updated l5 rmd eg

.Rproj.user/ABE7B653/console06/E8FBF1BE

@@ -1215,4 +1215,43 @@ remote:
 To https://github.com/darwinanddavis/EmoRyCodingClub
    5a6f108..d2418d2  master -> master
 ]0;~/Documents/Emory/admin/ecc6300L-127771-M:ecc malishev$ git pushcommit -m 'l6 yyaml'add .
-
+
+]0;~/Documents/Emory/admin/ecc6300L-127771-M:ecc malishev$ git add .pushcommit -m 'l6 yyaml'''''' '
+'r'e' n''d'e'r' 's'i't'e' 'l'6'
+[master 06169fa] render site l6
+ 30 files changed, 1943 insertions(+), 157 deletions(-)
+ rewrite Lesson5_files/figure-html/unnamed-chunk-3-1.png (66%)
+ create mode 100644 Lesson5_rmd.log
+ create mode 100644 Lesson5_rmd_files/figure-docx/unnamed-chunk-1-1.png
+ create mode 100644 Lesson5_rmd_files/figure-docx/unnamed-chunk-2-1.png
+ create mode 100644 Lesson5_rmd_files/figure-html/unnamed-chunk-1-1.png
+ create mode 100644 Lesson5_rmd_files/figure-html/unnamed-chunk-2-1.png
+ create mode 100644 Lesson5_rmd_files/figure-markdown_github/unnamed-chunk-1-1.png
+ create mode 100644 Lesson5_rmd_files/figure-markdown_github/unnamed-chunk-2-1.png
+ rewrite docs/Lesson3_files/figure-html/unnamed-chunk-2-1.png (97%)
+ delete mode 100644 docs/Lesson4_files/figure-html/unnamed-chunk-1-1.png
+ rewrite docs/Lesson5_files/figure-html/unnamed-chunk-3-1.png (66%)
+ create mode 100644 docs/Lesson5_rmd.docx
+ create mode 100644 docs/Lesson5_rmd.log
+ create mode 100644 docs/Lesson5_rmd.md
+ create mode 100644 docs/Lesson5_rmd.pdf
+ create mode 100644 docs/Lesson5_rmd_files/figure-docx/unnamed-chunk-1-1.png
+ create mode 100644 docs/Lesson5_rmd_files/figure-docx/unnamed-chunk-2-1.png
+ create mode 100644 docs/Lesson5_rmd_files/figure-markdown_github/unnamed-chunk-1-1.png
+ create mode 100644 docs/Lesson5_rmd_files/figure-markdown_github/unnamed-chunk-2-1.png
+]0;~/Documents/Emory/admin/ecc6300L-127771-M:ecc malishev$ ig tpgit push
+Counting objects: 35, done.
+Delta compression using up to 4 threads.
+Compressing objects:   3% (1/32)   Compressing objects:   6% (2/32)   Compressing objects:   9% (3/32)   Compressing objects:  12% (4/32)   Compressing objects:  15% (5/32)   Compressing objects:  18% (6/32)   Compressing objects:  21% (7/32)   Compressing objects:  25% (8/32)   Compressing objects:  28% (9/32)   Compressing objects:  31% (10/32)   Compressing objects:  34% (11/32)   Compressing objects:  37% (12/32)   Compressing objects:  40% (13/32)   Compressing objects:  43% (14/32)   Compressing objects:  46% (15/32)   Compressing objects:  50% (16/32)   Compressing objects:  53% (17/32)   Compressing objects:  56% (18/32)   Compressing objects:  59% (19/32)   Compressing objects:  62% (20/32)   Compressing objects:  65% (21/32)   Compressing objects:  68% (22/32)   Compressing objects:  71% (23/32)   Compressing objects:  75% (24/32)   Compressing objects:  78% (25/32)   Compressing objects:  81% (26/32)   Compressing objects:  84% (27/32)   Compressing objects:  87% (28/32)   Compressing objects:  90% (29/32)   Compressing objects:  93% (30/32)   Compressing objects:  96% (31/32)   Compressing objects: 100% (32/32)   Compressing objects: 100% (32/32), done.
+Writing objects:   2% (1/35)   Writing objects:   5% (2/35)   Writing objects:   8% (3/35)   Writing objects:  11% (4/35)   Writing objects:  14% (5/35)   Writing objects:  17% (6/35)   Writing objects:  20% (7/35)   Writing objects:  22% (8/35)   Writing objects:  25% (9/35)   Writing objects:  28% (10/35)   Writing objects:  31% (11/35)   Writing objects:  34% (12/35)   Writing objects:  37% (13/35)   Writing objects:  40% (14/35)   Writing objects:  42% (15/35)   Writing objects:  45% (16/35)   Writing objects:  48% (17/35)   Writing objects:  51% (18/35)   Writing objects:  54% (19/35)   Writing objects:  57% (20/35)   Writing objects:  60% (21/35)   Writing objects:  62% (22/35)   Writing objects:  65% (23/35)   Writing objects:  68% (24/35)   Writing objects:  71% (25/35)   Writing objects:  74% (26/35)   Writing objects:  77% (27/35)   Writing objects:  80% (28/35)   Writing objects:  80% (28/35), 1.07 MiB | 230.00 KiB/s   Writing objects:  82% (29/35), 1.07 MiB | 230.00 KiB/s   Writing objects:  85% (30/35), 1.07 MiB | 230.00 KiB/s   Writing objects:  88% (31/35), 1.07 MiB | 230.00 KiB/s   Writing objects:  91% (32/35), 1.07 MiB | 230.00 KiB/s   Writing objects:  94% (33/35), 1.07 MiB | 230.00 KiB/s   Writing objects:  97% (34/35), 1.07 MiB | 230.00 KiB/s   Writing objects: 100% (35/35), 1.07 MiB | 230.00 KiB/s   Writing objects: 100% (35/35), 1.94 MiB | 230.00 KiB/s, done.
+Total 35 (delta 15), reused 0 (delta 0)
+remote: Resolving deltas:   0% (0/15)remote: Resolving deltas:   6% (1/15)remote: Resolving deltas:  13% (2/15)remote: Resolving deltas:  20% (3/15)remote: Resolving deltas:  26% (4/15)remote: Resolving deltas:  33% (5/15)remote: Resolving deltas:  40% (6/15)remote: Resolving deltas:  46% (7/15)remote: Resolving deltas:  53% (8/15)remote: Resolving deltas:  60% (9/15)remote: Resolving deltas:  66% (10/15)remote: Resolving deltas:  73% (11/15)remote: Resolving deltas:  80% (12/15)remote: Resolving deltas:  86% (13/15)remote: Resolving deltas:  93% (14/15)remote: Resolving deltas: 100% (15/15)remote: Resolving deltas: 100% (15/15), completed with 15 local objects.
+remote: 
+remote: GitHub found 2 vulnerabilities on darwinanddavis/EmoRyCodingClub's default branch (2 moderate). To find out more, visit:
+remote:      https://github.com/darwinanddavis/EmoRyCodingClub/network/alerts
+remote: 
+To https://github.com/darwinanddavis/EmoRyCodingClub
+   d2418d2..06169fa  master -> master
+]0;~/Documents/Emory/admin/ecc6300L-127771-M:ecc malishev$ peopen _site.yml 
+]0;~/Documents/Emory/admin/ecc6300L-127771-M:ecc malishev$ open _site.yml 
+]0;~/Documents/Emory/admin/ecc6300L-127771-M:ecc malishev$ git add .

.Rproj.user/ABE7B653/sources/prop/INDEX

@@ -5,6 +5,7 @@
 ~%2FDocuments%2FEmory%2Fadmin%2Fecc%2FLesson5.Rmd="6A63A69"
 ~%2FDocuments%2FEmory%2Fadmin%2Fecc%2FLesson5_rmd.Rmd="76C81E37"
 ~%2FDocuments%2FEmory%2Fadmin%2Fecc%2FLesson6.Rmd="1AA4DEB8"
+~%2FDocuments%2FEmory%2Fadmin%2Fecc%2FLesson7.Rmd="D245CEC4"
 ~%2FDocuments%2FEmory%2Fadmin%2Fecc%2Fadmin%2F_ecc_master1.Rmd="D4A80BDA"
 ~%2FDocuments%2FEmory%2Fadmin%2Fecc%2Fadmin%2Fecc_master1.Rmd="86A44BC0"
 ~%2FDocuments%2FEmory%2Fadmin%2Fecc%2Fadmin_%2Fairbnbdata_test.R="7160458D"

.Rproj.user/shared/notebooks/paths

@@ -5,6 +5,7 @@
 /Users/malishev/Documents/Emory/admin/ecc/Lesson5.Rmd="18E98FB2"
 /Users/malishev/Documents/Emory/admin/ecc/Lesson5_rmd.Rmd="622DEF85"
 /Users/malishev/Documents/Emory/admin/ecc/Lesson6.Rmd="2D08C0EF"
+/Users/malishev/Documents/Emory/admin/ecc/Lesson7.Rmd="5F2E2BA4"
 /Users/malishev/Documents/Emory/admin/ecc/admin/_ecc_master1.Rmd="ADA1EBE5"
 /Users/malishev/Documents/Emory/admin/ecc/admin_/airbnbdata_test.R="DD9B31B9"
 /Users/malishev/Documents/Emory/admin/ecc/admin_/atl_breweries.Rmd="3D591BD"

Lesson5.Rmd

@@ -2,7 +2,7 @@
 params:
   lesson: "Lesson 5"
   title: "Turning code into reproducible documents with `Rmarkdown`"
-  bookchapter_name: "Download the `RMarkdown` template here"    
+  bookchapter_name: "Download the `RMarkdown` template here (right click > Save Link As")      
   bookchapter_section: "https://github.com/darwinanddavis/EmoRyCodingClub/raw/master/Lesson5_rmd.Rmd"
   functions: "`here`, `summarise`"
   packages: "`here`, `set_here`, `dr_here`, `dplyr`"      
@@ -141,6 +141,7 @@ Have a look through each section of the raw `.Rmd` file to see what the code doe
 
 # Exercises  
 
+* Knit a PDF, HTML, and Word doc. Use the hotkey `Cmd/Ctrl + Shift + K`  
 * Create a 'EmoRy Coding Club notes' document (PDF or HTML document)  
 * Create your own parameter in the yaml   
 * Create a code chunk that shows the code and output, but masks any warnings
@@ -154,7 +155,9 @@ url <- "http://data.insideairbnb.com/united-states/ny/new-york-city/2019-06-02/d
 nyc_full <- read_csv(url) # reads in data
 nyc_full %>% glimpse
 ```
-* Change the above figure dimensions in the knitted document      
+* Change the above figure dimensions in the knitted document     
+* Create a table with the title in bold text and one of the rows italicised 
+* Write an inline equation and a idented equation  
 
 
 <!-- end body -->

Lesson5_rmd.Rmd

@@ -5,13 +5,6 @@ author: |
  |  
  | Your affiliation here
 output:
-  html_document: # html options 
-    highlight: tango
-    code_folding: show
-    toc: yes
-    toc_depth: 4
-    number_sections: no
-    toc_float: yes
   pdf_document: # pdf options
     highlight: tango
     template: null
@@ -21,13 +14,28 @@ output:
     fig_width: 4
     fig_height: 5
     fig_caption: true
+    df_print: tibble 
+    latex_engine: xelatex #pdflatex # lualatex
+  html_document: # html options 
+    highlight: tango
+    code_folding: show
+    toc: yes
+    toc_depth: 4
+    number_sections: no
+    toc_float: yes
   word_document: # ms word options
     highlight: tango
     keep_md: yes
     pandoc_args: --smart
     toc: yes
   md_document: # markdown options
     variant: markdown_github 
+inludes:
+  before_body: before_body.tex
+subtitle: 
+tags:
+- nothing
+- nothingness
 params: 
   email: "your email here"
   date: !r Sys.Date()
@@ -40,7 +48,7 @@ classoption: portrait
   MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "all"} } });
 </script>
 
-```{r, set-options, echo = F, cache = F}
+```{r, set-options, echo = F, cache = T}
 options(width=100)
 knitr::opts_chunk$set(
  eval = TRUE, # run all code
@@ -51,6 +59,15 @@ knitr::opts_chunk$set(
  size="small" # set code chunk size
 )
 
+### run this once  
+# tinytex::install_tinytex()
+
+packages <- c("DT","htmlwidgets")
+
+ppp <- lapply(packages,require,character.only=T)
+names(ppp) <- packages
+if(any(ppp==F)){cbind(packages,ppp);cat("\n\n\n ---> Check packages are loaded properly <--- \n\n\n")}
+
 # knitr::opts_knit$set(root.dir=paste0(params$dir,"/")) # set working dir
 # setwd(paste0(params$dir,"/")) # for running just in R not knitr
 ```
@@ -67,36 +84,50 @@ R version: `r params$version`
 
 This document showcases how to create and use `RMarkdown` documents.    
 
+You can write in **bold** and *italicised* text (in _two_ different __ways__).  
+
 You can write in-line `code` if you want to differentiate between when you are typing normally or highlighting `model parameters`, for example.    
 
 Equations like this $t' = \gamma(t - vx/c^{2})$, to appear within text lines.  
 
 Create links to your [website](https://github.com/darwinanddavis).  
 
-Make footnotes^[Where the footnote goes here and it is automatically formatted].    
+Make footnotes^[Here is the footnote you created earlier, automatically formatted].    
 
-## Use different headings  
+# You can easily create headings. This is the same font size as the 'Overview' above    
+
+## Then move down in font size    
 
 ### Like this subheading  
 
-# Just like \LaTeX{}, but _more versatile_.      
+#### And this fourth order heading   
+
+Insert line breaks <br>  between text like this    
+
+Insert a horizontal line break using five asterisks ('*****')  
+
+*****        
+
+(There is also a page break here. Best seen in PDF. Check the raw Rmd file to see the code)  
+
+The raw Rmd file also has the code for inserting user comments, 
+<!-- To do this, place the cursor on the text and type 'Cmd/Ctl + Shift + C' -->
+
+\newpage    
 
-\newpage     
-
 ## Define equations      
 
-Accordingly, we write the eigenfunction of a spinless particle as the superposition of plane wave states of momentum ($\pi$) and energy ($Ej$) having amplitudes $a(\pi,Ej)$  
+Accordingly, we write the eigenfunction of a spinless particle as the superposition of plane wave states of momentum ($\pi$) and energy ($Ej$) having amplitudes $a(\pi,Ej)$ (from^[Efthimiades, S., Physical meaning and derivation of Schrodinger and Dirac equations, Department of Natural Sciences, Fordham University. [doi: d34464566](https://arxiv.org/vc/quant-ph/papers/0607/0607001v1.pdf).])     
 
 $$  
 \phi n(r,t) =  
-\sum_{i, j} a(p_{i},E_{j})
-e^{
-\frac{i}
-{h}
-(p_{i} \cdot r - E_{j}t) 
+  \sum_{i, j} a(p_{i},E_{j})
+  e^{
+  \frac{i}
+  {h}
+  (p_{i} \cdot r - E_{j}t) 
 }
 $$
-\  
 \    
 
 ## Embed images/gifs:  
@@ -148,7 +179,7 @@ Figure 2. Example of a plot with improved graphics and its associated code embed
 Table 1. Definitions of model parameters for individual hosts and **parasites**. Dimensions and units: -, dimensionless; cm, centimetres; J, Joules; L, length.    
 
 | Parameter | Definition | Dimension<br/>(unit) | 
-| :---: | :--- | :---: |    
+| :---: | :--- | ---: |    
 | _L_ | structural length | cm |
 | _ee_ | scaled reserve density | J (cm^3^) |
 | _D_ | host development | --- |
@@ -157,6 +188,47 @@ Table 1. Definitions of model parameters for individual hosts and **parasites**.
 \newpage  
 
 
+
+## Use buttons or tabs for sub-chapters {.tabset .tabset-fade .tabset-pills}  
+
+### Chapter 1  
+*Then you can add whatever you want here* like you would normally write in the `Rmd` file.  
+\  
+
+### Chapter 2 (with new code)  
+Here's an Easter egg for you ...  
+
+```{r,echo=F}
+require(ggplot2)
+require(plotly)
+nn <- 100
+p <- ggplot() +
+  geom_point(aes(rnorm(nn),sample(nn/2,nn,replace=T)),colour = rainbow(nn),size=sample(nn/2,nn,replace=T)/5,alpha=abs(rnorm(nn))) +
+  labs(x = "Random normally distributed data",
+       y = "Sampled integers") +
+  theme_minimal()
+ggplotly(p)
+```
+
+### More tables   
+Here's a new way of creating tables using the `DT` package  
+
+```{r,cache=T,warning=F, echo=F}
+require(DT)
+require(htmlwidgets)
+datatable(mtcars, 
+          rownames = T, 
+          filter="top", 
+          options = list(pageLength = 5, scrollX=T),
+          class = 'cell-border stripe',
+          editable = 'cell',
+          caption = "Table 1. The 'mtcars' dataset presented in a datatable. Try editing the columns and cells."  
+          )
+```
+
+
+***      
+
 ## Embed code from different languages  
 
 ### This is `R` code  
@@ -209,8 +281,16 @@ x = A \ b     # Solve the system Ax = b
 
 ### CSS
 ```{css, eval=F}
-body {
-  color: red;
+# custom code for the tabs in this file
+.btn {
+    border-width: 0 0px 0px 0px;
+    font-weight: normal;
+    text-transform: ;
+}
+.btn-default {
+    color: #f08080;
+    background-color: #ffffff;
+    border-color: #ffffff;
 }
 ```
 

Lesson5_rmd_cache/html/__packages

@@ -0,0 +1,8 @@
+base
+viridisLite
+viridis
+ggplot2
+plotly
+DT
+htmlwidgets
+nycflights13

Lesson6.Rmd

@@ -1,7 +1,7 @@
 ---
 params:
   lesson: "Lesson 6"
-  title: "Applying functions with `purrr`"
+  title: "Lists, lists, lists and applying functions with `purrr`"
   bookchapter_name: "Cheat sheet for the `purrr` package"    
   bookchapter_section: "https://purrr.tidyverse.org/"  
   functions: "`map`, `map2`"
@@ -68,7 +68,7 @@ Use the `purrr` package to apply functions to lists and vectors.
 
 # Do First    
 
-Recreate the below plot using the smaller NYC Airbnb dataset. To change the legend title, add the (unintuitive) `colour = "your legend text"` argument to the `labs()` function.  
+Recreate the below plot using the smaller NYC Airbnb dataset. The curve is a 'loess'. To change the legend title, add the (unintuitive) `colour = "your legend title"` argument to the `labs()` function.  
 
 ```{r}
 # smaller csv file (16 cols)
@@ -78,9 +78,7 @@ nyc <- nyc[nyc$id < 1000000,] # get smaller subet of data
 ```
 
 ```{r, echo=F, eval=T, out.width="100%"}
-require(ggthemes)
-require(ggplot2)
-require(readr)
+require(ggthemes,ggplot2,readr)
 
 # smaller csv file (16 cols)
 url <- "http://data.insideairbnb.com/united-states/ny/new-york-city/2019-06-02/visualisations/listings.csv"
@@ -130,7 +128,9 @@ map2(ls1,ls2,sum)
 `head_while` Return head elements until one does not pass. Also `tail_while`.   
 
 ```{r,eval=F}
-pluck(ls1,1)
+pluck(ls1,3) # advantage = returns numeric 
+ls1[3][[1]] # this is the same as above
+
 keep(ls2, is.na)
 discard(ls1, is.na)
 compact(ls1)