Merge branch 'wip' after adding notebooks and Rmd

 Conflicts:
	Graphs.R
	Graphs.Rmd
	ReadMe.Rmd
	ReadMe.html
	ReadMe.md
	data/Covid19ECDC_days.csv
	data/Covid19JHH_days.csv
	definitions.R
	deprecated.R
	loadData.R
	output.Rmd
	requirements.R
	wip.R

 On branch master
 Your branch is up to date with 'origin/master'.

 All conflicts fixed but you are still merging.

 Changes to be committed:
	modified:   Graphs.R
	modified:   Graphs.Rmd
	new file:   Graphs.ipynb
	new file:   Graphs.md
	modified:   ReadMe.Rmd
	new file:   ReadMe.html
	modified:   ReadMe.md
	modified:   data/Covid19ECDC_days.csv
	modified:   data/Covid19JHH_days.csv
	modified:   definitions.R
	new file:   deprecated.R
	deleted:    gifit.R
	new file:   gifit.Rmd
	new file:   graphit.R
	modified:   loadData.R
	modified:   output.Rmd
	new file:   output.ipynb
	new file:   output.tex
	modified:   requirements.R
	modified:   unittests.R
	modified:   wip.R

Graphs.R

@@ -3,26 +3,20 @@
 #for publication 
 rm(list = setdiff(ls(), c('ECDC0', 'JHH0', 'JHH', 'ECDC', 'JHHRegios', 'ECDCRegios','testing')))
 options(warn = 0)
-source("loadData.R")  #also loads the requirements and the definitions 
+if (!exists('JHH')) source('loadData.R') else 
+  if (max(JHH$Date) < Sys.Date() - 1) {source('loadData.R') 
+    }else if (!exists('graphit')) source('definitions.R')
+
+#also loads the requirements and the definitions 
 
 #make all graphs
 tim = Sys.time()
-#curGraph(lpdf = ECDC, regions = ECDCRegios, graphlist = myGraphNrs, ordre = 'GR')
 walkThrough(lpdf = ECDC, regions = ECDCRegios, graphlist = myGraphNrs, myFolderDate  = 'current', ordre = 'RG')
 reportDiffTime('ECDC graphs',tim, units = 'mins')
 
 tim = Sys.time()
-#curGraph( lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, ordre = 'RG')
 walkThrough( lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, myFolderDate  = 'current', ordre = 'RG')
 reportDiffTime('JHH graphs',tim,units = 'mins')
 
-
-
-#do a month
-walkThrough(lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, from = "2020-01-01", to = '2020-01-31', myFolderDate = 'January', ordre = 'RG')
-walkThrough(lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, from = "2020-04-01", to = '2020-04-30', myFolderDate = 'April', ordre = 'RG')
-walkThrough(lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, from = "2020-06-01", to = '2020-06-30', myFolderDate = 'June', ordre = 'RG')
-
-
 writeWithCounters(ECDC,name = "Covid19ECDC")
 writeWithCounters(JHH,name = "Covid19JHH") 

Graphs.Rmd

@@ -4,55 +4,66 @@ author: "VF"
 date: "9 July 2020"
 output: html_document
 ---
+##Graphs
+
 Run loadData.R or output.Rmd first to load the latest Data and the definitions. 
 Please make sure myPlotPath is correct!
 
-```{r, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-if (!exists('graphit')) source('definitions.R')
-if (!exists('JHH')) source('loadData.R')
-switch(get_os(), 
-       windows = {print("I run MS Windows.");myPlotPath <- "G:/My Drive/Covid19_plots"},
-       linux   = {print("I'm a penguin."); myPlotPath <- "~/Covid19_plots"},
-       osx     = {print("I'm a Mac.");myPlotPath <- "~/Covid19_plots"},
-       ...     = {print('not recognized OS');myPlotPath <- "~/Covid19_plots"})
+```{r init, include=FALSE}
+#knitrr::opts_chunk$set(echo = TRUE)
 
-if (!dir.exists(myPlotPath %//% 'data')) dir.create(myPlotPath %//% 'data', recursive = TRUE)
+if (!exists('JHH')) source('loadData.R') else 
+  if (max(JHH$Date) < Sys.Date() - 1) {source('loadData.R')  
+   } else source('definitions.R')
+save.image(".RData") #D:/gits/Covid19/
+#switch(get_os(), 
+#       windows = {print("I run MS Windows.");
+#                  myPlotPath <- "G:/My Drive/Covid19_plots"},
+#       linux   = {print("I'm a penguin."); myPlotPath <- "~/Covid19_plots"},
+#       osx     = {print("I'm a Mac.");myPlotPath <- "~/Covid19_plots"},
+#       ...     = {print('not recognized OS');myPlotPath <- "~/Covid19_plots"})
 
+if (!dir.exists(myPlotPath %//% 'data')) dir.create(myPlotPath %//% 'data', recursive = TRUE)
+writeWithCounters(ECDC,name = "Covid19ECDC")
+writeWithCounters(JHH,name = "Covid19JHH") 
 ```
 
 Graph and save lots of graphs on all regions present, paginated by size of the Covid impact (total confirmed cases), and on each page, territory graphs are sorted by decreasing value of the first graphed variable on the latest date in that territory.
 
 
-```{r , echo = FALSE} 
-
+```{r graphs walkthrough, echo=FALSE}
+print("results of" % % Sys.Date())
+verbose = 0
 tim = Sys.time()
-#curGraph(lpdf = ECDC, regions = ECDCRegios, graphlist = myGraphNrs, ordre = 'GR')
-walkThrough(lpdf = ECDC, regions = ECDCRegios, graphlist = myGraphNrs, myFolderDate  = 'current', ordre = 'RG')
+walkThrough(lpdf = ECDC, regions = ECDCRegios, graphlist = myGraphNrs, myFolderDate  = 'current', ordre = 'GR')
 reportDiffTime('ECDC graphs',tim, units = 'mins')
 
 tim = Sys.time()
-#curGraph( lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, ordre = 'RG')
-walkThrough( lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, myFolderDate  = 'current', ordre = 'RG')
+walkThrough( lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, myFolderDate  = 'current', ordre = 'GR')
 reportDiffTime('JHH graphs',tim,units = 'mins')
-``` 
+
+```
 
 Development one month at a time
-```{r}
-walkThrough(lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, from = "2020-01-01", to = '2020-01-31', myFolderDate = 'January', ordre = 'RG')
-walkThrough(lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, from = "2020-04-01", to = '2020-04-30', myFolderDate = 'April', ordre = 'RG')
-walkThrough(lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, from = "2020-06-01", to = '2020-06-30', myFolderDate = 'June', ordre = 'RG')
+```{r one month, include=FALSE, eval=FALSE}
+if ( mday(Sys.Date() ) <= 03) {#uses lubridate
+  walkThrough(lpdf = JHH, regions = JHHRegios, graphlist = myGraphNrs, 
+              from = floor_date(Sys.Date() %m-% months(1), 'month'), 
+              to = ceiling_date(Sys.Date() %m-% months(1), 'month')-1, 
+              myFolderDate = year(Sys.Date() %m-% months(1)) %-% sprintf("%02d", month(Sys.Date() %m-% months(1))), 
+              ordre = 'RG')
+  }
 ```
 
-do all months up to today
-```{r}
+Do all months up to today
+```{r all months, include=FALSE, eval=FALSE}
 verbose = 1
 makeHistoryGraphs(JHH, regions = JHHRegios, fromDates = seq(as.Date('2020-01-01'),Sys.Date(),  by = '1 month'), ordre = 'GR')  
 makeHistoryGraphs(ECDC, regions = ECDCRegios, fromDates = seq(as.Date('2020-01-01'),Sys.Date(),  by = '1 month'))  
 
 ```
-A more convoluted way: 
-```{r}
+A more convoluted way, just for the record: 
+```{r all months convoluted, include=FALSE, eval=FALSE}
 startDate = "2020-01-01"
 fromDates <- as.character(seq(as.Date(startDate), length = 12, by = "1 month"))
 toDates <- as.character(seq(as.Date(fromDates[2]), length = 12, by = "1 month") - 1)
@@ -66,13 +77,14 @@ makeHistoryGraphs(JHH,JHHRegios, graphlist = myGraphNrs,
 ```
 This do once in a while, to do all the non-numbererd graphs. 
 
-```{r}
+```{r byDate once a week}
 if ( weekdays( Sys.Date() , abbreviate = FALSE) == "Friday")  
-  walkThrough(ECDC, ECDCRegios, graphlist = myGraphListbyDate, myFoldetDate = 'weekly')
+  walkThrough(JHH, JHHRegios[1:10], graphlist = myGraphListbyDate,
+              myFolderDate = 'weekly')
 ```
 
 Simulate how the non-social distancing situation would have turned out: deaths, recovered, and confirmed   
-```{r}
+```{r sims, include=FALSE, eval=FALSE}
 graphDddp_fyl(JHH,regios$Vincent,savename  = "deaths missed") 
 walkThrough(JHH, regions = JHHRegios,graphlist = 'graphDccprr_fyl')
 
@@ -81,10 +93,12 @@ walkThrough(ECDC , ECDCRegios,ext = '_endsim',graphlist = c('graphDccprr_fiyl',
 
 
 ```
-## R Markdown
+## R Markdown and Jupyter Notebook: sync with Jupytext. 
 
-This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+This is an R Markdown document, linked to the same document as Jupyter notebook, using Jupytext. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
 
 When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
 
-Note that the `{r, echo = FALSE}` parameter can be added to the code chunk to prevent printing of the R code that generated the plot.
+Note that the `{r, echo = FALSE}` parameter can be added to the code chunk to prevent printing of the R code that generated the plot. And Include = false prevents automatic execution of the block.
+
+Second, note that for git, the ipynb files containing output are much heavier than the Rmd files which contain the inputs only, according to Jupytext faq (https://jupytext.readthedocs.io/en/latest/faq.html). I commit both just to be sure at this moment.