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----
-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
-![Reported Cases](Graphs\Campy_seasonal_reported){width=40%}
-
-../Graphs/Campy_seasonal_adjusted.tiff
-![Adjusted Cases](Graphs\Campy_seasonal_adjusted){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)
-```
-
-
-=======
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