R Lesson 17: ANOVA Part 1

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Hello everybody,

It’s Michael, and today I will be discussing ANOVA in R. ANOVA is a statisical technique in R that stands for analysis of variance. ANOVA is used to analyze data in R by comparing the means of subsets in the data. There are two types of ANOVA-one way and two way-the first of which I’ll discuss in this post. I’ll discuss two-way ANOVA in my next post.

Here’s the dataset-US Cities.

This dataset contains information about 150 randomly selected US cities (three for each state) such as population and climate. As always let’s load our file into R and learn more about our data:

Screen Shot 2019-06-28 at 1.09.41 PM

There are 150 observations of 11 variables. Here’s a detailed breakdown of each variable:

  • City-the name of the US city
    • The reason R says City only displays 149 levels, despite there being 150 cities is because I used “Jackson” twice  (for Jackson, Mississippi and Jackson, Wyoming).
  • State-I used the state’s postal code here, rather than the state’s name. For instance, Alaska is AK, Alabama is AL, and so on.
  • Population-the city’s population; I tried to get the most recent data possible, but in some cases, I had to rely on data from the 2010 US Census.
  • January.High and January.Low-The city’s high & low temperatures for the month of January, respectively.
  • July.High and July.Low-The city’s high & low temperatures for the month of July, respectively.
    • I chose January and July to get a gauge of a city’s climate since they are the coldest and hottest months of the year, respectively.
  • Time.Zone-the time zone where the city is located. I used single letters to represent each time zone, which are as follows:
    • A-Alaska (the state has its own time zone)
    • H-Hawaii (the one other state with its own time zone)
    • E-Eastern
    • C-Central
    • M-Mountain
    • P-Pacific
  • Elevation-How many feet a city is above sea level.
    • There is one negative number in the dataset-(-6)-which corresponds to New Orleans. This means that New Orleans is the only city in this dataset that is below sea level.
  • Landlocked-Whether or not the city is located in a landlocked state-0 means the state isn’t landlocked while 1 means the state is landlocked.
  • Founded-the year a city was founded/settled. Sometimes I used the settlement year if I couldn’t find the year a city was founded.

Now let’s start the ANOVA. I will start with one-way ANOVA, which is just ANOVA using  one independent variable.

Here’s our model along with the model’s summary:

In this model, I used January.Low as a dependent variable and State as an independent variable. If you’re wondering what I’m trying to analyze, I’m looking the relationship between states and the pleasantness/misery of their winters. I used January.Low rather than January.Highbecause I felt that the former would be a better measure of how good/bad a state’s winter is.

Now, before I discuss the output below summary, let me explain the concepts of null hypothesis and alternative hypothesis, as they are important to one-way ANOVA. A null hypothesis states that there is NO statistical significance between the dependent and independent variable. In this case, the null hypothesis is that there is no statistically significant relationship between a state and the pleasantness/misery of their winters.This is the hypothesis that we are trying to disprove.

On the other hand, the alternative hypothesis is simply the opposite of the null hypothesis; this hypothesis states that there is a statistically significant relationship between our dependent variable (January.Low) and our independent variable (State).

Now let’s explain the output below summary. First of all, the Df stands for degrees of freedom, which represents the amount of values that are free to vary in a dataset. The Df for State is 49, which means that there are 49 values in State that may vary.

We got 49 degrees of freedom because there are 50 possible values for State. Degrees of freedom for a variable/dataset will always be equal to N-1, with N being either the number of possible values in a variable or number of observations in a dataset. Why do we always subtract by 1? Here’s why:

Let’s say we’re looking for a set a four numbers that add up to 100. Some possibilities include (15, 20, 25, 40) or (15, 18, 30, 37) or (15, 16, 30, 39). However, notice that only three of the four numbers in each set vary, while the fourth is fixed, since it will always be 15. Therefore, only three of the four numbers are free to vary.

The f-value is 17.46 which is highly significant, given that the corresponding p-value is much less than the benchmark* level of significance-0.01 or 1%. This means that there is a statistically significant relationship between a state and how good/bad their winters are.

  • The “benchmark level of significance” refers to the threshold where you should reject the null hypothesis. Remember that if the Pr(>f)-which refers to the p-value of your independent variable-is less than 0.01 for your independent variable, reject the null hypothesis.

The Sum Sq and Mean Sq columns, which represent sum of squares and mean of sqaures, respectively (for both the independent variable and the residuals(, aren’t important for our ANOVA analysis.

Now it’s time to analyze pair-wise differences. In this case, we are analyzing the pair-wise differences between states to see which state pair has the greatest winter temperature difference. To analyze pair-wise differences, let’s use Tukey’s HSD test, which stands for Tukey’s Honest Significance Test. Here’s how it works (and I couldn’t post a screenshot since the output is too long). By the way, the line to set up the Tukey’s HSD test is TukeyHSD(model, conf.level=0.99)-remember that we’re analyzing our data with a 99% confidence level:

diff lwr upr p adj
AL-AK 34.33333333 15.0921361 53.574530535 0.0000000
AR-AK 26.90000000 7.6588028 46.141197201 0.0000048
AZ-AK 42.16666667 22.9254695 61.407863868 0.0000000
CA-AK 43.03333333 23.7921361 62.274530535 0.0000000
CO-AK 16.86666667 -2.3745305 36.107863868 0.0650303
CT-AK 18.80000000 -0.4411972 38.041197201 0.0145141
DE-AK 25.06666667 5.8254695 44.307863868 0.0000350
FL-AK 48.80000000 29.5588028 68.041197201 0.0000000
GA-AK 33.16666667 13.9254695 52.407863868 0.0000000
HI-AK 61.10000000 41.8588028 80.341197201 0.0000000
IA-AK 10.23333333 -9.0078639 29.474530535 0.9446692
ID-AK 13.10000000 -6.1411972 32.341197201 0.5202584
IL-AK 13.83333333 -5.4078639 33.074530535 0.3867198
IN-AK 16.80000000 -2.4411972 36.041197201 0.0681855
KS-AK 18.13333333 -1.1078639 37.374530535 0.0249778
KY-AK 22.23333333 2.9921361 41.474530535 0.0006339
LA-AK 39.13333333 19.8921361 58.374530535 0.0000000
MA-AK 18.06666667 -1.1745305 37.307863868 0.0263343
MD-AK 23.90000000 4.6588028 43.141197201 0.0001185
ME-AK 13.50000000 -5.7411972 32.741197201 0.4457807
MI-AK 15.26666667 -3.9745305 34.507863868 0.1844181
MN-AK 5.33333333 -13.9078639 24.574530535 1.0000000
MO-AK 20.20000000 0.9588028 39.441197201 0.0043056
MS-AK 36.26666667 17.0254695 55.507863868 0.0000000
MT-AK 12.33333333 -6.9078639 31.574530535 0.6652421
NC-AK 28.03333333 8.7921361 47.274530535 0.0000014
ND-AK -2.43333333 -21.6745305 16.807863868 1.0000000
NE-AK 11.63333333 -7.6078639 30.874530535 0.7858266
NH-AK 11.86666667 -7.3745305 31.107863868 0.7478742
NJ-AK 23.30000000 4.0588028 42.541197201 0.0002188
NM-AK 21.06666667 1.8254695 40.307863868 0.0019407
NV-AK 26.66666667 7.4254695 45.907863868 0.0000062
NY-AK 19.76666667 0.5254695 39.007863868 0.0063352
OH-AK 19.10000000 -0.1411972 38.341197201 0.0112786
OK-AK 24.00000000 4.7588028 43.241197201 0.0001069
OR-AK 32.00000000 12.7588028 51.241197201 0.0000000
PA-AK 20.33333333 1.0921361 39.574530535 0.0038167
RI-AK 20.50000000 1.2588028 39.741197201 0.0032794
SC-AK 32.90000000 13.6588028 52.141197201 0.0000000
SD-AK 7.70000000 -11.5411972 26.941197201 0.9996197
TN-AK 25.93333333 6.6921361 45.174530535 0.0000138
TX-AK 36.00000000 16.7588028 55.241197201 0.0000000
UT-AK 16.70000000 -2.5411972 35.941197201 0.0731639
VA-AK 27.16666667 7.9254695 46.407863868 0.0000036
VT-AK 7.56666667 -11.6745305 26.807863868 0.9997438
WA-AK 30.73333333 11.4921361 49.974530535 0.0000001
WI-AK 7.83333333 -11.4078639 27.074530535 0.9994447
WV-AK 21.60000000 2.3588028 40.841197201 0.0011709
WY-AK 10.26666667 -8.9745305 29.507863868 0.9423542
AR-AL -7.43333333 -26.6745305 11.807863868 0.9998304
AZ-AL 7.83333333 -11.4078639 27.074530535 0.9994447
CA-AL 8.70000000 -10.5411972 27.941197201 0.9954754
CO-AL -17.46666667 -36.7078639 1.774530535 0.0418707
CT-AL -15.53333333 -34.7745305 3.707863868 0.1572874
DE-AL -9.26666667 -28.5078639 9.974530535 0.9866689
FL-AL 14.46666667 -4.7745305 33.707863868 0.2858501
GA-AL -1.16666667 -20.4078639 18.074530535 1.0000000
HI-AL 26.76666667 7.5254695 46.007863868 0.0000056
IA-AL -24.10000000 -43.3411972 -4.858802799 0.0000964
ID-AL -21.23333333 -40.4745305 -1.992136132 0.0016592
IL-AL -20.50000000 -39.7411972 -1.258802799 0.0032794
IN-AL -17.53333333 -36.7745305 1.707863868 0.0398126
KS-AL -16.20000000 -35.4411972 3.041197201 0.1029146
KY-AL -12.10000000 -31.3411972 7.141197201 0.7075040
LA-AL 4.80000000 -14.4411972 24.041197201 1.0000000
MA-AL -16.26666667 -35.5078639 2.974530535 0.0984460
MD-AL -10.43333333 -29.6745305 8.807863868 0.9297498
ME-AL -20.83333333 -40.0745305 -1.592136132 0.0024125
MI-AL -19.06666667 -38.3078639 0.174530535 0.0116018
MN-AL -29.00000000 -48.2411972 -9.758802799 0.0000005
MO-AL -14.13333333 -33.3745305 5.107863868 0.3368657
MS-AL 1.93333333 -17.3078639 21.174530535 1.0000000
MT-AL -22.00000000 -41.2411972 -2.758802799 0.0007960
NC-AL -6.30000000 -25.5411972 12.941197201 0.9999977
ND-AL -36.76666667 -56.0078639 -17.525469465 0.0000000
NE-AL -22.70000000 -41.9411972 -3.458802799 0.0003998
NH-AL -22.46666667 -41.7078639 -3.225469465 0.0005039
NJ-AL -11.03333333 -30.2745305 8.207863868 0.8693993
NM-AL -13.26666667 -32.5078639 5.974530535 0.4888757
NV-AL -7.66666667 -26.9078639 11.574530535 0.9996549
NY-AL -14.56666667 -33.8078639 4.674530535 0.2715191
OH-AL -15.23333333 -34.4745305 4.007863868 0.1880399
OK-AL -10.33333333 -29.5745305 8.907863868 0.9375203
OR-AL -2.33333333 -21.5745305 16.907863868 1.0000000
PA-AL -14.00000000 -33.2411972 5.241197201 0.3585928
RI-AL -13.83333333 -33.0745305 5.407863868 0.3867198
SC-AL -1.43333333 -20.6745305 17.807863868 1.0000000
SD-AL -26.63333333 -45.8745305 -7.392136132 0.0000065
TN-AL -8.40000000 -27.6411972 10.841197201 0.9976614
TX-AL 1.66666667 -17.5745305 20.907863868 1.0000000
UT-AL -17.63333333 -36.8745305 1.607863868 0.0368937
VA-AL -7.16666667 -26.4078639 12.074530535 0.9999296
VT-AL -26.76666667 -46.0078639 -7.525469465 0.0000056
WA-AL -3.60000000 -22.8411972 15.641197201 1.0000000
WI-AL -26.50000000 -45.7411972 -7.258802799 0.0000075
WV-AL -12.73333333 -31.9745305 6.507863868 0.5900517
WY-AL -24.06666667 -43.3078639 -4.825469465 0.0000998
AZ-AR 15.26666667 -3.9745305 34.507863868 0.1844181
CA-AR 16.13333333 -3.1078639 35.374530535 0.1075485
CO-AR -10.03333333 -29.2745305 9.207863868 0.9571836
CT-AR -8.10000000 -27.3411972 11.141197201 0.9988710
DE-AR -1.83333333 -21.0745305 17.407863868 1.0000000
FL-AR 21.90000000 2.6588028 41.141197201 0.0008771
GA-AR 6.26666667 -12.9745305 25.507863868 0.9999981
HI-AR 34.20000000 14.9588028 53.441197201 0.0000000
IA-AR -16.66666667 -35.9078639 2.574530535 0.0748907
ID-AR -13.80000000 -33.0411972 5.441197201 0.3924661
IL-AR -13.06666667 -32.3078639 6.174530535 0.5265762
IN-AR -10.10000000 -29.3411972 9.141197201 0.9532685
KS-AR -8.76666667 -28.0078639 10.474530535 0.9948059
KY-AR -4.66666667 -23.9078639 14.574530535 1.0000000
LA-AR 12.23333333 -7.0078639 31.474530535 0.6835500
MA-AR -8.83333333 -28.0745305 10.407863868 0.9940553
MD-AR -3.00000000 -22.2411972 16.241197201 1.0000000
ME-AR -13.40000000 -32.6411972 5.841197201 0.4641051
MI-AR -11.63333333 -30.8745305 7.607863868 0.7858266
MN-AR -21.56666667 -40.8078639 -2.325469465 0.0012088
MO-AR -6.70000000 -25.9411972 12.541197201 0.9999875
MS-AR 9.36666667 -9.8745305 28.607863868 0.9841955
MT-AR -14.56666667 -33.8078639 4.674530535 0.2715191
NC-AR 1.13333333 -18.1078639 20.374530535 1.0000000
ND-AR -29.33333333 -48.5745305 -10.092136132 0.0000003
NE-AR -15.26666667 -34.5078639 3.974530535 0.1844181
NH-AR -15.03333333 -34.2745305 4.207863868 0.2108675
NJ-AR -3.60000000 -22.8411972 15.641197201 1.0000000
NM-AR -5.83333333 -25.0745305 13.407863868 0.9999998
NV-AR -0.23333333 -19.4745305 19.007863868 1.0000000
NY-AR -7.13333333 -26.3745305 12.107863868 0.9999373
OH-AR -7.80000000 -27.0411972 11.441197201 0.9994941
OK-AR -2.90000000 -22.1411972 16.341197201 1.0000000
OR-AR 5.10000000 -14.1411972 24.341197201 1.0000000
PA-AR -6.56666667 -25.8078639 12.674530535 0.9999928
RI-AR -6.40000000 -25.6411972 12.841197201 0.9999965
SC-AR 6.00000000 -13.2411972 25.241197201 0.9999995
SD-AR -19.20000000 -38.4411972 0.041197201 0.0103584
TN-AR -0.96666667 -20.2078639 18.274530535 1.0000000
TX-AR 9.10000000 -10.1411972 28.341197201 0.9900922
UT-AR -10.20000000 -29.4411972 9.041197201 0.9469173
VA-AR 0.26666667 -18.9745305 19.507863868 1.0000000
VT-AR -19.33333333 -38.5745305 -0.092136132 0.0092399
WA-AR 3.83333333 -15.4078639 23.074530535 1.0000000
WI-AR -19.06666667 -38.3078639 0.174530535 0.0116018
WV-AR -5.30000000 -24.5411972 13.941197201 1.0000000
WY-AR -16.63333333 -35.8745305 2.607863868 0.0766521
CA-AZ 0.86666667 -18.3745305 20.107863868 1.0000000
CO-AZ -25.30000000 -44.5411972 -6.058802799 0.0000273
CT-AZ -23.36666667 -42.6078639 -4.125469465 0.0002045
DE-AZ -17.10000000 -36.3411972 2.141197201 0.0549574
FL-AZ 6.63333333 -12.6078639 25.874530535 0.9999905
GA-AZ -9.00000000 -28.2411972 10.241197201 0.9917758
HI-AZ 18.93333333 -0.3078639 38.174530535 0.0129826
IA-AZ -31.93333333 -51.1745305 -12.692136132 0.0000000
ID-AZ -29.06666667 -48.3078639 -9.825469465 0.0000004
IL-AZ -28.33333333 -47.5745305 -9.092136132 0.0000010
IN-AZ -25.36666667 -44.6078639 -6.125469465 0.0000254
KS-AZ -24.03333333 -43.2745305 -4.792136132 0.0001033
KY-AZ -19.93333333 -39.1745305 -0.692136132 0.0054663
LA-AZ -3.03333333 -22.2745305 16.207863868 1.0000000
MA-AZ -24.10000000 -43.3411972 -4.858802799 0.0000964
MD-AZ -18.26666667 -37.5078639 0.974530535 0.0224533
ME-AZ -28.66666667 -47.9078639 -9.425469465 0.0000007
MI-AZ -26.90000000 -46.1411972 -7.658802799 0.0000048
MN-AZ -36.83333333 -56.0745305 -17.592136132 0.0000000
MO-AZ -21.96666667 -41.2078639 -2.725469465 0.0008222
MS-AZ -5.90000000 -25.1411972 13.341197201 0.9999997
MT-AZ -29.83333333 -49.0745305 -10.592136132 0.0000002
NC-AZ -14.13333333 -33.3745305 5.107863868 0.3368657
ND-AZ -44.60000000 -63.8411972 -25.358802799 0.0000000
NE-AZ -30.53333333 -49.7745305 -11.292136132 0.0000001
NH-AZ -30.30000000 -49.5411972 -11.058802799 0.0000001
NJ-AZ -18.86666667 -38.1078639 0.374530535 0.0137286
NM-AZ -21.10000000 -40.3411972 -1.858802799 0.0018810
NV-AZ -15.50000000 -34.7411972 3.741197201 0.1605020
NY-AZ -22.40000000 -41.6411972 -3.158802799 0.0005381
OH-AZ -23.06666667 -42.3078639 -3.825469465 0.0002770
OK-AZ -18.16666667 -37.4078639 1.074530535 0.0243236
OR-AZ -10.16666667 -29.4078639 9.074530535 0.9490994
PA-AZ -21.83333333 -41.0745305 -2.592136132 0.0009355
RI-AZ -21.66666667 -40.9078639 -2.425469465 0.0010984
SC-AZ -9.26666667 -28.5078639 9.974530535 0.9866689
SD-AZ -34.46666667 -53.7078639 -15.225469465 0.0000000
TN-AZ -16.23333333 -35.4745305 3.007863868 0.1006599
TX-AZ -6.16666667 -25.4078639 13.074530535 0.9999988
UT-AZ -25.46666667 -44.7078639 -6.225469465 0.0000228
VA-AZ -15.00000000 -34.2411972 4.241197201 0.2148563
VT-AZ -34.60000000 -53.8411972 -15.358802799 0.0000000
WA-AZ -11.43333333 -30.6745305 7.807863868 0.8160859
WI-AZ -34.33333333 -53.5745305 -15.092136132 0.0000000
WV-AZ -20.56666667 -39.8078639 -1.325469465 0.0030852
WY-AZ -31.90000000 -51.1411972 -12.658802799 0.0000000
CO-CA -26.16666667 -45.4078639 -6.925469465 0.0000107
CT-CA -24.23333333 -43.4745305 -4.992136132 0.0000839
DE-CA -17.96666667 -37.2078639 1.274530535 0.0284942
FL-CA 5.76666667 -13.4745305 25.007863868 0.9999998
GA-CA -9.86666667 -29.1078639 9.374530535 0.9659111
HI-CA 18.06666667 -1.1745305 37.307863868 0.0263343
IA-CA -32.80000000 -52.0411972 -13.558802799 0.0000000
ID-CA -29.93333333 -49.1745305 -10.692136132 0.0000002
IL-CA -29.20000000 -48.4411972 -9.958802799 0.0000004
IN-CA -26.23333333 -45.4745305 -6.992136132 0.0000100
KS-CA -24.90000000 -44.1411972 -5.658802799 0.0000417
KY-CA -20.80000000 -40.0411972 -1.558802799 0.0024882
LA-CA -3.90000000 -23.1411972 15.341197201 1.0000000
MA-CA -24.96666667 -44.2078639 -5.725469465 0.0000389
MD-CA -19.13333333 -38.3745305 0.107863868 0.0109637
ME-CA -29.53333333 -48.7745305 -10.292136132 0.0000003
MI-CA -27.76666667 -47.0078639 -8.525469465 0.0000018
MN-CA -37.70000000 -56.9411972 -18.458802799 0.0000000
MO-CA -22.83333333 -42.0745305 -3.592136132 0.0003500
MS-CA -6.76666667 -26.0078639 12.474530535 0.9999838
MT-CA -30.70000000 -49.9411972 -11.458802799 0.0000001
NC-CA -15.00000000 -34.2411972 4.241197201 0.2148563
ND-CA -45.46666667 -64.7078639 -26.225469465 0.0000000
NE-CA -31.40000000 -50.6411972 -12.158802799 0.0000000
NH-CA -31.16666667 -50.4078639 -11.925469465 0.0000000
NJ-CA -19.73333333 -38.9745305 -0.492136132 0.0065239
NM-CA -21.96666667 -41.2078639 -2.725469465 0.0008222
NV-CA -16.36666667 -35.6078639 2.874530535 0.0920448
NY-CA -23.26666667 -42.5078639 -4.025469465 0.0002264
OH-CA -23.93333333 -43.1745305 -4.692136132 0.0001145
OK-CA -19.03333333 -38.2745305 0.207863868 0.0119336
OR-CA -11.03333333 -30.2745305 8.207863868 0.8693993
PA-CA -22.70000000 -41.9411972 -3.458802799 0.0003998
RI-CA -22.53333333 -41.7745305 -3.292136132 0.0004718
SC-CA -10.13333333 -29.3745305 9.107863868 0.9512161
SD-CA -35.33333333 -54.5745305 -16.092136132 0.0000000
TN-CA -17.10000000 -36.3411972 2.141197201 0.0549574
TX-CA -7.03333333 -26.2745305 12.207863868 0.9999560
UT-CA -26.33333333 -45.5745305 -7.092136132 0.0000090
VA-CA -15.86666667 -35.1078639 3.374530535 0.1278119
VT-CA -35.46666667 -54.7078639 -16.225469465 0.0000000
WA-CA -12.30000000 -31.5411972 6.941197201 0.6713740
WI-CA -35.20000000 -54.4411972 -15.958802799 0.0000000
WV-CA -21.43333333 -40.6745305 -2.192136132 0.0013727
WY-CA -32.76666667 -52.0078639 -13.525469465 0.0000000
CT-CO 1.93333333 -17.3078639 21.174530535 1.0000000
DE-CO 8.20000000 -11.0411972 27.441197201 0.9985493
FL-CO 31.93333333 12.6921361 51.174530535 0.0000000
GA-CO 16.30000000 -2.9411972 35.541197201 0.0962725
HI-CO 44.23333333 24.9921361 63.474530535 0.0000000
IA-CO -6.63333333 -25.8745305 12.607863868 0.9999905
ID-CO -3.76666667 -23.0078639 15.474530535 1.0000000
IL-CO -3.03333333 -22.2745305 16.207863868 1.0000000
IN-CO -0.06666667 -19.3078639 19.174530535 1.0000000
KS-CO 1.26666667 -17.9745305 20.507863868 1.0000000
KY-CO 5.36666667 -13.8745305 24.607863868 1.0000000
LA-CO 22.26666667 3.0254695 41.507863868 0.0006135
MA-CO 1.20000000 -18.0411972 20.441197201 1.0000000
MD-CO 7.03333333 -12.2078639 26.274530535 0.9999560
ME-CO -3.36666667 -22.6078639 15.874530535 1.0000000
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WY-RI -10.23333333 -29.4745305 9.007863868 0.9446692
SD-SC -25.20000000 -44.4411972 -5.958802799 0.0000304
TN-SC -6.96666667 -26.2078639 12.274530535 0.9999654
TX-SC 3.10000000 -16.1411972 22.341197201 1.0000000
UT-SC -16.20000000 -35.4411972 3.041197201 0.1029146
VA-SC -5.73333333 -24.9745305 13.507863868 0.9999999
VT-SC -25.33333333 -44.5745305 -6.092136132 0.0000263
WA-SC -2.16666667 -21.4078639 17.074530535 1.0000000
WI-SC -25.06666667 -44.3078639 -5.825469465 0.0000350
WV-SC -11.30000000 -30.5411972 7.941197201 0.8349684
WY-SC -22.63333333 -41.8745305 -3.392136132 0.0004272
TN-SD 18.23333333 -1.0078639 37.474530535 0.0230616
TX-SD 28.30000000 9.0588028 47.541197201 0.0000010
UT-SD 9.00000000 -10.2411972 28.241197201 0.9917758
VA-SD 19.46666667 0.2254695 38.707863868 0.0082348
VT-SD -0.13333333 -19.3745305 19.107863868 1.0000000
WA-SD 23.03333333 3.7921361 42.274530535 0.0002864
WI-SD 0.13333333 -19.1078639 19.374530535 1.0000000
WV-SD 13.90000000 -5.3411972 33.141197201 0.3753454
WY-SD 2.56666667 -16.6745305 21.807863868 1.0000000
TX-TN 10.06666667 -9.1745305 29.307863868 0.9552573
UT-TN -9.23333333 -28.4745305 10.007863868 0.9874204
VA-TN 1.23333333 -18.0078639 20.474530535 1.0000000
VT-TN -18.36666667 -37.6078639 0.874530535 0.0207147
WA-TN 4.80000000 -14.4411972 24.041197201 1.0000000
WI-TN -18.10000000 -37.3411972 1.141197201 0.0256479
WV-TN -4.33333333 -23.5745305 14.907863868 1.0000000
WY-TN -15.66666667 -34.9078639 3.574530535 0.1449218
UT-TX -19.30000000 -38.5411972 -0.058802799 0.0095084
VA-TX -8.83333333 -28.0745305 10.407863868 0.9940553
VT-TX -28.43333333 -47.6745305 -9.192136132 0.0000009
WA-TX -5.26666667 -24.5078639 13.974530535 1.0000000
WI-TX -28.16666667 -47.4078639 -8.925469465 0.0000012
WV-TX -14.40000000 -33.6411972 4.841197201 0.2956591
WY-TX -25.73333333 -44.9745305 -6.492136132 0.0000172
VA-UT 10.46666667 -8.7745305 29.707863868 0.9270184
VT-UT -9.13333333 -28.3745305 10.107863868 0.9894722
WA-UT 14.03333333 -5.2078639 33.274530535 0.3530942
WI-UT -8.86666667 -28.1078639 10.374530535 0.9936474
WV-UT 4.90000000 -14.3411972 24.141197201 1.0000000
WY-UT -6.43333333 -25.6745305 12.807863868 0.9999959
VT-VA -19.60000000 -38.8411972 -0.358802799 0.0073328
WA-VA 3.56666667 -15.6745305 22.807863868 1.0000000
WI-VA -19.33333333 -38.5745305 -0.092136132 0.0092399
WV-VA -5.56666667 -24.8078639 13.674530535 0.9999999
WY-VA -16.90000000 -36.1411972 2.341197201 0.0635003
WA-VT 23.16666667 3.9254695 42.407863868 0.0002504
WI-VT 0.26666667 -18.9745305 19.507863868 1.0000000
WV-VT 14.03333333 -5.2078639 33.274530535 0.3530942
WY-VT 2.70000000 -16.5411972 21.941197201 1.0000000
WI-WA -22.90000000 -42.1411972 -3.658802799 0.0003275
WV-WA -9.13333333 -28.3745305 10.107863868 0.9894722
WY-WA -20.46666667 -39.7078639 -1.225469465 0.0033807
WV-WI 13.76666667 -5.4745305 33.007863868 0.3982507
WY-WI 2.43333333 -16.8078639 21.674530535 1.0000000
WY-WV -11.33333333 -30.5745305 7.907863868 0.8303487

In case you were wondering how many pairs are being analyzed, it’s 2450. How did I figure that out? Well, each state is paired up with every other state, so that makes for 49 possible pairings for each state, since states aren’t paired up with themselves. There are also 50 states with pairings, so multiply 49 by 50 to get 2450 pairings.

This table shows the pair-wise differences in average January low temperatures amongst pairs of states. The lwr and upr columns show the lower and upper 99% confidence bounds, respectively, for mean temperature differences between two states. The p adj column gives the p-values for each state pair adjusted for the number of comparisons made. Any p-value that is less than 0.01 means that the pair-wise difference is statistically significant. Some notably significant pair-wise differences include (rounded to two decimal places):

  • AZ-AK, Arizona-Alaska, 42.17
    • Makes sense. After all, Arizona is a dry desert, while Alaska is very close to the Arctic Circle
  • VT-HI, Vermont-Hawaii, -53.53
    • Vermont is in New England, which is known for cold winters, while Hawaii is made up of several islands that are situated on active volcanoes.
  • OR-MN, Oregon-Minnesota, 26.67
    • This one I found interesting, since both Oregon and Minnesota can get very cold winters, but if you live in Oregon, you’re likelier to experience rougher winters if you live west of the Cascade Mountains. Minnesota (and most of the Midwest for that matter) are known for their brutal winters.
  • LA-HI, Louisiana-Hawaii, -21.97
    • Another interesting observation, since neither state recieves plenty of snow (or gets very cold for that matter). Then again, Lousiana has lots of bayous, while Hawaii consists of several islands sitting on active volcanoes.

Thanks for reading, and stay tuned for my post on two-way ANOVA,

Michael

R Analysis 5: Random Forests, Decision Trees and Merit Badges

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Hello everybody,

Its Michael, and today’s post will be an R analysis about Boy Scout merit badges earned in 2018 utilizing random forests and decision trees. I thought this would be a fun analysis to do since I am an Eagle Scout (Class of ’14).  Also, since I haven’t done so yet, I will show you a regression random forest and a regression decision tree in this analysis.

Here’s the dataset-2018 merit badges.

As always, let’s load our file into R and try to understand our data:

So as you can see, we’ve got 137 observations of 7 variables. Here’s a variable-by-variable breakdown:

  • Rank-These badges are ranked based on how many Scouts earned them; the ranks go from 1 (most earned badge) to 137 (least earned badge)
    • The original dataset I found on ScoutingMagazine.org had 139 observations, but since the bottom 2 had discontinued or rebranded merit badges (Computers and Cinematography), I removed those two observations from the dataset
  • Merit.Badge-The name of the merit badge
  • X2018.earned-How many Scouts earned that particular badge
  • Year.Introduced-The year the badge was introduced into the BSA
  • Requirements.Revision-The year of the most recent requirements revision for the badge
  • Change.from.17-The percentage change of Scouts who earned a particular merit badge from 2017 to 2018
    • I mentioned that this variable was a percentage change, however I had to list these values as decimals so R would read them as num and not factor.
  • Eagle.Required-Whether or not a badge is required for the Eagle Scout rank; the two values are “Yes” and “No”
    • Just so you know, there are 21 merit badges required for the Eagle Scout rank.

Now let’s set up our model (remember to install the randomForest package). Since the model is fairly small-with only 137 observations-there’s no need to split the data into training and validation sets. So, here’s the model along with the corresponding summary:

In this model, I used X2018.earned as my dependent variable and Year.Introduced and Rank as my independent variables. In other words, I am attempting to figure out whether the amount of Scouts that earned a particular merit badge has to do with when the badge was introduced into the BSA and/or the badge’s rank of popularity. Since my dependent variable is non-binary, I will be performing a linear regression.

Now, you will see two unfamiliar terms at the bottom of the output. Here’s an explanation of each term:

  • The mean of squared residuals is the average of the squares of the residuals.
    • In regression analysis (linear & logistic), residuals are the differences between the observed value and the predicted value of the dependent variable-X2018.earned.
  • The % var explained is a measure  of how well out-of-bag predictions explain the variance of the training set; a low % var explained could be due to either true random behavior or a lack of fit. Our % var explained-97.07%-is high, which indicates plenty of fit in the model.

Now, you might recall that when dealing with classification random forests, we create several classification matrices. However, when dealing with regression random forests, we create a graph of the random forest using the handy ggplot2 package (which you must remember to install):

And here’s the actual graph:

OK, so what’s the deal with the actual and predicted columns? Both of these columns demonstrate the concepts of residuals. Remember that earlier in this post, I mentioned that residuals are the differences between the actual and predicted values of the dependent variable-X2018.earned.

This graph shows all of the predicted and actualvalues of X2018.earned. In case you were wondering, here are all of the predicted values of X2018.earned in order of their appearance on the dataset. Since I sorted all the badges (and other information in turn) alphabetically, the first number-2073.128-corresponds to the American Business merit badge, while each subsequent number corresponds to the next merit badge alphabetically. The last number-5492.116-corresponds to the alphabetically last merit badge-Woodworking:

  • In case you’re wondering how I got this output of numbers, I wrote the line file$predicted <- predict(model1) and then typed in file$predicted to get this output.

But that’s not all. See, we’re then going to take the predicted values and place them onto two separate graphs-one with Rank and the other with Year.Introduced. The predicted values will be the y-axis in both graphs, while the dependent variables will each serve as the x-axes. The whole point of making these graphs is to see how well the predicted values correlate with each of the independent variables.

First, here’s the code and the graph for Year.Introduced:

From this graph, you can see there is a small negative correlation between the predicted values and Year.Introduced. This implies that, even with all of the new merit badges that have been introduced in the last decade (e.g. Robotics, Game Design, etc.), many Scouts still went for the traditional merit badges (e.g. Archery, First Aid, Cycling) that have been around since the BSA’s founding in 1910. Most of the traditional badges, such as Swimming and Cooking, are Eagle-required badges, which could explain why plenty of Scouts earned them in 2018.

  • Granted, many of the traditional badges had been around since 1910, but their Year.Introduced is 1911, since that’s the year the first Scout handbook came out.

Want to figure out the exact correlation between Year.Introduced and the predicted values? Here’s how:

The number -0.1470237 indicates that there is some negative correlation between the predicted values and Year.Introduced. This means that the more recently a badge was introduced, the fewer scouts earned it-SOMETIMES. There are exceptions to this rule. For instance, twice as many Scouts earned the Chess badge-which was introduced in 2011-than the Aviation badge-which was introduced 59 years earlier. And here’s a more interesting example-four times as many Scouts earned the Exploration badge (which was just introduced in 2017) than the Stamp Collecting badge (which has been around since 1932).

Now here’s the code and the graph for Rank:

This graph shows that Rank has a much stronger correlation than Year.Introducedwith the predicted values. This makes perfect sense; after all, the higher a certain badge’s popularity ranking is, the more Scouts earned that badge in 2018, and vice versa.

Want to know the exact correlation? Check this out:

Just as with Year.Introduced, there is also a negative correlation. However, the number -0.8173855 implies a much stronger inverse correlation (stronger than the correlation with Year.Introduced).

Now let’s make some regression decision trees (remember to install the rpart package):

The formula used to create the tree is the same one you would use for classification decision trees, except use anova for the method.

  • ANOVA stands for analysis of variance, which is a type of regression that I will likely cover in a future R post.

You’ll recognize the pruning table at the bottom of the printcp(tree) output. Remember that the optimal place to prune the tree would be at the lowest level where  rel error-xstd < xerror.

Now let’s plot the pre-pruned tree (remember to keep the window with the tree open when you are writing the text line):

In this tree, only Rank was used, even though Year.Introduced was likely factored into the tree’s construction (though I’m not certain that it was). By the way, I’ll round up on all of the ranks.

Now, here’s a breakdown of the tree:

  • The top row contains all 137 observations and any badge ranked 22 or lower.
  • The top row splits into two branches:
    • The left branch contains badges ranked 55 or lower and 116 observations.
    • The right branch contains badges ranked 12 or lower and 21 observations.
  • The branch with the badges ranked 55 or higher is further split into two branches (this branch has 116 observations):
    • The left branch contains badges ranked 95 or lower and 83 observations.
      • This branch further splits into two terminal nodes, each containing the number of Scouts and the observations in the group.
        • The left node contains 2,587 Scouts and 43 merit badges.
        • The right node contains 6,563 Scouts and 40 merit badges.
    • The right branch contains badges ranked 31 or lower and 33 observations.
      • The right branch also further splits into two terminal nodes, each containing the number of Scouts and observations in the group.
        • The left node contains 1,287 Scouts and 24 merit badges.
        • The right node contains 2,083 scouts and 9 merit badges.
  • The branch containing badges ranked 12 or lower (and with 21 observations) splits into two terminal nodes.
    • The left node contains 3,424 Scouts and 9 merit badges.
    • The right node contains 5,364 Scouts and 12 merit badges.

So here’s a summary of all the groups in the tree, going from left to right:

  • Group 1 (the leftmost) contains 2,587 Scouts and 43 merit badges.
  • Group 2 contains 6,563 Scouts and 40 merit badges.
  • Group 3 contains 1,287 Scouts and 24 merit badges.
  • Group 4 contains 2,083 Scouts and 9 merit badges.
  • Group 5 contains 3,424 Scouts and 9 merit badges.
  • Group 6 (the rightmost) contains 5,364 Scouts and 12 merit badges.

Now let’s see if our tree needs pruning:

And here’s the pruned tree:

So as it turns out, this tree did need to be pruned. As you can see, there are only 3 terminal nodes now as opposed to the six that were in the pre-pruned tree. The top branch is still the same-all of the merit badges and ranking 22 or lower. The top branch’s splits are also the same-116 badges and ranking 55 or lower on the left, 21 badges on the right.

However, that’s where the similarities end. Unlike the pre-pruned tree, the right split from the top branch is a terminal node; this node contains 4,532 Scouts and 21 merit badges and doesn’t split any further. The left split, on the other hand, splits into two branches (just as it does in the pre-pruned tree), but unlike the pre-pruned tree, those branches are terminal nodes. Those two terminal nodes contain 83 badges/4,503 Scouts on the left split and 33 badges/1,504 Scouts on the right split.

So here’s a breakdown of each group in this tree:

  • Group 1 (left)-4,532 Scouts and 21 merit badges
  • Group 2 (center)-4,503 Scouts and 83 merit badges
  • Group 3 (right)-1,504 Scouts and 33 merit badges

How did I know where to prune the tree? Here’s how:

When I typed in plotcp(tree), I got this handy little diagram, which is a visual summary of the output I got with printcp(tree). The area I circled, which corresponds to Node 3, is the optimal place to prune the tree, since it’s the one closest above the dashed line (which I’ll call the pruning line). You might think Node 4 would have been a better place to prune the tree, but since it touches the pruning line, that would not have a good place to prune the tree.

So after determining the best place to prune the tree, I look up the CP for Node 3-0.061173-and use that for the pfit <- prune(tree, cp=0.061173) line (this is the line that prunes the tree-the CP tells it where to prune).

Thanks for reading,

Michael

Thank You For 1 Year

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Hello everybody,

This is Michael, and today is the one-year anniversary of this blog’s launch. To everybody who has ever read and/or subscribed to this blog, thank you. Thank you for reading all my data analytics and programming lessons this past year. I started this blog on June 13, 2018 not only to keep my analytical/programming skills sharp but also to show what I know and share my knowledge with others. I hope you all learned something from this blog too.

So, thank you all for reading, and here’s to more amazing content in the second year,

Michael

R Lesson 16: R Loops

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Hello everybody,

It’s Michael, and today’s lesson will be on loops in R. I’ve posted about loops before, but those were for my Java lessons. However, while there may be some differences between Java loops and R loops, the basic ideas are the same. In fact, two of the three main types of Java loops-while and for-are also the two main types of R loops. The do-while loop doesn’t exist in R…..at least not yet. In its place, R has something called the repeatloop.

Let’s demonstrate the forloop first:

In this for loop, the factorials for the numbers 1-10 are printed. The i is a common symbol in R loops-it represents the indexes (or elements) of a loop. The i will traverse through all 10 elements of the loop-in this case, the numbers 1 through 10-and print out the factorials of each number along with the corresponding text-The factorial for , i , is, factorial(i).

  • In case you weren’t aware, the factorial of a number is the product of that number and all numbers below it (stopping at 1). So 4 factorial would be 24, since 4*3*2*1 equals 24. Factorials are denoted with an exclamation point by the number, so 4 factorial would be written as 4!. You might have come across this concept in your algebra class.

Now let’s take a look at the differences in syntax between a Java for loop and an R for loop (using the same factorial output)

R for loop:

for (i in 1:10)

{print(paste(“The factorial for” , i , “is” , factorial(i)))}

Java for loop:

int fac = 1;

for (int i = 1; i <= 10; i++)

{

fac *= i;

System.out.println(“The factorial of  ” + i + ” is ” + fac );

}

So, where are all of the differences? Let me name 5:

  1. The commands to print the output are different. Java requires System.out.println (or System.out.print). R requires print(paste()).
  2. Java needs 6 lines of code to do what R can accomplish in two lines-which is to calculate the factorials of the numbers 1-10 and print the specified output.
  3. The way to concatenate strings and numbers is different-Java requires a plus sign while R uses a comma
  4. You will often need to declare a variable outside the loop in Java (like I did with fac = 1). That is usually not necessary in R.
  5. The forloop parameters in R are much simpler than those in Java. Here’s how:
    • The Java for loop parameters go (initializing condition; condition to stop the loop; action to perform after each iteration)
    • The R for loop parameters go (index variable in starting value:ending value). The starting value:ending value part tells the loop the startpoint and endpoint.

Next, let’s demonstrate a nested for loop. Just like in Java, you can make nested for loops:

And here’s the output (it was too large to capture in a single screenshot):

[1] “I times J is 6”
[1] “I times J is 8”
[1] “I times J is 10”
[1] “I times J is 12”
[1] “I times J is 14”
[1] “I times J is 16”
[1] “I times J is 18”
[1] “I times J is 9”
[1] “I times J is 12”
[1] “I times J is 15”
[1] “I times J is 18”
[1] “I times J is 21”
[1] “I times J is 24”
[1] “I times J is 27”
[1] “I times J is 12”
[1] “I times J is 16”
[1] “I times J is 20”
[1] “I times J is 24”
[1] “I times J is 28”
[1] “I times J is 32”
[1] “I times J is 36”
[1] “I times J is 15”
[1] “I times J is 20”
[1] “I times J is 25”
[1] “I times J is 30”
[1] “I times J is 35”
[1] “I times J is 40”
[1] “I times J is 45”
[1] “I times J is 18”
[1] “I times J is 24”
[1] “I times J is 30”
[1] “I times J is 36”
[1] “I times J is 42”
[1] “I times J is 48”
[1] “I times J is 54”
[1] “I times J is 21”
[1] “I times J is 28”
[1] “I times J is 35”
[1] “I times J is 42”
[1] “I times J is 49”
[1] “I times J is 56”
[1] “I times J is 63”
[1] “I times J is 24”
[1] “I times J is 32”
[1] “I times J is 40”
[1] “I times J is 48”
[1] “I times J is 56”
[1] “I times J is 64”
[1] “I times J is 72”

In this nested forloop, I have two important segments. The I segment traverses through the numbers 2-8 while the J segment traverses through the numbers 3-9. However, the statements on their own are useless. The only line that really matters is the output line-"I times J is" , i*j. This line will print out the product of i and j.

OK, so that isn’t as simple as it looks. That is because the loop will traverse through every element of the I and J statements. In other words, the products of every element in the I statement and every element in the J statement will be displayed. For instance, the answer to 2*3 will be displayed, followed by 2*4, 2*5, all the way up to 2*9. Then all of the products from 3*3 to 3*9 will be displayed, and so forth, until you hit the 8 range (meaning from 8*3 to 8*9).

Now let’s create a while loop:

And here is the output (it was too long to fit on the same screenshot as the loop):

In this loop, I use 1902 as a starting point and 2018 as a stopping point. For each iteration, num will increase by 4 (starting from 1902) until 2018 is reached. In case you are wondering where I’m going with this, I’m printing out every even-numbered non-leap year between 1902 and 2018 inclusive.

  • Unfortunately, R doesn’t recognize increment/decrement symbols like ++, --, +=, -=, /=, *= the way Java does. So you’ll just have to increment/decrement in long form, as I did with the num <- num + 4 line.

Unlike for loops between Java and R, while loops between Java and R are very similar. Here’s the R loop for this program:

num <- 1902

while (num <= 2018)

{

print (num)

num <- num + 4

}

And here’s a Java whileloop that will do the exact same thing as the R loop:

num = 1902;

while (num <= 2018)

{

System.out.println(num)

num += 4;

}

One of the similarities between the two while loops are the parameters of the loop. In both loops, the lone parameter is what I’d like to call the running condition, which is the condition that tells the loop that while that condition is true, keep the loop running. In both cases, the running condition is num <= 2018.

The differences between the two loops are related to the difference in functions between Java and R. For instance, Java output requires System.out.printlnwhile R output simply requires print(or print(paste()) for outputs with strings). The other main difference is how to denote incrementing/decrementing in the loop, which I already discussed earlier in this post.

The third type of R loop is the repeat; this is the loop that is exclusive to R (just as the do-while loop is exclusive to Java). In R, a repeat loop is similar to a while loop in the sense that both loops have a stop condition (which is the condition that stops the loop from running). However, in while loops, the stop condition also functions as the running condition. For instance, the statement num <= 2018acts as both a running condition and a stop condition, since it tells the loop to keep running as long as num is less than or equal to 2018 but it also tells the loop to stop running as soon as 2018 (or the closest number to it) is reached.

Repeat loops don’t have a running condition per se, since they can be infinite. As a result, including a stop condition is totally optional. However, if you wish to include a stop condition, write an ifstatement (they’re formatted just like Java if statements) ending with the word break, which indicates that the loop will stop if the if statement condition is met.

Here’s an example of a repeat loop with a breakclause:

In this loop, I start with num <- 5 just outside the loop. Once I get inside the loop, numkeeps getting multiplied by 2 until a number that is either greater than or equal to 1000 is reached. All of the products of num * 2 are printed, and the last output is 1280, which is 640*2.

  • Had I not included a breakstatement, this loop would have gone on and on. Inf would be displayed after a certain point to denote that the loop would be infinite.

Thanks for reading,

Michael