help.Rmd

---
title: "FAQ / Help"
output: 
  html_document:
    toc: true
---

<br>
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```{css, echo=FALSE}
.bg-error {
  background-color: #fde4e4;
  border: 2px solid #ce0707;
  color: #ce0707
}
code{
  background-color: #ffffff;
  color: #000
}
```

# **Common Issues**

***
## **I'm getting an error related to something called Rtools**

You probably need some add-on software for a Windows machine. Note that this is _not_ an additional R package to install. Here is a quick guide to installing Rtools: [link](https://docs.google.com/viewer?url=https://raw.githubusercontent.com/jhudsl/intro_to_r/main/resources/rtools_windows.pdf).

***
## **What packages are part of the Tidyverse**?

If you need to check what packages are part of the `tidyverse`, you can do so at this [link](https://www.tidyverse.org/packages/).

***
## **Why are my changes not taking effect? It's making my results look weird!**

**Forgetting to assign your data to an object**

Often we are just printing our data and not either reassigning an existing object or creating a new object.

Here we are creating a new object from an existing one:

```{r}
new_rivers <- sample(rivers, 5)
new_rivers
```

Using just this will only print the result and not actually change `new_rivers`:

```{r}
new_rivers + 1
```

If we want to modify `new_rivers` and save that modified version, then we need to reassign `new_rivers` like so:

```{r}
new_rivers <- new_rivers + 1
new_rivers
```

If we forget to reassign this can cause subsequent steps to not work as expected because we will not be working with the data that has been modified.

***
## **Why do I have a `+`  sign instead of the cursor `>` in the console?**

**Trouble with parentheses**

You may get a `+`  sign instead of the cursor `>` in the console suggesting that you have not closed an open parentheses. Each instance of `(` should be followed by `)`. 

Hit the "esc" key to restore your `>`, then fix/rerun your code.

***
## **When should I use quotes ("") or backticks (``)?**

Check out our [Guide on when to use quotes or backticks](https://jhudatascience.org/intro_to_r/resources/quotes_vs_backticks.html).

***
## **How do I know when to use the `pull()` function, instead of just using `select()`?**

Check out our [Guide on what functions require pulling values out first](https://jhudatascience.org/intro_to_r/resources/functions_for_vectors.html).

<br><br><br>

# **Common Errors**

***
## **Error in x : could not find function "y"**

**Forgetting to load a library or misspelling a function or package**

For example, we forgot `library(tidyverse)` below:

```{r, echo = FALSE}
unloadNamespace("tidyverse")
```

```{r, error = TRUE, class.error="bg-error"}
iris %>% pull(Species) 
```

Below will not work because `str_detect` is missing a `t` at the end:

```{r, error = TRUE, message = FALSE, class.error="bg-error"}
library(tidyverse) # need this! This can be at the top of your file
iris %>% pull(Species) %>% str_detec("setosa")
```

This will not work because `library()` is misspelled:

```{r, error = TRUE, class.error="bg-error"}
libary(tidyverse)
```

***
## **Error: object 'X' not found**

**Forgetting to assign an object to start with**

This error is usually caused by forgetting to assign an object to start with, or not running the piece of code that assigns an object. If you never created `rivers2` and try to modify it like so:

```{r, error = TRUE, class.error="bg-error"}
rivers2 + 1
```

Make sure you run something like this, with the `<-` operator:

```{r}
rivers2 <- new_rivers + 1
rivers2
```

***
## **Error: unexpected ',' in ... / Error: unexpected ')' in ... / Error: unexpected 'X' in ...**

**Trouble with parentheses**

This error can be caused by missing parentheses. Such as:

```{r, error = TRUE, class.error="bg-error"}
library(dplyr)
all.equal((rivers+1, rivers)
```

It should be:

```{r}
all.equal((rivers+1), rivers)
```

You will also often get this error if you have the correct number of parentheses but wrong placement:

```{r, error = TRUE, class.error="bg-error"}
all.equal((rivers+1, rivers))
```

If you have too many parentheses like this (the last one is extra)... you will get this error:

```{r, error = TRUE, class.error="bg-error"}
all_equal((rivers+1), rivers))
```

***
## **Error: unexpected symbol in "x"**

**Not using quotes or backticks when needed**  

You will need to use quotes for variable names that have spaces or unusual punctuation. It is best to avoid these and rename variables if a variable name has spaces.

```{r, echo = FALSE, class.error="bg-error"}
library(tibble)
df_quotes <- tibble("The Values" = c(1,2,3), "names" = c("A", "B", "C"))
```

```{r}
df_quotes

```

If we want to specifically pull out the column with the variable named `The Values` we need to use quotes or back ticks.

```{r}
df_quotes %>% pull(names) # this works fine! no spaces in `names`
```

```{r}
df_quotes %>% pull("The Values") # this works
```

```{r}
df_quotes %>% pull(`The Values`) # this works
```

```{r, error = TRUE, class.error="bg-error"}
df_quotes %>% pull(The Values) # this does not work!
```

***
## **Error: unexpected input in "x"**

**Copy+pasting quotation marks**

If you copy paste code form somewhere with curly quotation marks, it will not work.

```{r}
df_quotes %>% pull("The Values") # this works
```

```{r, error = TRUE, class.error="bg-error"}
df_quotes %>% pull(“The Values”) # this doesn't work
```

***
## **Error: `mapping` must be created by `aes()` / `ℹ` Did you use '%>%' or '|>' instead of '+'?**

**Forgetting to use `+` to add `ggplot2` layers**

This will not work:

```{r, error = TRUE, class.error="bg-error"}
ggplot(data = iris, aes(x = Species, y = Petal.Length)) %>%
  geom_boxplot()
```

This will work:

```{r, out.width = "30%"}
ggplot(data = iris, aes(x = Species, y = Petal.Length)) +
  geom_boxplot()
```

***
## **Error in +.gg: `ℹ` Did you accidentally put '+' on a new line?**

This will not work:

```{r, error = TRUE, class.error="bg-error", out.width = "30%"}
ggplot(data = iris, aes(x = Species, y = Petal.Length))
 +  geom_boxplot()
```

This will work:

```{r, out.width = "30%", class.error="bg-error"}
ggplot(data = iris, aes(x = Species, y = Petal.Length)) +
  geom_boxplot()
```

# **Preference Changes**

***
## **How do I get output to stop printing inside the Rmarkdown and only show it in the console? (How Ava has her setup?)**

**To change this, you will need to adjust the RStudio Settings.**

![Click the gear icon beside the knit button to expand the options menu. Select "Chunk Output in Console".](images/console_output1.jpg)
  
![You can select Remove Output. You should now see output in the console.](images/console_output2.jpg)

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***
## **How do I change the color / theme?**

Go to the menu Tools > Global Options > Appearance. Choose a theme and apply!

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