amended to enable a way to force report update; pdf still fails, unclear why;...

amended to enable a way to force report update; pdf still fails, unclear why; render is still ignoring floating ToC. Have seen this before, can't remember the cause/fix

Rmd/cleaningFeederData.Rmd

@@ -9,7 +9,7 @@ author: '`r params$authors`'
 date: 'Last run at: `r Sys.time()`'
 output:
   bookdown::html_document2:
-    self_contained: TRUE
+    self_contained: no
     fig_caption: yes
     code_folding: hide
     number_sections: yes
@@ -305,13 +305,17 @@ aggDT[, propExpected := sumOK/(uniqueN(feederDT$feeder_ID)*24*4)] # we expect 25
 summary(aggDT)
 
 message("How many days have 100%?")
-nrow(aggDT[propExpected == 1])
+n <- nrow(aggDT[propExpected == 1])
+n
 ```
 
+So, there are `r n` days with 100% data...
+
 If we plot the mean then we will see which days get closest to having a full dataset.
 
 ```{r bestDaysMean, fig.width=8}
 ggplot2::ggplot(aggDT, aes(x = rDate, colour = season, y = meanOK)) + geom_point()
+
 ```
 
 Re-plot by the % of expected if we assume we _should_ have 25 feeders * 24 hours * 4 per hour (will be the same shape):
@@ -319,6 +323,27 @@ Re-plot by the % of expected if we assume we _should_ have 25 feeders * 24 hours
 ```{r bestDaysProp, fig.width=8}
 ggplot2::ggplot(aggDT, aes(x = rDate, colour = season, y = 100*propExpected)) + geom_point() +
   labs(y = "%")
+
+aggDT[, rDoW := lubridate::wday(rDate, lab = TRUE)]
+h <- head(aggDT[season == "Spring"][order(-propExpected)])
+kableExtra::kable(h, caption = "Best Spring days overall", 
+                  digits = 3) %>%
+  kable_styling()
+
+h <- head(aggDT[season == "Summer"][order(-propExpected)])
+kableExtra::kable(h, caption = "Best Summer days overall", 
+                  digits = 3) %>%
+  kable_styling()
+
+h <- head(aggDT[season == "Autumn"][order(-propExpected)])
+kableExtra::kable(h, caption = "Best Autumn days overall",
+                  digits = 3) %>%
+  kable_styling()
+
+h <- head(aggDT[season == "Winter"][order(-propExpected)])
+kableExtra::kable(h, caption = "Best Winter days overall", 
+                  digits = 3) %>%
+  kable_styling()
 ```
 
 This also tells us that there is some reason why we get fluctations in the number of data points per hour after 2003.

Rmd/cleaningFeederData_allData.log

-This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) (format=pdflatex 2020.4.15)  8 JUL 2020 22:59
+This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) (format=pdflatex 2020.4.15)  9 JUL 2020 00:11
 entering extended mode
  restricted \write18 enabled.
  %&-line parsing enabled.

_drakeCleanFeeders.R

@@ -54,7 +54,7 @@ addSeason <- function(dt,dateVar,h){
 }
 
 
-getData <- function(f,update){
+getData <- function(f,updateData){
   # gets the data
   dt <- data.table::fread(f)
   dt[, rDateTime := lubridate::as_datetime(Time)] # the dateTime is now called Time!!!
@@ -120,7 +120,7 @@ saveData <- function(dt, which){
   }
 }
 
-makeReport <- function(f,version, type = "html"){
+makeReport <- function(f,version, type = "html", updateReport){
   # default = html
   message("Rendering ", f, ".Rmd (version: ", version, ") to ", type)
   if(type == "html"){
@@ -149,14 +149,14 @@ makeReport <- function(f,version, type = "html"){
 
 # Set the drake plan ----
 my_plan <- drake::drake_plan(
-  origData = getData(dFile, update), # returns data as data.table. If you edit 'update' in any way it will reload - drake is watching you!
+  origData = getData(dFile, updateData), # returns data as data.table. If you edit 'update' in any way it will reload - drake is watching you!
   uniqData = makeUniq(origData), # remove duplicates
   wideData = toWide(uniqData),
   saveLong = saveData(uniqData, "L"), # doesn't actually return anything
   saveWide = saveData(wideData, "W"), # doesn't actually return anything
   # pdf output fails
-  #pdfOut = makeReport(rmdFile, version, "pdf"), # pdf - must be some way to do this without re-running the whole thing
-  htmlOut = makeReport(rmdFile, version, "html") # html output
+  pdfOut = makeReport(rmdFile, version, "pdf", updateReport), # pdf - must be some way to do this without re-running the whole thing
+  htmlOut = makeReport(rmdFile, version, "html", updateReport) # html output
 )
 
 # see https://books.ropensci.org/drake/projects.html#usage

make_cleanFeeders.R

@@ -3,7 +3,9 @@
 
 # Set up ----
 startTime <- proc.time()
-update <- "yes" # edit this in any way (at all) to get drake to re-load the data
+updateData <- "yes" # edit this in any way (at all) to get drake to re-load the data
+updateReport <- "yes" # edit this to force re-render of .Rmd
+
 library(drake)
 # use r_make to run the plan inside a clean R session so nothing gets contaminated
 drake::r_make(source = "_drakeCleanFeeders.R") # where we keep the drake plan etc