R

We’ve talked a lot around here about the reasons to use syntax — not only menus — in your statistical analyses.

Regardless of which software you use, the syntax file is pretty much always a text file. This is true for R, SPSS, SAS, Stata — just about all of them.

This is important because it means you can use an unlikely tool to help you code: Microsoft Word.

I know what you’re thinking. Word? Really?

Yep, it’s true. Essentially it’s because Word has much better Search-and-Replace options than your stat software’s editor.

Here are a couple features of Word’s search-and-replace that I use to help me code faster:

(more…)

12 comments

In our last post, we calculated Pearson and Spearman correlation coefficients in R and got a surprising result.

So let’s investigate the data a little more with a scatter plot.

We use the same version of the data set of tourists. We have data on tourists from different nations, their gender, number of children, and how much they spent on their trip.

Again we copy and paste the following array into R.


M <- structure(list(COUNTRY = structure(c(3L, 3L, 3L, 3L, 1L, 3L, 2L, 3L, 1L, 3L, 3L, 1L, 2L, 2L, 3L, 3L, 3L, 2L, 3L, 1L, 1L, 3L,
1L, 2L), .Label = c("AUS", "JAPAN", "USA"), class = "factor"),GENDER = structure(c(2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L), .Label = c("F", "M"), class = "factor"), CHILDREN = c(2L, 1L, 3L, 2L, 2L, 3L, 1L, 0L, 1L, 0L, 1L, 2L, 2L, 1L, 1L, 1L, 0L, 2L, 1L, 2L, 4L, 2L, 5L, 1L), SPEND = c(8500L, 23000L, 4000L, 9800L, 2200L, 4800L, 12300L, 8000L, 7100L, 10000L, 7800L, 7100L, 7900L, 7000L, 14200L, 11000L, 7900L, 2300L, 7000L, 8800L, 7500L, 15300L, 8000L, 7900L)), .Names = c("COUNTRY", "GENDER", "CHILDREN", "SPEND"), class = "data.frame", row.names = c(NA, -24L))



M
attach(M)

plot(CHILDREN, SPEND)

(more…)

1 comment

Let’s use R to explore bivariate relationships among variables.

Part 7 of this series showed how to do a nice bivariate plot, but it’s also useful to have a correlation statistic.

We use a new version of the data set we used in Part 20 of tourists from different nations, their gender, and number of children. Here, we have a new variable – the amount of money they spend while on vacation.

First, if the data object (A) for the previous version of the tourists data set is present in your R workspace, it is a good idea to remove it because it has some of the same variable names as the data set that you are about to read in. We remove A as follows:

rm(A)

Removing the object A ensures no confusion between different data objects that contain variables with similar names.

Now copy and paste the following array into R.

M <- structure(list(COUNTRY = structure(c(3L, 3L, 3L, 3L, 1L, 3L, 2L, 3L, 1L, 3L, 3L, 1L, 2L, 2L, 3L, 3L, 3L, 2L, 3L, 1L, 1L, 3L,
1L, 2L), .Label = c("AUS", "JAPAN", "USA"), class = "factor"),GENDER = structure(c(2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L), .Label = c("F", "M"), class = "factor"), CHILDREN = c(2L, 1L, 3L, 2L, 2L, 3L, 1L, 0L, 1L, 0L, 1L, 2L, 2L, 1L, 1L, 1L, 0L, 2L, 1L, 2L, 4L, 2L, 5L, 1L), SPEND = c(8500L, 23000L, 4000L, 9800L, 2200L, 4800L, 12300L, 8000L, 7100L, 10000L, 7800L, 7100L, 7900L, 7000L, 14200L, 11000L, 7900L, 2300L, 7000L, 8800L, 7500L, 15300L, 8000L, 7900L)), .Names = c("COUNTRY", "GENDER", "CHILDREN", "SPEND"), class = "data.frame", row.names = c(NA, -24L))


M
attach(M)

Do tourists with greater numbers of children spend more? Let’s calculate the correlation between CHILDREN and SPEND, using the cor() function.

R <- cor(CHILDREN, SPEND)
[1] -0.2612796


We have a weak correlation, but it’s negative! Tourists with a greater number of children tend to spend less rather than more!

(Even so, we’ll plot this in our next post to explore this unexpected finding).

We can round to any number of decimal places using the round() command.

round(R, 2)
[1] -0.26

The percentage of shared variance (100*r²) is:
100 * (R**2)
[1] 6.826704

To test whether your correlation coefficient differs from 0, use the cor.test() command.

cor.test(CHILDREN, SPEND)
Pearson's product-moment correlation
data: CHILDREN and SPEND
t = -1.2696, df = 22, p-value = 0.2175
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.6012997 0.1588609
sample estimates:
cor
-0.2612796

The cor.test() command returns the correlation coefficient, but also gives the p-value for the correlation. In this case, we see that the correlation is not significantly different from 0 (p is approximately 0.22).

Of course we have only a few values of the variable CHILDREN, and this fact will influence the correlation. Just how many values of CHILDREN do we have? Can we use the levels() command directly? (Recall that the term “level” has a few meanings in statistics, once of which is the values of a categorical variable, aka “factor“).

levels(CHILDREN)
NULL

R does not recognize CHILDREN as a factor. In order to use the levels() command, we must turn CHILDREN into a factor temporarily, using as.factor().

levels(as.factor(CHILDREN))
[1] "0" "1" "2" "3" "4" "5"

So we have six levels of CHILDREN. CHILDREN is a discrete variable without many values, so a Spearman correlation can be a better option. Let’s see how to implement a Spearman correlation:

cor(CHILDREN, SPEND, method ="spearman")
[1] -0.3116905

We have obtained a similar but slightly different correlation coefficient estimate because the Spearman correlation is indeed calculated differently than the Pearson.

Why not plot the data? We will do so in our next post.

About the Author: David Lillis has taught R to many researchers and statisticians. His company, Sigma Statistics and Research Limited, provides both on-line instruction and face-to-face workshops on R, and coding services in R. David holds a doctorate in applied statistics.

See our full R Tutorial Series and other blog posts regarding R programming.

No comments yet

Sometimes when you’re learning a new stat software package, the most frustrating part is not knowing how to do very basic things. This is especially frustrating if you already know how to do them in some other software.

Let’s look at some basic but very useful commands that are available in R.

We will use the following data set of tourists from different nations, their gender and numbers of children. Copy and paste the following array into R.

A <- structure(list(NATION = structure(c(3L, 3L, 3L, 1L, 3L, 2L, 3L,
1L, 3L, 3L, 1L, 2L, 2L, 3L, 3L, 3L, 2L), .Label = c("CHINA",
"GERMANY", "FRANCE"), class = "factor"), GENDER = structure(c(1L,
2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L
), .Label = c("F", "M"), class = "factor"), CHILDREN = c(1L,
3L, 2L, 2L, 3L, 1L, 0L, 1L, 0L, 1L, 2L, 2L, 1L, 1L, 1L, 0L, 2L
)), .Names = c("NATION", "GENDER", "CHILDREN"), row.names = 2:18, class = "data.frame")

Want to check that R read the variables correctly? We can look at the first 3 rows using the head() command, as follows:

head(A, 3)
  NATION   GENDER   CHILDREN
2 FRANCE      F        1
3 FRANCE      M        3
4 FRANCE      M        2

Now we look at the last 4 rows using the tail() command:

tail(A, 4)
    NATION   GENDER  CHILDREN
15  FRANCE      F        1
16  FRANCE      M        1
17  FRANCE      F        0
18 GERMANY      F        2

Now we find the number of rows and number of columns using nrow() and ncol().

nrow(A)
[1] 17

ncol(A)
[1] 3

So we have 17 rows (cases) and three columns (variables). These functions look very basic, but they turn out to be very useful if you want to write R-based software to analyse data sets of different dimensions.

Now let’s attach A and check for the existence of particular data.

attach(A)

As you may know, attaching a data object makes it possible to refer to any variable by name, without having to specify the data object which contains that variable.

Does the USA appear in the NATION variable? We use the any() command and put USA inside quotation marks.

any(NATION == "USA")
[1] FALSE

Clearly, we do not have any data pertaining to the USA.

What are the values of the variable NATION?

levels(NATION)
[1] "CHINA"   "GERMANY" "FRANCE"

How many non-missing observations do we have in the variable NATION?

length(NATION)
[1] 17

OK, but how many different values of NATION do we have?

length(levels(NATION))
[1] 3

We have three different values.

Do we have tourists with more than three children? We use the any() command to find out.

any(CHILDREN > 3)
[1] FALSE

None of the tourists in this data set have more than three children.

Do we have any missing data in this data set?

In R, missing data is indicated in the data set with NA.

any(is.na(A))
[1] FALSE

We have no missing data here.

Which observations involve FRANCE? We use the which() command to identify the relevant indices, counting column-wise.

which(A == "FRANCE")
[1]  1  2  3  5  7  9 10 14 15 16

How many observations involve FRANCE? We wrap the above syntax inside the length() command to perform this calculation.

length(which(A == "FRANCE"))
[1] 10

We have a total of ten such observations.

That wasn’t so hard! In our next post we will look at further analytic techniques in R.

About the Author: David Lillis has taught R to many researchers and statisticians. His company, Sigma Statistics and Research Limited, provides both on-line instruction and face-to-face workshops on R, and coding services in R. David holds a doctorate in applied statistics.

See our full R Tutorial Series and other blog posts regarding R programming.

2 comments

I received a question recently about R Commander, a free R package.

R Commander overlays a menu-based interface to R, so just like SPSS or JMP, you can run analyses using menus.  Nice, huh?

The question was whether R Commander does everything R does, or just a small subset.

Unfortunately, R Commander can’t do everything R does. Not even close.

But it does a lot. More than just the basics.

So I thought I would show you some of the things R Commander can do entirely through menus–no programming required, just so you can see just how unbelievably useful it is.

Since R commander is a free R package, it can be installed easily through R! Just type install.packages("Rcmdr") in the command line the first time you use it, then type library("Rcmdr") each time you want to launch the menus.

Data Sets and Variables

Import data sets from other software:

• SPSS
• Stata
• Excel
• Minitab
• Text
• SAS Xport
  

Define Numerical Variables as categorical and label the values

Open the data sets that come with R packages

Merge Data Sets

Edit and show the data in a data spreadsheet

Personally, I think that if this was all R Commander did, it would be incredibly useful. These are the types of things I just cannot remember all the commands for, since I just don’t use R often enough.

Data Analysis

Yes, R Commander does many of the simple statistical tests you’d expect:

• Chi-square tests
• Paired and Independent Samples t-tests
• Tests of Proportions
• Common nonparametrics, like Friedman, Wilcoxon, and Kruskal-Wallis tests
• One-way ANOVA and simple linear regression

What is surprising though, is how many higher-level statistics and models it runs:

• Hierarchical and K-Means Cluster analysis (with 7 linkage methods and 4 options of distance measures)
• Principal Components and Factor Analysis
• Linear Regression (with model selection, influence statistics, and multicollinearity diagnostic options, among others)
• Logistic regression for binary, ordinal, and multinomial responses
• Generalized linear models, including Gamma and Poisson models

In other words–you can use R Commander to run in R most of the analyses that most researchers need.

Graphs

A sample of the types of graphs R Commander creates in R without you having to write any code:

• QQ Plots
• Scatter plots
• Histograms
• Box Plots
• Bar Charts

The nice part is that it does not only do simple versions of these plots.  You can, for example, add regression lines to a scatter plot or run histograms by a grouping factor.

If you’re ready to get started practicing, click here to learn about making scatterplots in R commander, or click here to learn how to use R commander to sample from a uniform distribution.

4 comments

In my last blog post we fitted a generalized linear model to count data using a Poisson error structure.

We found, however, that there was over-dispersion in the data – the variance was larger than the mean in our dependent variable.

(more…)

9 comments