updates tos ite

Author: taddallas

.gitignore

@@ -0,0 +1,27 @@
+content/inClassProblems/week2.Rmd
+content/inClassProblems/week3.Rmd
+content/inClassProblems/week4.Rmd
+content/inClassProblems/week5.Rmd
+content/inClassProblems/week6.Rmd
+content/inClassProblems/week7.Rmd
+content/inClassProblems/week8.Rmd
+content/inClassProblems/week9.Rmd
+content/inClassProblems/week10.Rmd
+content/inClassProblems/week11.Rmd
+content/inClassProblems/week12.Rmd
+content/inClassProblems/week13.Rmd
+content/inClassProblems/week14.Rmd
+
+content/inClassProblems/week2.html
+content/inClassProblems/week3.html
+content/inClassProblems/week4.html
+content/inClassProblems/week5.html
+content/inClassProblems/week6.html
+content/inClassProblems/week7.html
+content/inClassProblems/week8.html
+content/inClassProblems/week9.html
+content/inClassProblems/week10.html
+content/inClassProblems/week11.html
+content/inClassProblems/week12.html
+content/inClassProblems/week13.html
+content/inClassProblems/week14.html

content/code/api.Rmd

@@ -165,6 +165,7 @@ tadInfo <- jsonlite::fromJSON(content(tad, "text"), simplifyVector = FALSE)
 
 
 
+
 ### Class problem:
 
 How long as Tad been on GitHub?
@@ -176,9 +177,16 @@ How long as Tad been on GitHub?
 ```
 
 
+That list (`tadInfo`) also has some links to other API calls that could be made. Use the `organizations_url` to get a list of the organizations that Tad is a member of.
+
+
+```{r class.source = 'fold-hide'}
 
 
 
+```
+
+
 
 
 
@@ -419,7 +427,7 @@ Now that we know we can connect to the database, let's explore how to get the da
 
 ### Querying the database with the SQL syntax
 
-To connect to tables within a database, you can use the `tbl()` function from `dplyr`. This function can be used to send SQL queries to the database. To demonstrate this functionality, let’s select the columns "year", "species_id", and "plot_id" from the surveys table:
+To connect to tables within a database, you can use the `tbl()` function from `dplyr`. This function can be used to send SQL queries to the database. To demonstrate this functionality, let's select the columns "year", "species_id", and "plot_id" from the surveys table:
 
 
 ```{r}

content/code/git.Rmd

@@ -8,10 +8,6 @@ output: pdf_document
 
 
 
-
-
-
-
 ## Unix (bash) shell
 
 The best way to directly interact with your computer is through the terminal window. This terminal (in Mac and Linux OSs) is the unix shell, and is commonly referred to as the bash shell, though bash is only one flavor of unix shell (e.g., Ksh shell, fish). 
@@ -25,7 +21,7 @@ We will use the bash shell to run some of our programs, and help with makefiles
 
 Open up the terminal. 
 
-You should see, at least in Ubuntu, your username followed by a "@" and the name of your machine (e.g., `tad@poe`), followed by ":~$" and a blinking cursor. You are in the home directory by default. To see this, issue the command 
+You should see, at least in Ubuntu, your username followed by a "@" and the name of your machine (e.g., `tad@tadComputer`), followed by ":~$" and a blinking cursor. You are in the home directory by default. To see this, issue the command 
 
 ```
 pwd
@@ -159,7 +155,7 @@ sudo apt install htop
 
 You also do not strictly need the "-get" part of that. This is a holdover from an earlier version, and I just stuck with it due to muscle memory. 
 
-Finally, this should rarely (fingers crossed) be the case when working on these lab computers for people in the course, as I requested that all (hopefully) necessary packages and such be installed prior to you sitting in that seat. 
+Finally, this should rarely (fingers crossed) be the case when working on these lab computers for people in the course, as I requested that all (hopefully) necessary packages and such be installed prior to you sitting in that seat. For instance, you should have `htop` installed already. You can check on this by typing `htop` into the terminal. What does the output look like? 
 
 
 
@@ -195,13 +191,9 @@ Finally, this should rarely (fingers crossed) be the case when working on these
 Now we will demonstrate how to use command line utilities. These are things that do not have a GUI (graphical user interface), and therefore must be run through the command line (e.g., nano). The thing we will learn to use through command line is a version control software called `git`. 
 
 
-
-
-
 ### What is version control?
 
-Version control is a system that records changes to a file or set of files over time so that you can recall specific versions later.
-
+Version control is a system that records changes to a file or set of files over time so that you can recall specific versions later. 
 
 ### Why does it matter?
 
@@ -210,10 +202,6 @@ Version control is important both for collaborative coding with team members, an
 
 
 
-
-
-
-
 ### How do I do it?
 
 I want you to use the folder you made above called `firstRepo` as your first GitHub repo. So navigate to it from command line. Now, initiate the folder as a git repository (i.e., repo).
@@ -293,7 +281,6 @@ To do this, we will navigate to our account on Github, and click the `+` dropdow
 git remote add origin https://github.com/userName/repoName.git
 ```
 
-
 Now, when we go through the `add, commit, push` process of staging and making a commit (as described above), you will be prompted for your Github username and password. 
 
 _you may also need to set some global options of your name and email address when first pushing to Github, but you will be instructed on how exactly to do this_
@@ -307,9 +294,7 @@ Github allows for collaborative coding, meaning that people distributed across t
 
 **What does this mean for you?**
 
-Probably nothing, but it means something for how you will collaborate with your classmates, and how you will turn in assignments. All your dev work for your assignments will be version controlled on Github. 
-
-
+Probably nothing, but it means something for how you will collaborate with your classmates, and how you will turn in assignments. All your dev work for your assignments will be version controlled on Github. On an individual level, especially to graduate researchers in the room, this tool could save you, in the case of poor data backups (how often do you backup your data?), code changes that break functionality (meaning that you probably want to revert), and collaborating with your advisor and others (easier to send a link to a GitHub to demonstrate progress than manuscript drafts called `manuscriptTD_v2_final_final(2).docx`).
 
 
 

content/code/git.html

@@ -370,9 +370,9 @@ <h2>Unix (bash) shell</h2>
 <h3>Tutorial</h3>
 <p>Open up the terminal.</p>
 <p>You should see, at least in Ubuntu, your username followed by a “@”
-and the name of your machine (e.g., <code>tad@poe</code>), followed by
-“:~$” and a blinking cursor. You are in the home directory by default.
-To see this, issue the command</p>
+and the name of your machine (e.g., <code>tad@tadComputer</code>),
+followed by “:~$” and a blinking cursor. You are in the home directory
+by default. To see this, issue the command</p>
 <pre><code>pwd</code></pre>
 <p>which should output “/home/name”, where “name” is your username
 (again, this may be specific to Linux OSs).</p>
@@ -460,7 +460,9 @@ <h2>Downloading programs that you need</h2>
 <p>Finally, this should rarely (fingers crossed) be the case when
 working on these lab computers for people in the course, as I requested
 that all (hopefully) necessary packages and such be installed prior to
-you sitting in that seat.</p>
+you sitting in that seat. For instance, you should have
+<code>htop</code> installed already. You can check on this by typing
+<code>htop</code> into the terminal. What does the output look like?</p>
 <hr />
 </div>
 <div id="git" class="section level1">
@@ -569,7 +571,14 @@ <h3>Benefits of Github</h3>
 <p><strong>What does this mean for you?</strong></p>
 <p>Probably nothing, but it means something for how you will collaborate
 with your classmates, and how you will turn in assignments. All your dev
-work for your assignments will be version controlled on Github.</p>
+work for your assignments will be version controlled on Github. On an
+individual level, especially to graduate researchers in the room, this
+tool could save you, in the case of poor data backups (how often do you
+backup your data?), code changes that break functionality (meaning that
+you probably want to revert), and collaborating with your advisor and
+others (easier to send a link to a GitHub to demonstrate progress than
+manuscript drafts called
+<code>manuscriptTD_v2_final_final(2).docx</code>).</p>
 </div>
 </div>
 <div id="so-lets-take-a-tour-of-github" class="section level2">
@@ -602,26 +611,14 @@ <h2>sessionInfo</h2>
 ## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-##  [1] tidyr_1.3.1    dplyr_1.1.4    plyr_1.8.9     DBI_1.2.3      geodata_0.5-8 
-##  [6] terra_1.8-50   sf_1.0-21      rgbif_3.7.7    jsonlite_1.8.9 httr_1.4.7    
+## [1] rmarkdown_2.29
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] gtable_0.3.6       xfun_0.49          bslib_0.8.0        ggplot2_3.5.1     
-##  [5] vctrs_0.6.5        tools_4.5.0        generics_0.1.4     curl_6.0.1        
-##  [9] tibble_3.2.1       proxy_0.4-27       RSQLite_2.3.7      blob_1.2.4        
-## [13] pkgconfig_2.0.3    KernSmooth_2.23-26 data.table_1.16.2  dbplyr_2.5.0      
-## [17] lifecycle_1.0.4    compiler_4.5.0     stringr_1.5.1      munsell_0.5.1     
-## [21] codetools_0.2-19   htmltools_0.5.8.1  maps_3.4.1         class_7.3-23      
-## [25] sass_0.4.9         yaml_2.3.10        lazyeval_0.2.2     pillar_1.10.2     
-## [29] jquerylib_0.1.4    whisker_0.4.1      classInt_0.4-11    cachem_1.1.0      
-## [33] tidyselect_1.2.1   digest_0.6.37      stringi_1.8.4      purrr_1.0.2       
-## [37] fastmap_1.2.0      grid_4.5.0         colorspace_2.1-1   cli_3.6.5         
-## [41] magrittr_2.0.3     utf8_1.2.5         triebeard_0.4.1    crul_1.5.0        
-## [45] e1071_1.7-16       withr_3.0.2        scales_1.3.0       bit64_4.5.2       
-## [49] oai_0.4.0          rmarkdown_2.29     bit_4.5.0          memoise_2.0.1     
-## [53] evaluate_1.0.1     knitr_1.49         rlang_1.1.6        urltools_1.7.3    
-## [57] Rcpp_1.0.14        glue_1.8.0         httpcode_0.3.0     xml2_1.3.6        
-## [61] R6_2.6.1           units_0.8-7</code></pre>
+##  [1] digest_0.6.37     R6_2.6.1          fastmap_1.2.0     xfun_0.52        
+##  [5] cachem_1.1.0      knitr_1.50        htmltools_0.5.8.1 lifecycle_1.0.4  
+##  [9] cli_3.6.5         sass_0.4.10       jquerylib_0.1.4   compiler_4.5.0   
+## [13] tools_4.5.0       evaluate_1.0.3    bslib_0.9.0       yaml_2.3.10      
+## [17] rlang_1.1.6       jsonlite_2.0.0</code></pre>
 </div>
 </div>
 

content/code/iteration.Rmd

@@ -129,10 +129,13 @@ tmp3 <- dat |>
 
 ```
 
-So summarise expects the output to be a vector (note that there are ways around this, by pulling out the information we want from the cor.test)
 
 
-```{r}
+So `summarise` expects the output to be a vector (note that there are ways around this, by pulling out the information we want from the cor.test)
+
+
+```{r class.source = 'fold-hide'}
+
 tmp3 <- dat |>
 	dplyr::group_by(country) |>
 	dplyr::summarise(cor.test(year, lifeExp)$estimate)
@@ -141,7 +144,7 @@ tmp3 <- dat |>
 
 But how we do pull out multiple values from the same test? And how do we handle and diagnose potential errors when we don't work through each test sequentially? 
 
-```{r}
+```{r class.source = 'fold-hide'}
 
 lifeExpTime <- matrix(0, ncol=4, nrow=length(countries))
 
@@ -165,7 +168,7 @@ lifeExpTime$country <- countries
 
 And we can explore these data, to determine which countries have increasing or decreasing life expectancy values as a function of time. 
 
-```{r}
+```{r class.source = 'fold-hide'}
 
 lifeExpTime[which.min(lifeExpTime$pearsonEst),]
 
@@ -176,7 +179,9 @@ This may seem like a lot of work when we could have done a bit less using `dplyr
 
 Let's say we want to create a Fibonacci sequence. This is a vector of numbers in which each number is the sum of the two preceding numbers in the vector. For the example, we will limit the length of the vector to be length 1000. 
 
-```{r}
+
+
+```{r class.source = 'fold-hide'}
 
 fib <- c(0,1)
 for(i in 3:1000){
@@ -185,10 +190,18 @@ for(i in 3:1000){
 
 ```
 
+
+
 And now we have a Fibonacci sequence starting with `c(0,1)`. 
 
+
 > Why do I start the `for` loop above at 3, and how else could you approach this same problem (there are many ways)? 
 
+```{r class.source = 'fold-hide'}
+
+# You do it. 
+
+```
 
 
 
@@ -226,6 +239,7 @@ lapply(X=testList2, FUN=nrow)
 
 ```
 
+
 The output of `lapply` will always be a list, which is nice in some instances and not nice in others. `sapply` is a wrapper for `lapply` which always returns a vector of values.
 
 
@@ -275,8 +289,12 @@ sapply(X=testDF, FUN=mean)
 
 
 
+
+
+
 ## Some practice problems 
 
+
 1. Above, we defined a data set as a list on ringtail diet changes as a function of time. Using those data, calculate the mean dry fragment weight for each of the fragment types.
 
 ```{r}
@@ -315,7 +333,8 @@ sapply(X=testDF, FUN=mean)
 You are creating a game of rock-paper-scissors. In the game, each player can select their strategy, and the strategy can be different in each trial (where there can be 100s of trials). 
 
 I think that the outcome is random, so as a player, I already have decided what I'm going to play before the game starts. 
-```{r}
+
+```{r class.source = 'fold-hide'}
 
 strat <- sample(c('rock','paper', 'scissors'), 100, replace=TRUE)
 
@@ -325,15 +344,20 @@ strat <- sample(c('rock','paper', 'scissors'), 100, replace=TRUE)
 
 Write a for loop to simulate rock-paper-scissors game of 500 trials between two players, where my strategy above is one of the players. 
 
-```{r}
+```{r class.source = 'fold-hide'}
 
 newStrat <- c()
 for(i in 1:length(strat)){
   newStrat[i] <- sample(c('rock','paper','scissors'),1)
 }
 
-# but this is just the same as above. And we need a way to score the result to see who won right? Let's do that now. Write a function that determines who wins each round (so the inputs would be something like x='rock',y='scissors', and it would output `y` or `2` to indicate the winner)
+```
+
+
 
+But this is just the same as above. And we need a way to score the result to see who won right? Let's do that now. Write a function that determines who wins each round (so the inputs would be something like x='rock',y='scissors', and it would output `y` or `2` to indicate the winner)
+
+```{r class.source = 'fold-hide'}
 
 getScore <- function(x,y){
   xScore <- yScore <- c()
@@ -352,10 +376,9 @@ getScore <- function(x,y){
 
 
 
-How would you go about changing the strategy of the other player to beat my strategy? 
-
-```{r}
+How would you go about changing the strategy of the other player to beat my strategy? I'm basically asking you to write code to play the winning move against the opponent when you know the opponent's strategy. 
 
+```{r class.source = 'fold-hide'}
 
 tadStrat <- function(opp){
   opts <- c('rock', 'paper', 'scissors')
@@ -374,9 +397,9 @@ tadStrat <- function(opp){
   return(ret)
 }
 
+```
 
 
-```
 
 
 
@@ -404,7 +427,6 @@ What other way could we approach this problem?
 
 ```{r}
 
-
 # a bit obvious, but I can break down each play and test all 3 strategies, picking the one that works best. 
 
 ret <- c()