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Source  : 6fc2cb9
Branch  : main
Author  : Christian Knudsen <[email protected]>
Time    : 2024-11-08 13:40:54 +0000
Message : Merge pull request #171 from chrbknudsen/main

primært chunk-naming

clt.md

@@ -45,7 +45,7 @@ mean(random_numbers)
 ```
 
 ``` output
-[1] 0.5095871
+[1] 0.4877989
 ```
 The important point of the Central Limit Theorem is, that if we take a large
 number of random samples, and calculate the mean of each of these samples,
@@ -59,7 +59,7 @@ mean(runif(100))
 ```
 
 ``` output
-[1] 0.4959613
+[1] 0.4897284
 ```
 And we can use the `replicate()` function to repeat that calculation several times, in this case 1000 times:
 

index.md

@@ -8,7 +8,7 @@ This site is a collection of individual episodes. It is not intended
 as a single course. The concept is for this site to act as the  foundation for made-to-measure courses.
 Based on the individual and specific needs in a given situation, we will make a 
 selection of relevant episodes, and string them together to form a tailored 
-course,.
+course.
 
 The episodes are under construction, and will continue to be, as we will
 add new content until we have covered any subject that might arise working with

kmeans.md

@@ -144,31 +144,31 @@ clustering
 ```
 
 ``` output
-K-means clustering with 3 clusters of sizes 62, 69, 47
+K-means clustering with 3 clusters of sizes 69, 47, 62
 
 Cluster means:
    Alcohol Malicacid      Ash Alcalinityofash Magnesium Totalphenols Flavanoids
-1 12.92984  2.504032 2.408065        19.89032 103.59677     2.111129   1.584032
-2 12.51667  2.494203 2.288551        20.82319  92.34783     2.070725   1.758406
-3 13.80447  1.883404 2.426170        17.02340 105.51064     2.867234   3.014255
+1 12.51667  2.494203 2.288551        20.82319  92.34783     2.070725   1.758406
+2 13.80447  1.883404 2.426170        17.02340 105.51064     2.867234   3.014255
+3 12.92984  2.504032 2.408065        19.89032 103.59677     2.111129   1.584032
   Nonflavanoidphenols Proanthocyanins Colorintensity       Hue
-1           0.3883871        1.503387       5.650323 0.8839677
-2           0.3901449        1.451884       4.086957 0.9411594
-3           0.2853191        1.910426       5.702553 1.0782979
+1           0.3901449        1.451884       4.086957 0.9411594
+2           0.2853191        1.910426       5.702553 1.0782979
+3           0.3883871        1.503387       5.650323 0.8839677
   OD280OD315ofdilutedwines   Proline
-1                 2.365484  728.3387
-2                 2.490725  458.2319
-3                 3.114043 1195.1489
+1                 2.490725  458.2319
+2                 3.114043 1195.1489
+3                 2.365484  728.3387
 
 Clustering vector:
-  [1] 3 3 3 3 1 3 3 3 3 3 3 3 3 3 3 3 3 3 3 1 1 1 3 3 1 1 3 3 1 3 3 3 3 3 3 1 1
- [38] 3 3 1 1 3 3 1 1 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 1 2 1 2 2 1 2 2 1 1 1 2 2 3
- [75] 1 2 2 2 1 2 2 1 1 2 2 2 2 2 1 1 2 2 2 2 2 1 1 2 1 2 1 2 2 2 1 2 2 2 2 1 2
-[112] 2 1 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 2 1 1 1 1 2 2 2 1 1 2 2 1 1 2 1
-[149] 1 2 2 2 2 1 1 1 2 1 1 1 2 1 2 1 1 2 1 1 1 1 2 2 1 1 1 1 1 2
+  [1] 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 2 2 3 3 2 2 3 2 2 2 2 2 2 3 3
+ [38] 2 2 3 3 2 2 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 3 1 3 1 1 3 1 1 3 3 3 1 1 2
+ [75] 3 1 1 1 3 1 1 3 3 1 1 1 1 1 3 3 1 1 1 1 1 3 3 1 3 1 3 1 1 1 3 1 1 1 1 3 1
+[112] 1 3 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 3 1 1 3 3 3 3 1 1 1 3 3 1 1 3 3 1 3
+[149] 3 1 1 1 1 3 3 3 1 3 3 3 1 3 1 3 3 1 3 3 3 3 1 1 3 3 3 3 3 1
 
 Within cluster sum of squares by cluster:
-[1]  566572.5  443166.7 1360950.5
+[1]  443166.7 1360950.5  566572.5
  (between_SS / total_SS =  86.5 %)
 
 Available components:
@@ -188,9 +188,9 @@ table()
 ``` output
      true
 quess  1  2  3
-    1 13 20 29
-    2  0 50 19
-    3 46  1  0
+    1  0 50 19
+    2 46  1  0
+    3 13 20 29
 ```
 
 The algorithm have no idea about the numbering, the three groups are numbered 

md5sum.txt

@@ -2,10 +2,10 @@
 "CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-11-08"
 "LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-11-08"
 "config.yaml" "76188894d250a68fbdf65206cee2d873" "site/built/config.yaml" "2024-11-08"
-"index.md" "e4e80431f54f0c27189828975817535f" "site/built/index.md" "2024-11-08"
+"index.md" "61394b6d8242b2ec5c69d9c2493cd74b" "site/built/index.md" "2024-11-08"
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-11-08"
-"episodes/reproducible-analysis.Rmd" "c35d8069a53be38e0fc226243af7fc12" "site/built/reproducible-analysis.md" "2024-11-08"
-"episodes/reading-files.Rmd" "f16cdf18bbcf52659587b4f4b0985461" "site/built/reading-files.md" "2024-11-08"
+"episodes/reproducible-analysis.Rmd" "976433176d38ef5f97b18f2b25794941" "site/built/reproducible-analysis.md" "2024-11-08"
+"episodes/reading-files.Rmd" "16728c259f424282058f7c80997900d2" "site/built/reading-files.md" "2024-11-08"
 "episodes/descript-stat.Rmd" "828abde6deb35bebf2b60f730d6eaff7" "site/built/descript-stat.md" "2024-11-08"
 "episodes/table1.Rmd" "1615b0b67bb2e6a3d9a992a00d3edde3" "site/built/table1.md" "2024-11-08"
 "episodes/tidy-data.Rmd" "32109e710bb7b47451b8783b246aa857" "site/built/tidy-data.md" "2024-11-08"
@@ -30,7 +30,7 @@
 "learners/CLT-en.md" "8ae8f14f05472820ef155acf980ae06f" "site/built/CLT-en.md" "2024-11-08"
 "learners/data.md" "629a1935166e040d5aa8832446946310" "site/built/data.md" "2024-11-08"
 "learners/reference.md" "527a12e217602daae51c5fd9ef8958df" "site/built/reference.md" "2024-11-08"
-"learners/setup.md" "0c80507a6a78380e67338e8e60563b20" "site/built/setup.md" "2024-11-08"
+"learners/setup.md" "9b1b924cf88e06b154562a92250fcb76" "site/built/setup.md" "2024-11-08"
 "poster/poster_dk.Rmd" "721a2b68eeb0b61308158bce41c6ae21" "site/built/poster_dk.md" "2024-11-08"
 "profiles/learner-profiles.md" "5fe5bf7537072422b91ed393ada03f9a" "site/built/learner-profiles.md" "2024-11-08"
 "renv/profiles/lesson-requirements/renv.lock" "18fc1cfeec6bf26f24f2759c070cc46a" "site/built/renv.lock" "2024-11-08"

normal-distribution.md

@@ -196,7 +196,7 @@ rnorm(5, mean = 0, sd = 1 )
 ```
 
 ``` output
-[1] -0.49124146 -0.04092335  0.55254473  1.66132290 -0.01081915
+[1] -0.3687852  0.2342679  1.4054515  2.5355764  0.4683077
 ```
 Den returnerer (her) fem tilfældige værdier fra en normalfordeling med (her) 
 middelværdi 0 og standardafvigelse 1.

reading-files.md

@@ -8,7 +8,7 @@ editor_options:
 ---
 
 ::: questions
--   How do you read in data from files??
+-   How do you read in data from files?
 :::
 
 ::: objectives

reproducible-analysis.md

@@ -39,7 +39,7 @@ is not working. Doing the same analysis tomorrow, we should reach the same resul
 And that can be surprisingly difficult!
 
 There are a lot of pitfalls, ranging from accessibility to incentive structures
-in academia. But the two areas where R can help us are:
+in academia. But the three areas where R can help us are:
 
 * Software Environment
 * Documentation and Metadata
@@ -82,7 +82,7 @@ computer crashes.
 
 
 
-## Documentation and Metadata:
+## Documentation and Metadata
 
 What did we actually do in the analysis? Why did we do it? Why are we reaching the conclusion we've arrived at?
 
@@ -166,7 +166,9 @@ data set.
 
 Make a new RMarkdown document - File -> New File -> R Markdown.
 
-Change the final code chunk to include `plot(cars$dist)` instead of plot(pressure)
+Change the final code chunk to include `plot(cars$dist)` instead of plot(pressure),
+and add `library(tidyverse)`.
+
 
 ::::
 

setup.md

@@ -2,6 +2,130 @@
 title: Setup
 ---
 
-## Setup
+## Software Setup
+
+::::::::::::::::::::::::: callout
+
+### Warning
+
+Please do NOT install R and RStudio on Onedrive or other clouddrives.
+R will work but you will not be able to install the extensions to R
+that you will need in this course!
+
+::::::::::::
+
+::::::::::::::::::::::::::::::::::::::: discussion
+
+### Installing R and RStudio
+
+**R** and **RStudio** are separate downloads and installations. R is the
+underlying statistical computing environment, but using R alone is no
+fun. RStudio is a graphical integrated development environment (IDE) that makes
+using R much easier and more interactive. You need to install R before you
+install RStudio. Once installed, because RStudio is an IDE, RStudio will run R in 
+the background.  You do not need to run it separately. 
+
+
+
+:::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::: solution
+
+### Online
+Rather than installing R and RStudio on your personal computer, 
+[Posit Cloud](https://posit.cloud//) offers a free, online alternative,
+where you will be able to run R and RStudio in your browser. 
+Sign up with your Google/Gmail account if you have one, or with any other email.
+
+The free version of RStudio Cloud places limitations on the number of projects you
+can work on, and the amount of memory and processing power you can access. For the 
+purposes of following these lessons, RStudio Cloud is perfectly adequate, and what we
+recommend if you have any problems installing R and RStudio on your personal computer.
+
+:::::::::::::::::::::::::
+
+:::::::::::::::: solution
+
+### Windows
+
+#### If you already have R and RStudio installed
+
+* Open RStudio, and click on "Help" > "Check for updates". If a new version is
+	available, quit RStudio, and download the latest version for RStudio.
+* To check which version of R you are using, start RStudio and the first thing
+  that appears in the console indicates the version of R you are
+  running. Alternatively, you can type `sessionInfo()`, which will also display
+  which version of R you are running. Go on
+  the [CRAN website](https://cran.r-project.org/bin/windows/base/) and check
+  whether a more recent version is available. If so, please download and install
+  it. You can [check here](https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f) for
+  more information on how to remove old versions from your system if you wish to do so.
+
+#### If you don't have R and RStudio installed
+
+* Download R from
+  the [CRAN website](https://cran.r-project.org/bin/windows/base/release.htm).
+* Run the `.exe` file that was just downloaded.
+* Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download).
+* Under *Installers* select **RStudio x.yy.zzz - Windows.
+  Vista/7/8/10** (where x, y, and z represent version numbers).
+* Double click the file to install it.
+* Once it's installed, open RStudio to make sure it works and you don't get any
+  error messages.
+
+:::::::::::::::::::::::::
+
+:::::::::::::::: solution
+
+### MacOS
+
+#### If you already have R and RStudio installed
+
+* Open RStudio, and click on "Help" > "Check for updates". If a new version is
+	available, quit RStudio, and download the latest version for RStudio.
+* To check the version of R you are using, start RStudio and the first thing
+  that appears on the terminal indicates the version of R you are running. Alternatively, you can type `sessionInfo()`, which will also display which version of R you are running. Go on
+  the [CRAN website](https://cran.r-project.org/bin/macosx/) and check
+  whether a more recent version is available. If so, please download and install
+  it. In any case, make sure you have at least R 3.2.
+
+#### If you don't have R and RStudio installed
+
+* Download R from
+  the [CRAN website](https://cran.r-project.org/bin/macosx/).
+* Select the `.pkg` file for the latest R version.
+* Double click on the downloaded file to install R.
+* It is also a good idea to install [XQuartz](https://www.xquartz.org/) (needed
+  by some packages).
+* Go to the [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download).
+* Under *Installers* select **RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit)**
+  (where x, y, and z represent version numbers).
+* Double click the file to install RStudio.
+* Once it's installed, open RStudio to make sure it works and you don't get any
+  error messages.
+
+:::::::::::::::::::::::::
+
+
+:::::::::::::::: solution
+
+### Linux
+
+* Follow the instructions for your distribution
+  from [CRAN](https://cloud.r-project.org/bin/linux), they provide information
+  to get the most recent version of R for common distributions. For most
+  distributions, you could use your package manager (e.g., for Debian/Ubuntu run
+  `sudo apt-get install r-base`, and for Fedora `sudo yum install R`), but we
+  don't recommend this approach as the versions provided by this approach are
+  usually out of date. In any case, make sure you have at least R 3.2.
+* Go to the
+  [RStudio download page](https://www.rstudio.com/products/rstudio/download/#download).
+* Under *Installers* select the version that matches your distribution, and
+  install it with your preferred method (e.g., with Debian/Ubuntu `sudo dpkg -i
+  rstudio-x.yy.zzz-amd64.deb` at the terminal).
+* Once it's installed, open RStudio to make sure it works and you don't get any
+  error messages.
+
+:::::::::::::::::::::::::