
var.id = c("host_groupNumber"))
names(input.data.events)
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))),
var.id = c("host_groupNumber"))
source("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/LocalAlgorithm.R", echo=TRUE)
arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))),
var.id = c("host_groupNumber"))
input.data.events$inoculation_type
host.event.data
sample(c("S","I"), length(input.data.events$inoculation_type))
sample(c("S","I"), length(input.data.events$inoculation_type),replace = TRUE)
input.data.events$inoculation_type <- sample(c("S","I"), length(input.data.events$inoculation_type),replace = TRUE)
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))),
var.id = c("host_groupNumber"))
arranged.data
arranged.data[[1]]
arranged.data[[1]]$arranged.data
arranged.data[[2]]
raw.plot(arranged.data[[2]])
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
transform.data.for.plot(arranged.data[[2]])
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
transform.data.for.plot(arranged.data[[2]])
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
transform.data.for.plot(arranged.data[[2]])
sirdata
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
transform.data.for.plot(arranged.data[[2]])
sirdata
host.data[1,"inoculation_type"]
host.data
sirdata%>%filter(host_id ==i)
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
transform.data.for.plot(arranged.data[[2]])
single.host.data
out
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
transform.data.for.plot(arranged.data[[2]])
debugSource("C:/Users/fisch106/surfdrive - Fischer, E.A.J. (Egil)@surfdrive.surf.nl/Projecten/SUMMERFAIR/ProjectShareSUMMERFAIR/Syntax/autumn-fair/src/WorkingExample/ExperimentalPlots.R", echo=TRUE)
transform.data.for.plot(arranged.data[[2]])
single.host.data
sirdata
sirdata%>%filter(host_id ==i)
host.data
input.data.events
input.data.events%>%mutate(.by = host_id,
inoculation_type = sample(c("S","I"),1))
input.data.events <- input.data.events%>%mutate(.by = host_id,
inoculation_type = sample(c("S","I"),1))
input.data.events
#filter out only relevant information. Here the count of ESBL producing E.coli
input.data.events <- host.event.data%>%filter(measurement_type == "esbl_count")
#When only using host data for measurements use function join_host_environment
input.data.events <- join_host_environment(input.data.events,
environment.event.data)
#add additional data of the hosts
input.data.events <- left_join(x = input.data.events,
y = host.data)
head(input.data.events)
#treatment_type and inoculation_type is required to have at least a value
input.data.events$treatment_type <- "control"
input.data.events <- input.data.events%>%mutate(.by = host_id,
inoculation_type = sample(c("S","I"),1))
#apply rule and arrange data
arranged.data <- arrangeData(input.data.events,
eval(str2expression(paste0("rule.",settings$rule_name))),
var.id = c("host_groupNumber"))
transform.data.for.plot(arranged.data[[2]])
transform.data.for.plot(arranged.data[[2]])