class: center, middle  <!-- Do not forget to adapt the presentation title in the header! --> <!-- Adjust the presentation to the session. Focus on the challenges, this is not a coding tutorial. Note, to include figures, store the image in the `/docs/assets/images/yyyymmdd/` folder and use the jekyll base.url reference as done in this template or see https://jekyllrb.com/docs/liquid/tags/#links. using the scale attribute , you can adjust the image size. --> <!-- Adjust the day, month --> # 27 OCTOBER 2020 ## INBO coding club <!-- Adjust the room number and name --> Exclusively on INBOflix --- class: center, middle <!-- Create a new badge using Inkscape or other programs based on the assets/images/coding_club_badges.svg file -->  --- class: center, middle  <br> [xkcd comics](https://xkcd.com/1179) --- class: center, middle  <br> [lubridate](https://lubridate.tidyverse.org/) --- class: center, middle  [Download cheatsheet here](https://github.com/inbo/coding-club/blob/master/cheat_sheets/20180426_cheat_sheet_lubridate.pdf) --- class: center, middle ### How to get started? Check the [Each session setup](https://inbo.github.io/coding-club/gettingstarted.html#each-session-setup) to get started. ### First time coding club? Check the [First time setup](https://inbo.github.io/coding-club/gettingstarted.html#first-time-setup) section to setup. --- class: left, middle  <br> No yellow sticky notes online :-( We use hackmd (see next slide) but basic principle doesn't change. --- class: center, middle ### Share your code during the coding session! <!-- Create a new hackmd file and replace this link (twice!) --> Go to https://hackmd.io/@CX5eR_y9TP2KGHs5tv61pw/Bke_b0cPw/edit <iframe src="https://hackmd.io/@CX5eR_y9TP2KGHs5tv61pw/Bke_b0cPw/edit" height="400px" width="800px"></iframe> --- class: left, middle ## Install required packages Packages we need: ``` install.packages(c("lubridate", "suncalc")) # add tidyverse if still not installed ``` ## Load the required packages ``` library(lubridate) library(suncalc) library(tidyverse) ``` --- class: left, middle # Download data and code Just as during the last coding cub session, instead of downloading the files manually we test a new inborutils function called `setup_codingclub_session()`. If you have not used this function yet, restart your R session and update the inborutils package by running: ```r if (!"remotes" %in% rownames(installed.packages())) { install.packages("remotes") } remotes::install_github("inbo/inborutils") ``` To download the coding club material of today, just run `setup_codingclub_session()`. In general, you can use the date in "YYYYMMDD" format , e.g. `setup_codingclub_session("20201027")`, to download the coding club material of October, 27. For all options, check the [documentation online](https://inbo.github.io/inborutils/reference/setup_codingclub_session.html). Of course, you can download [data](https://github.com/inbo/coding-club/blob/master/data/20201027/20201027_cameratrap_df.txt) and [scripts](https://github.com/inbo/coding-club/blob/master/src/20201027/20201027_challenges.R) manually* as we did before! <small>* __Note__: check the getting started instructions on [how to download a single file](https://inbo.github.io/coding-club/gettingstarted.html#each-session-setup)</small> --- background-image: url(/assets/images/background_challenge_1.png) class: left, middle # Challenge 1 1. The first thing you should do while working with datetimes is converting (_parsing_) characters to date(time) objects. Discover the potential of the lubridate package by parsing all columns of dataframe `datetimes_to_parse` 2. INBO is born on 2006-04-01 as the fusion of two institutes: the _Instituut voor Natuurbehoud_ (IN) and the _Instituut voor Bosbouw en Wildbeheer_ (IBW). IN is born on 1985-07-17, while IBW on 1991-03-13. On which day of the week (Monday, Tuesday, ...) are these three institutes born? Tip: use [day.html](https://lubridate.tidyverse.org/reference/day.html) or the lubridate cheat sheet 3. Use a _stamp_ to print the dates of IN, IBW and INBO as in this example: `"The institute was founded on Monday, Jan 1, 1900"` 4. How long have IN and IBW existed? What's the difference between basic `difftime` and lubridate `duration` classes? --- class: left, middle ## Intermezzo. UTC, time zones & Daylight Saving Time Some definitions: - UTC (Coordinated Universal Time): not a time zone, but THE ** time standard**. See https://24timezones.com/time-zone/utc - GMT (Greenwich Mean Time) : one of the well-known names of UTC+0 ** time zone**). GMT does observe Daylight Saving Time (unlike UTC), more on https://24timezones.com/gmt-vs-utc - World time zone map: https://24timezones.com/timezone-map - DST (Daylight Saving Time): “spring forward, fall back". [EU ends the use of DST in 2021](https://www.timetemperature.com/europe/eu-ends-summer-time.shtml). <p> --- class: left, middle ## Intermezzo. UTC, time zones & Daylight Saving Time - Where is Daylight Saving Time used?  --- class: left, middle ## Intermezzo. UTC, time zones & Daylight Saving Time - How to define time zones? Typically `"Continent/City"` works well: ```r as_datetime("2020-08-01 09:00:00", tz = "Asia/Tehran") [1] "2020-08-01 09:00:00 +0430" as_datetime("2020-08-01 09:00:00", tz = "Europe/Brussels") [1] "2020-08-01 09:00:00 CEST" ``` or a time zone abbreviation: ```r as_datetime("2020-08-01 09:00:00", tz = "CET") [1] "2020-08-01 09:00:00 CEST" ``` Note the authomatic conversion to CEST (Central Europe *Summer* Time). However, if you use CEST it will not work, and you get the GMT version: ```r as_datetime("2020-08-01 09:00:00", tz = "CEST") [1] "2020-08-01 07:00:00 GMT" Warning message: In as.POSIXlt.POSIXct(x, tz) : unknown timezone 'CEST' ``` CEST is ** NOT ** a time zone! --- background-image: url(/assets/images/background_challenge_2.png) class: left, middle # Challenge 2 We need to get a better insight of the behavior of the mammals of the [Red Forest](https://en.wikipedia.org/wiki/Red_Forest) in Ukraine, one of the most contaminated areas in the world today. To do so, brave Emma, Jim and Sander (FIS team) went there in 2018 and installed a camera trap deployment. The data are stored in `20201027_cameratrap_df.txt`, which you have just downloaded. 1. The datetime of the observations are stored in column `image_sequence` and are in UTC. Get correspondent clock times. 2. Contrary to `image_sequence_datetime`, the datetimes in `camera_deployment_start` and `camera_deployment_end` are already in clock time. Add the timezone information to these columns. --- background-image: url(/assets/images/background_challenge_3.png) class: left, middle # Challenge 3 Use the same data as for Challenge 2. 1. Get hour and day information of the observations. You can store them as additional columns 2. For each observation find whether it happened during "dawn" (between `dawn` and `sunriseEnd`), "day" (between `sunriseEnd` and `sunset`), "evening" (between `sunset` and `nightStart`) or "night" (from midnight to `dawn` or after `night`). You can do it by using the function `getSunlightTimes()` from the [suncalc](https://github.com/datastorm-open/suncalc#suncalc) package.* <small>* __Note__: this challenge could require basic knowledge of data manipulation (e.g. `dplyr` package) </small> --- class: left, middle # The future of UTC: to leap or not to leap? UTC is based on time as measured by atomic clocks so it is independent of Earth's rotation. The [leap second](https://en.wikipedia.org/wiki/Leap_second) is a one-second adjustment that is occasionally applied to Coordinated Universal Time (UTC), to accommodate the imprecise observed solar time (irregularities and slowdown in the Earth's rotation).  So, what to do with these annoying leap seconds? Should the standard UTC be getting rid of them or not? --- class: left, middle ## Resources - `lubridate` website: https://lubridate.tidyverse.org/ - Summary of all formats recognized by lubridate: https://lubridate.tidyverse.org/reference/parse_date_time.html#details - Commented [solutions](https://github.com/inbo/coding-club/blob/master/src/20201027/20201027_challenges_solutions.R) of the challenges - Video recording of the coding club session: https://vimeo.com/473564881 - R for Data Science. [Chapter 16: Dates and times](https://r4ds.had.co.nz/dates-and-times.html) - One useful internet site about time measurement and time zones: https://24timezones.com/ - Definition of UTC standard: https://24timezones.com/time-zone/utc - Difference between GMT vs UTC: https://24timezones.com/gmt-vs-utc - EU and the end of daylight saving time: https://www.timetemperature.com/europe/eu-ends-summer-time.shtml - World time zone map: https://24timezones.com/timezone-map --- class: center, middle  <!-- Adjust the room and date --> Room: 01.72 (Kaat Tilley)?? & online <br> Date: __24/11/2020__, van 10:00 tot 12:00<br> Subject: ggplot for dummies (registration announced via DG_useR@inbo.be)