library(tidyr)
library(matrixcalc)
library(corrplot)
## corrplot 0.84 loaded
library(MASS)

Problem 1

Generate random variable

Using R, generate a random variable X that has 10,000 random uniform numbers from 1 to N, where N can be any number of your choosing greater than or equal to 6. Then generate a random variable Y that has 10,000 random normal numbers with a mean of \(\mu = \sigma = (N+1)/2\)

N <- 10
n <- 10000
X <- runif(n = n, min = 1, max = N)
Y <- rnorm(n, mean=(N+1)/2, sd = (N+1)/2)

Probability.

Calculate as a minimum the below probabilities a through c. Assume the small letter “x” is estimated as the median of the X variable, and the small letter “y” is estimated as the 1st quartile of the Y variable. Interpret the meaning of all probabilities.

x <- median(X)
y <- quantile(Y)[2]

df <- data.frame(X, Y)

a. P(X>x | X>y)

Identify first the Probability of X>y

dfXy <- subset(df, df$X>y)

Identify the Probability of X>x in the above subset

n2 <- nrow(subset(dfXy, df$X>x))
n2/n
## [1] 0.5

b. P(X>x, Y>y)

n2 <- nrow(subset(df, df$X>x & df$Y>y))
Pxny <- n2/n
Pxny
## [1] 0.3776

c. P(X<x | X>y)

n2 <- nrow(subset(dfXy, df$X<x))
n2/n
## [1] 0.5

Marginal and joint probabilities

Investigate whether P(X>x and Y>y)=P(X>x)P(Y>y) by building a table and evaluating the marginal and joint probabilities.

Px <- nrow(subset(df, df$X>x))/n
Py <- nrow(subset(df, df$Y>y))/n

Px*Py
## [1] 0.375
dfPtableValues <- matrix(c( nrow( df %>% subset(df$X < x & df$Y < y) ), 
                 nrow( df %>% subset(df$X > x & df$Y < y)), 
                 nrow( df %>% subset(df$X < x & df$Y > y)), 
                 nrow( df %>% subset(df$X > x & df$Y > y)) 
              ))
              

table <- matrix(dfPtableValues , nrow=2)

colnames(table) <- c('Y < y','Y > y')
rownames(table) <- c('X < x','X > x')
table
##       Y < y Y > y
## X < x  1276  3724
## X > x  1224  3776
dfPtable <- c( nrow( df %>% subset(df$X < x & df$Y < y) )/n, 
                 nrow( df %>% subset(df$X > x & df$Y < y))/n, 
                 nrow( df %>% subset(df$X < x & df$Y > y))/n, 
                 nrow( df %>% subset(df$X > x & df$Y > y))/n 
              )
              
table <- matrix(dfPtable , nrow=2)

colnames(table) <- c('Y < y','Y > y')
rownames(table) <- c('X < x','X > x')
table
##        Y < y  Y > y
## X < x 0.1276 0.3724
## X > x 0.1224 0.3776

Looking at the individual values, marginal and joint probabilities are almost similar i.e., 0.375 vs 0.3776

Fisher and Chi square test

Check to see if independence holds by using Fisher’s Exact Test and the Chi Square Test. What is the difference between the two? Which is most appropriate?

Fisher’s test is used

pTable <- matrix(dfPtableValues , nrow=2)
fisher.test(pTable)
## 
##  Fisher's Exact Test for Count Data
## 
## data:  pTable
## p-value = 0.2389
## alternative hypothesis: true odds ratio is not equal to 1
## 95 percent confidence interval:
##  0.964496 1.158476
## sample estimates:
## odds ratio 
##   1.057068

Chi Square test is used

chisq.test(pTable)
## 
##  Pearson's Chi-squared test with Yates' continuity correction
## 
## data:  pTable
## X-squared = 1.3872, df = 1, p-value = 0.2389

Since both tests return higher p value, they fail to reject the null hypothesis.

Problem 2

Descriptive and Inferential Statistics

Provide univariate descriptive statistics and appropriate plots for the training data set. Provide a scatterplot matrix for at least two of the independent variables and the dependent variable. Derive a correlation matrix for any three quantitative variables in the dataset. Test the hypotheses that the correlations between each pairwise set of variables is 0 and provide an 80% confidence interval. Discuss the meaning of your analysis. Would you be worried about familywise error? Why or why not?

#Load the training dataset
trainData <- read.csv("kaggle/train.csv")
#Show summary of the dataset
summary(trainData)
##        Id           MSSubClass       MSZoning     LotFrontage    
##  Min.   :   1.0   Min.   : 20.0   C (all):  10   Min.   : 21.00  
##  1st Qu.: 365.8   1st Qu.: 20.0   FV     :  65   1st Qu.: 59.00  
##  Median : 730.5   Median : 50.0   RH     :  16   Median : 69.00  
##  Mean   : 730.5   Mean   : 56.9   RL     :1151   Mean   : 70.05  
##  3rd Qu.:1095.2   3rd Qu.: 70.0   RM     : 218   3rd Qu.: 80.00  
##  Max.   :1460.0   Max.   :190.0                  Max.   :313.00  
##                                                  NA's   :259     
##     LotArea        Street      Alley      LotShape  LandContour  Utilities   
##  Min.   :  1300   Grvl:   6   Grvl:  50   IR1:484   Bnk:  63    AllPub:1459  
##  1st Qu.:  7554   Pave:1454   Pave:  41   IR2: 41   HLS:  50    NoSeWa:   1  
##  Median :  9478               NA's:1369   IR3: 10   Low:  36                 
##  Mean   : 10517                           Reg:925   Lvl:1311                 
##  3rd Qu.: 11602                                                              
##  Max.   :215245                                                              
##                                                                              
##    LotConfig    LandSlope   Neighborhood   Condition1     Condition2  
##  Corner : 263   Gtl:1382   NAmes  :225   Norm   :1260   Norm   :1445  
##  CulDSac:  94   Mod:  65   CollgCr:150   Feedr  :  81   Feedr  :   6  
##  FR2    :  47   Sev:  13   OldTown:113   Artery :  48   Artery :   2  
##  FR3    :   4              Edwards:100   RRAn   :  26   PosN   :   2  
##  Inside :1052              Somerst: 86   PosN   :  19   RRNn   :   2  
##                            Gilbert: 79   RRAe   :  11   PosA   :   1  
##                            (Other):707   (Other):  15   (Other):   2  
##    BldgType      HouseStyle   OverallQual      OverallCond      YearBuilt   
##  1Fam  :1220   1Story :726   Min.   : 1.000   Min.   :1.000   Min.   :1872  
##  2fmCon:  31   2Story :445   1st Qu.: 5.000   1st Qu.:5.000   1st Qu.:1954  
##  Duplex:  52   1.5Fin :154   Median : 6.000   Median :5.000   Median :1973  
##  Twnhs :  43   SLvl   : 65   Mean   : 6.099   Mean   :5.575   Mean   :1971  
##  TwnhsE: 114   SFoyer : 37   3rd Qu.: 7.000   3rd Qu.:6.000   3rd Qu.:2000  
##                1.5Unf : 14   Max.   :10.000   Max.   :9.000   Max.   :2010  
##                (Other): 19                                                  
##   YearRemodAdd    RoofStyle       RoofMatl     Exterior1st   Exterior2nd 
##  Min.   :1950   Flat   :  13   CompShg:1434   VinylSd:515   VinylSd:504  
##  1st Qu.:1967   Gable  :1141   Tar&Grv:  11   HdBoard:222   MetalSd:214  
##  Median :1994   Gambrel:  11   WdShngl:   6   MetalSd:220   HdBoard:207  
##  Mean   :1985   Hip    : 286   WdShake:   5   Wd Sdng:206   Wd Sdng:197  
##  3rd Qu.:2004   Mansard:   7   ClyTile:   1   Plywood:108   Plywood:142  
##  Max.   :2010   Shed   :   2   Membran:   1   CemntBd: 61   CmentBd: 60  
##                                (Other):   2   (Other):128   (Other):136  
##    MasVnrType    MasVnrArea     ExterQual ExterCond  Foundation  BsmtQual  
##  BrkCmn : 15   Min.   :   0.0   Ex: 52    Ex:   3   BrkTil:146   Ex  :121  
##  BrkFace:445   1st Qu.:   0.0   Fa: 14    Fa:  28   CBlock:634   Fa  : 35  
##  None   :864   Median :   0.0   Gd:488    Gd: 146   PConc :647   Gd  :618  
##  Stone  :128   Mean   : 103.7   TA:906    Po:   1   Slab  : 24   TA  :649  
##  NA's   :  8   3rd Qu.: 166.0             TA:1282   Stone :  6   NA's: 37  
##                Max.   :1600.0                       Wood  :  3             
##                NA's   :8                                                   
##  BsmtCond    BsmtExposure BsmtFinType1   BsmtFinSF1     BsmtFinType2
##  Fa  :  45   Av  :221     ALQ :220     Min.   :   0.0   ALQ :  19   
##  Gd  :  65   Gd  :134     BLQ :148     1st Qu.:   0.0   BLQ :  33   
##  Po  :   2   Mn  :114     GLQ :418     Median : 383.5   GLQ :  14   
##  TA  :1311   No  :953     LwQ : 74     Mean   : 443.6   LwQ :  46   
##  NA's:  37   NA's: 38     Rec :133     3rd Qu.: 712.2   Rec :  54   
##                           Unf :430     Max.   :5644.0   Unf :1256   
##                           NA's: 37                      NA's:  38   
##    BsmtFinSF2        BsmtUnfSF       TotalBsmtSF      Heating     HeatingQC
##  Min.   :   0.00   Min.   :   0.0   Min.   :   0.0   Floor:   1   Ex:741   
##  1st Qu.:   0.00   1st Qu.: 223.0   1st Qu.: 795.8   GasA :1428   Fa: 49   
##  Median :   0.00   Median : 477.5   Median : 991.5   GasW :  18   Gd:241   
##  Mean   :  46.55   Mean   : 567.2   Mean   :1057.4   Grav :   7   Po:  1   
##  3rd Qu.:   0.00   3rd Qu.: 808.0   3rd Qu.:1298.2   OthW :   2   TA:428   
##  Max.   :1474.00   Max.   :2336.0   Max.   :6110.0   Wall :   4            
##                                                                            
##  CentralAir Electrical     X1stFlrSF      X2ndFlrSF     LowQualFinSF    
##  N:  95     FuseA:  94   Min.   : 334   Min.   :   0   Min.   :  0.000  
##  Y:1365     FuseF:  27   1st Qu.: 882   1st Qu.:   0   1st Qu.:  0.000  
##             FuseP:   3   Median :1087   Median :   0   Median :  0.000  
##             Mix  :   1   Mean   :1163   Mean   : 347   Mean   :  5.845  
##             SBrkr:1334   3rd Qu.:1391   3rd Qu.: 728   3rd Qu.:  0.000  
##             NA's :   1   Max.   :4692   Max.   :2065   Max.   :572.000  
##                                                                         
##    GrLivArea     BsmtFullBath     BsmtHalfBath        FullBath    
##  Min.   : 334   Min.   :0.0000   Min.   :0.00000   Min.   :0.000  
##  1st Qu.:1130   1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:1.000  
##  Median :1464   Median :0.0000   Median :0.00000   Median :2.000  
##  Mean   :1515   Mean   :0.4253   Mean   :0.05753   Mean   :1.565  
##  3rd Qu.:1777   3rd Qu.:1.0000   3rd Qu.:0.00000   3rd Qu.:2.000  
##  Max.   :5642   Max.   :3.0000   Max.   :2.00000   Max.   :3.000  
##                                                                   
##     HalfBath       BedroomAbvGr    KitchenAbvGr   KitchenQual  TotRmsAbvGrd   
##  Min.   :0.0000   Min.   :0.000   Min.   :0.000   Ex:100      Min.   : 2.000  
##  1st Qu.:0.0000   1st Qu.:2.000   1st Qu.:1.000   Fa: 39      1st Qu.: 5.000  
##  Median :0.0000   Median :3.000   Median :1.000   Gd:586      Median : 6.000  
##  Mean   :0.3829   Mean   :2.866   Mean   :1.047   TA:735      Mean   : 6.518  
##  3rd Qu.:1.0000   3rd Qu.:3.000   3rd Qu.:1.000               3rd Qu.: 7.000  
##  Max.   :2.0000   Max.   :8.000   Max.   :3.000               Max.   :14.000  
##                                                                               
##  Functional    Fireplaces    FireplaceQu   GarageType   GarageYrBlt  
##  Maj1:  14   Min.   :0.000   Ex  : 24    2Types :  6   Min.   :1900  
##  Maj2:   5   1st Qu.:0.000   Fa  : 33    Attchd :870   1st Qu.:1961  
##  Min1:  31   Median :1.000   Gd  :380    Basment: 19   Median :1980  
##  Min2:  34   Mean   :0.613   Po  : 20    BuiltIn: 88   Mean   :1979  
##  Mod :  15   3rd Qu.:1.000   TA  :313    CarPort:  9   3rd Qu.:2002  
##  Sev :   1   Max.   :3.000   NA's:690    Detchd :387   Max.   :2010  
##  Typ :1360                               NA's   : 81   NA's   :81    
##  GarageFinish   GarageCars      GarageArea     GarageQual  GarageCond 
##  Fin :352     Min.   :0.000   Min.   :   0.0   Ex  :   3   Ex  :   2  
##  RFn :422     1st Qu.:1.000   1st Qu.: 334.5   Fa  :  48   Fa  :  35  
##  Unf :605     Median :2.000   Median : 480.0   Gd  :  14   Gd  :   9  
##  NA's: 81     Mean   :1.767   Mean   : 473.0   Po  :   3   Po  :   7  
##               3rd Qu.:2.000   3rd Qu.: 576.0   TA  :1311   TA  :1326  
##               Max.   :4.000   Max.   :1418.0   NA's:  81   NA's:  81  
##                                                                       
##  PavedDrive   WoodDeckSF      OpenPorchSF     EnclosedPorch      X3SsnPorch    
##  N:  90     Min.   :  0.00   Min.   :  0.00   Min.   :  0.00   Min.   :  0.00  
##  P:  30     1st Qu.:  0.00   1st Qu.:  0.00   1st Qu.:  0.00   1st Qu.:  0.00  
##  Y:1340     Median :  0.00   Median : 25.00   Median :  0.00   Median :  0.00  
##             Mean   : 94.24   Mean   : 46.66   Mean   : 21.95   Mean   :  3.41  
##             3rd Qu.:168.00   3rd Qu.: 68.00   3rd Qu.:  0.00   3rd Qu.:  0.00  
##             Max.   :857.00   Max.   :547.00   Max.   :552.00   Max.   :508.00  
##                                                                                
##   ScreenPorch        PoolArea        PoolQC       Fence      MiscFeature
##  Min.   :  0.00   Min.   :  0.000   Ex  :   2   GdPrv:  59   Gar2:   2  
##  1st Qu.:  0.00   1st Qu.:  0.000   Fa  :   2   GdWo :  54   Othr:   2  
##  Median :  0.00   Median :  0.000   Gd  :   3   MnPrv: 157   Shed:  49  
##  Mean   : 15.06   Mean   :  2.759   NA's:1453   MnWw :  11   TenC:   1  
##  3rd Qu.:  0.00   3rd Qu.:  0.000               NA's :1179   NA's:1406  
##  Max.   :480.00   Max.   :738.000                                       
##                                                                         
##     MiscVal             MoSold           YrSold        SaleType   
##  Min.   :    0.00   Min.   : 1.000   Min.   :2006   WD     :1267  
##  1st Qu.:    0.00   1st Qu.: 5.000   1st Qu.:2007   New    : 122  
##  Median :    0.00   Median : 6.000   Median :2008   COD    :  43  
##  Mean   :   43.49   Mean   : 6.322   Mean   :2008   ConLD  :   9  
##  3rd Qu.:    0.00   3rd Qu.: 8.000   3rd Qu.:2009   ConLI  :   5  
##  Max.   :15500.00   Max.   :12.000   Max.   :2010   ConLw  :   5  
##                                                     (Other):   9  
##  SaleCondition    SalePrice     
##  Abnorml: 101   Min.   : 34900  
##  AdjLand:   4   1st Qu.:129975  
##  Alloca :  12   Median :163000  
##  Family :  20   Mean   :180921  
##  Normal :1198   3rd Qu.:214000  
##  Partial: 125   Max.   :755000  
## 

univariate statistics and plots

par(mfrow=c(2,3))
plot(trainData$MSZoning, main = 'Zoning')

hist(trainData$LotArea, main = 'Lot Area')

hist(trainData$TotalBsmtSF, main = 'Basement sqft')

plot(trainData$Neighborhood, main = 'Neighborhood')

hist(trainData$SalePrice, main = 'Sale price')

hist(trainData$BedroomAbvGr, main = 'Bedroom count')

Independent and response variables

#Select 2 independent variables i.e., 'GrLivArea' and 'SaleCondition', and a response variable 'SalePrice'
plot(trainData$GrLivArea, trainData$SalePrice, xlab = "Gr LivingArea", ylab = "Sale price", main='LivingArea vs Sale price')

plot(trainData$SaleCondition, trainData$SalePrice,  xlab = "Sale condition", ylab = "Sale price", main='Sale condition  vs Sale price')

subsetData <- trainData[c('BedroomAbvGr', 'GrLivArea', 'SalePrice')]

#Calculate the co-relations between the 3 variables
corMatrix <- cor(subsetData)
corMatrix
##              BedroomAbvGr GrLivArea SalePrice
## BedroomAbvGr    1.0000000 0.5212695 0.1682132
## GrLivArea       0.5212695 1.0000000 0.7086245
## SalePrice       0.1682132 0.7086245 1.0000000
# Plot the co-relations
corrplot(corMatrix)

#Test the co-relations for a confidence level of 0.8
cor.test(subsetData$BedroomAbvGr, subsetData$SalePrice, conf.level = .8)
## 
##  Pearson's product-moment correlation
## 
## data:  subsetData$BedroomAbvGr and subsetData$SalePrice
## t = 6.5159, df = 1458, p-value = 9.927e-11
## alternative hypothesis: true correlation is not equal to 0
## 80 percent confidence interval:
##  0.1354160 0.2006421
## sample estimates:
##       cor 
## 0.1682132
cor.test(subsetData$GrLivArea, subsetData$SalePrice, conf.level = .8)
## 
##  Pearson's product-moment correlation
## 
## data:  subsetData$GrLivArea and subsetData$SalePrice
## t = 38.348, df = 1458, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 80 percent confidence interval:
##  0.6915087 0.7249450
## sample estimates:
##       cor 
## 0.7086245
cor.test(subsetData$BedroomAbvGr, subsetData$GrLivArea, conf.level = .8)
## 
##  Pearson's product-moment correlation
## 
## data:  subsetData$BedroomAbvGr and subsetData$GrLivArea
## t = 23.323, df = 1458, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 80 percent confidence interval:
##  0.4963921 0.5452915
## sample estimates:
##       cor 
## 0.5212695

Would you be worried about familywise error? Due to the high number of variables available, and many of which are categorical nature and as I’m focussed on quantitative variables for this analysis, it is possible that I might be making false assumptions leading to FWE.

Linear Algebra and Correlation

Invert your correlation matrix from above. (This is known as the precision matrix and contains variance inflation factors on the diagonal.) Multiply the correlation matrix by the precision matrix, and then multiply the precision matrix by the correlation matrix. Conduct LU decomposition on the matrix.

inverseCorMatrix <- solve(corMatrix)
x <- round(corMatrix %*% inverseCorMatrix, 1)
x
##              BedroomAbvGr GrLivArea SalePrice
## BedroomAbvGr            1         0         0
## GrLivArea               0         1         0
## SalePrice               0         0         1
y <- round(inverseCorMatrix %*% corMatrix, 1)
y
##              BedroomAbvGr GrLivArea SalePrice
## BedroomAbvGr            1         0         0
## GrLivArea               0         1         0
## SalePrice               0         0         1
lu.decomposition(x)
## $L
##      [,1] [,2] [,3]
## [1,]    1    0    0
## [2,]    0    1    0
## [3,]    0    0    1
## 
## $U
##      [,1] [,2] [,3]
## [1,]    1    0    0
## [2,]    0    1    0
## [3,]    0    0    1
lu.decomposition(y)
## $L
##      [,1] [,2] [,3]
## [1,]    1    0    0
## [2,]    0    1    0
## [3,]    0    0    1
## 
## $U
##      [,1] [,2] [,3]
## [1,]    1    0    0
## [2,]    0    1    0
## [3,]    0    0    1

The decomposition of both x and y matrix resolve to same value.

Calculus-Based Probability & Statistics

Find the optimal value of \(\lambda\) for this distribution, and then take 1000 samples from this exponential distribution using this value (e.g., rexp(1000, \(\lambda\))). Plot a histogram and compare it with a histogram of your original variable. Using the exponential pdf, find the 5th and 95th percentiles using the cumulative distribution function (CDF). Also generate a 95% confidence interval from the empirical data, assuming normality. Finally, provide the empirical 5th percentile and 95th percentile of the data. Discuss.

a <- fitdistr(x=trainData$SalePrice, densfun = "exponential")
value <- a$estimate 

data <- rexp(1000, value)
quantile(data, c(.05,.95))
##        5%       95% 
##  10542.15 547971.98
#Plot graphs
par(mfrow=c(1,2))
hist(trainData$SalePrice,main = "Actual train data")
#hist(trainData$SalePrice_log,main = "Skew adjusted train data")
hist(data,main = "distrbution data")

5th and 95th percentiles using the cumulative distribution function (CDF)

quantile(data, c(.05,.95))
##        5%       95% 
##  10542.15 547971.98

Empirical 5th percentile and 95th percentile of the data

quantile(trainData$SalePrice, c(.05,.95))
##     5%    95% 
##  88000 326100
data <- rnorm(length(trainData$SalePrice), mean = mean(trainData$SalePrice), sd=sd(trainData$SalePrice))
hist(data, main = "Normalized data")

Modeling

Build some type of multiple regression model and submit your model to the competition board. Provide your complete model summary and results with analysis. Report your Kaggle.com user name and score.

I observed there are high statistical outliers in the data in certain cases and calculated the quantile data for each variable I’m considering for this regression model. Based on my observation, I have mostly selected 98 percentile data and removed first 5 percentile data for a particular variable (yearbuild)

#Calculate and remove observations with outliers for variables 'GrLivArea','TotalBsmtSF','TotRmsAbvGrd','GarageArea','YearBuilt'

# Showcasing quantile data for Living area
quantile(trainData$GrLivArea, c(1:100)/100)
##      1%      2%      3%      4%      5%      6%      7%      8%      9%     10% 
##  692.18  768.00  796.00  828.80  848.00  864.00  864.00  885.44  895.55  912.00 
##     11%     12%     13%     14%     15%     16%     17%     18%     19%     20% 
##  924.49  948.00  960.00  980.00  988.00 1004.00 1034.00 1040.00 1054.00 1066.60 
##     21%     22%     23%     24%     25%     26%     27%     28%     29%     30% 
## 1078.78 1092.00 1109.57 1120.00 1129.50 1144.00 1154.93 1178.00 1196.22 1208.00 
##     31%     32%     33%     34%     35%     36%     37%     38%     39%     40% 
## 1217.29 1224.00 1236.00 1251.06 1262.00 1279.96 1300.49 1311.68 1324.00 1339.00 
##     41%     42%     43%     44%     45%     46%     47%     48%     49%     50% 
## 1348.00 1360.00 1368.00 1382.00 1392.55 1414.00 1427.46 1437.96 1452.91 1464.00 
##     51%     52%     53%     54%     55%     56%     57%     58%     59%     60% 
## 1474.09 1483.36 1494.00 1501.86 1509.45 1525.00 1540.26 1557.22 1571.00 1578.00 
##     61%     62%     63%     64%     65%     66%     67%     68%     69%     70% 
## 1599.95 1612.74 1626.51 1639.76 1651.35 1660.00 1668.00 1683.12 1694.00 1709.30 
##     71%     72%     73%     74%     75%     76%     77%     78%     79%     80% 
## 1717.00 1728.00 1739.07 1765.32 1776.75 1792.00 1803.43 1836.00 1849.22 1869.00 
##     81%     82%     83%     84%     85%     86%     87%     88%     89%     90% 
## 1907.37 1928.00 1949.97 1966.24 1987.30 2020.74 2058.66 2090.00 2120.02 2158.30 
##     91%     92%     93%     94%     95%     96%     97%     98%     99%    100% 
## 2221.14 2264.12 2328.35 2385.52 2466.10 2545.72 2633.23 2782.38 3123.48 5642.00
trainData_nonOutlier <- trainData[c('SalePrice','GrLivArea','TotalBsmtSF','TotRmsAbvGrd','GarageArea','YearBuilt')]
trainData_nonOutlier <- subset(trainData_nonOutlier, trainData_nonOutlier$GrLivArea<quantile(trainData_nonOutlier$GrLivArea, c(1:100)/100)[98][1])
trainData_nonOutlier <- subset(trainData_nonOutlier, trainData_nonOutlier$TotalBsmtSF<quantile(trainData_nonOutlier$TotalBsmtSF, c(1:100)/100)[98][1])
trainData_nonOutlier <- subset(trainData_nonOutlier, trainData_nonOutlier$TotRmsAbvGrd<quantile(trainData_nonOutlier$TotRmsAbvGrd, c(1:100)/100)[98][1])
trainData_nonOutlier <- subset(trainData_nonOutlier, trainData_nonOutlier$GarageArea<quantile(trainData_nonOutlier$GarageArea, c(1:100)/100)[98][1])
trainData_nonOutlier <- subset(trainData_nonOutlier, trainData_nonOutlier$YearBuilt>quantile(trainData_nonOutlier$YearBuilt, c(1:100)/100)[5][1])
m2 <- lm(SalePrice ~ ., data=trainData_nonOutlier)
summary(m2)
## 
## Call:
## lm(formula = SalePrice ~ ., data = trainData_nonOutlier)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -118635  -15917   -1968   14031  179803 
## 
## Coefficients:
##                Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  -1.162e+06  7.416e+04 -15.674  < 2e-16 ***
## GrLivArea     7.944e+01  3.635e+00  21.851  < 2e-16 ***
## TotalBsmtSF   4.537e+01  2.612e+00  17.370  < 2e-16 ***
## TotRmsAbvGrd -3.449e+03  1.052e+03  -3.280  0.00107 ** 
## GarageArea    5.171e+01  5.846e+00   8.846  < 2e-16 ***
## YearBuilt     5.940e+02  3.835e+01  15.491  < 2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 29430 on 1248 degrees of freedom
## Multiple R-squared:  0.7678, Adjusted R-squared:  0.7669 
## F-statistic: 825.6 on 5 and 1248 DF,  p-value: < 2.2e-16
plot(m2$residuals, main='Residuals')

res <- resid(m2)
qqnorm(res)
qqline(res)

testData <- read.csv("kaggle/test.csv")
pred <- predict(m2, testData)
kaggleResult <- data.frame( Id = testData[,"Id"],  SalePrice =pred)
kaggleResult[kaggleResult<0] <- 0
kaggleResult <- replace(kaggleResult,is.na(kaggleResult),0)
write.csv(kaggleResult, file="kaggleResult.csv", row.names = FALSE)

Kaggle score

My username is Cheruku and I scored .49038 in first attempt. Will making few more tries to improve my score.