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Commit a6db3391 authored by B.Anderson's avatar B.Anderson
Browse files

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
parent c4ff5901
......@@ -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.
......
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.
......
......@@ -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
......
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......@@ -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
......
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