diff --git a/Content of Codes used in the Campylobacter project.Rmd b/Content of Codes used in the Campylobacter project.Rmd deleted file mode 100644 index b39893bdd22c087250a4249b9730bea8f9b91cb5..0000000000000000000000000000000000000000 --- a/Content of Codes used in the Campylobacter project.Rmd +++ /dev/null @@ -1,180 +0,0 @@ ---- -title: "Content of Codes used in Campylobacter project" -author: "Gianni Lo Iacono" -bibliography: campylobacter.bib -output: - pdf_document: - toc: yes - highlight: tango - fig_caption: yes - citation_package: natbib -date: '2023-01-06' ---- - -```{r setup, include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -``` - - - -# Description of the files in this folder - -## _File name:_ remove_incubation_reporting_Campylobacter.R -### _Brief Description:_ -The code adjust the Campylobacter data, to remove the incubation period and reporting delay. - -### _Key Features:_ -The distributions of the incubation period were assumed to be log-normal [@Sartwell1995] with location parameter, $\mu$, and the scale parameter, $\sigma$ inferred by the mean, $m$, and standard deviation, $s$, of the observed data of Horn and Lake [@Horn2013] for the incubation period. -Delay in reporting was assumed to follow a uniform distribution between 1-4 days, based on informed opinion of one of the authors (G. Nichols). - -### _Input Files:_ (with examples) -../Data_Base/Incubation_period_Horn_Lake.csv -```{r input, echo = FALSE} -file_name<-paste("Data_Base/Incubation_period_Horn_Lake.csv",sep="") -Incub_data<-read.csv( file_name ) -head(Incub_data) -``` - -### Plot of Incubation Period - -```{r incubation, echo=FALSE} -plot(Incub_data$day,Incub_data$freq,xlab="Day",ylab="Frequency") -``` - -../Data_Base/Campylobacter_reported.csv -```{r input2, echo = FALSE} -Campylobacter_data_df<-read.csv(file="Data_Base/Campylobacter_reported.csv",sep=",") -colnames(Campylobacter_data_df)<-c("Spec_Date", "POSTCODE") -head(Campylobacter_data_df) -``` - - -### _Output Files:_ (with example) -../Data_Base/Campylobacter_adjusted_date_df.csv -```{r output, echo = FALSE} -Campylobacter_adjusted_date_df<-read.csv(file="Data_Base/Campylobacter_adjusted_date.csv",sep=",") -head(Campylobacter_adjusted_date_df[,-1]) -``` - -<<<<<<< HEAD -<!---Different File ---> - - - -## _File name:_ [Plot_reported_and_adjusted_campylobacter_cases.R](Codes/Plot_reported_and_adjusted_campylobacter_cases.R) -### _Brief Description:_ -The code plots reported and adjusted campylobacter cases. - -### _Key Features:_ -Data aggregated monthly - -### _Input Files:_ (with examples) -../Data_Base/Campylobacter_adjusted_date.csv -```{r input3, echo = FALSE} -Campylobacter_adjusted_date_df<-read.csv("Data_Base/Campylobacter_adjusted_date.csv") -head(Campylobacter_adjusted_date_df) -``` - -### _Output Files:_ -../Graphs/Campy_seasonal_reported.tiff -{width=40%} - -../Graphs/Campy_seasonal_adjusted.tiff -{width=40%} - - -## _File name:_ [Pathogen_Linkage_fixed_time_lag.R](Codes/Pathogen_Linkage_fixed_time_lag.R) -### _Brief Description:_ -The code associates the value of selected environmental variables to the Campylobacter cases at the location of the diagnostic laboratory postcode and date of occurrence with a chosen time-time_lag. It also associate the corresponding yearly population in the catchment areas corresponding to the diagnostic laboratory postcode. - - -### _Key Features:_ -The time lag is an input (line 180, e.g. time_lag<-7 will take 7 days time-lag) and calculate the enviromental variables averaged (expect for cululative rainfall which calculate the cumulative sum of rain) over the past time-lag days. - -The code also extract iformation about the latitude and longitude of the laboratory location. -It also estimmate the day-length based on latitude from laboratory location and time of the year. - -### _Input Files:_ (with examples for humidity) -../Data_Base/MEDMI/,_variable_,.csv -where _variable_ can be: - -- humidity -- max_air_temp -- min_air_temp -- rain -- wind_speed - - -```{r input4, echo = FALSE} -variable<-"humidity" -file<-paste("Data_Base/MEDMI/",variable,".csv",sep="") -variable_df_1<-read.csv(file) -head(variable_df_1[,c(1:7)]) -``` -../Data_Base/Population_catchments_1989_2016.csv - -```{r input5, echo = FALSE} -catchment_population_df<-read.csv(paste("Data_Base/Population_catchments_1989_2016.csv",sep="")) -colnames(catchment_population_df)<-c("PostCode", - "residents_1989", - "residents_1990", - "residents_1991", - "residents_1992", - "residents_1993", - "residents_1994", - "residents_1995", - "residents_1996", - "residents_1997", - "residents_1998", - "residents_1999", - "residents_2000", - "residents_2001", - "residents_2002", - "residents_2003", - "residents_2004", - "residents_2005", - "residents_2006", - "residents_2007", - "residents_2008", - "residents_2009", - "residents_2010", - "residents_2011", - "residents_2012", - "residents_2013", - "residents_2014", - "residents_2015", - "residents_2016") - -head(catchment_population_df) -``` -../Data_Base/Campylobacter_Adjusted_date.csv - -```{r input6, echo = FALSE} -Campylobacter_cases<-read.csv("Data_Base/Campylobacter_Adjusted_date.csv") -colnames(Campylobacter_cases)<-c("Date","Spec_Date", "PostCode") -head(Campylobacter_cases) -``` - -### _Output Files:_ -../Data_Base/Laboratory_environment_,_time_lag_char_,".csv -where _time_lag_char_ is the timelag in days -```{r output2 , echo = FALSE} -time_lag_char<-"7" -merged_lab_time_lag<-read.csv(paste("Data_Base/Laboratory_environment_",time_lag_char,".csv",sep="")) -head(merged_lab_time_lag) -``` -../Data_Base/Campylobacter_environment_,_time_lag_char_,".csv -where _time_lag_char_ is the timelag in days - -```{r output3 , echo = FALSE} -time_lag_char<-"7" -Campylobacter_cases_df2<-read.csv(paste("Data_Base/Campylobacter_environment_",time_lag_char,".csv",sep="")) -head(Campylobacter_cases_df2) -``` - - -======= ->>>>>>> 7ba923ff14a4c44a060bb1910e03bac7800d2cfe - - -