diff --git a/StudentNotebooks/Assignment01/zhaot4-f24-assignment1.Rmd b/StudentNotebooks/Assignment01/zhaot4-f24-assignment1.Rmd index 274fea4..97b62d6 100644 --- a/StudentNotebooks/Assignment01/zhaot4-f24-assignment1.Rmd +++ b/StudentNotebooks/Assignment01/zhaot4-f24-assignment1.Rmd @@ -354,7 +354,21 @@ What do the clustering and PCA results tell us about the data detected by the The clustering and PCA results from the M20 PIXL experiment data reveal a heterogeneous composition in the Martian surface samples, indicating diverse geological processes and materials. The three distinct clusters point to different rock or soil types, suggesting a complex geological history involving various environmental conditions and processes. ```{r} - +library(ggplot2) +library(factoextra) +library(dplyr) +summary(pixl_trim.mat.pca) +loadings <- pixl_trim.mat.pca$rotation +print("PCA Loadings:") +print(loadings) +data <- as.factor(km$cluster) +fviz_pca_biplot(pixl_trim.mat.pca, +geom.ind = "point", +col.ind = data, # Color by clusters +palette = "jco", +addEllipses = FALSE, +label = "var", +title = "PCA Biplot of Martian Geochemical Data") ``` ## SAVE, COMMIT and PUSH YOUR CHANGES! diff --git a/StudentNotebooks/Assignment01/zhaot4-f24-assignment1.html b/StudentNotebooks/Assignment01/zhaot4-f24-assignment1.html index a39bb51..09d77ae 100644 --- a/StudentNotebooks/Assignment01/zhaot4-f24-assignment1.html +++ b/StudentNotebooks/Assignment01/zhaot4-f24-assignment1.html @@ -11,9 +11,9 @@ - + -RPI github and Mars 2020 PIXL Example Notebook: +RPI github and Mars 2020 PIXL-zhaot4 Notebook: + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + +
+ +
+ +
+

1 DAR ASSIGNMENT 2 +(Introduction): Introductory DAR Notebook

+

This notebook is broken into two main parts:

+ +

NOTE: The RPI github repository for all the code and +data required for this notebook may be found at:

+ +
+
+

2 DAR ASSIGNMENT 2 (Part +1): Preparing your local repo for Assignment 2

+

In this assignment you’ll start by making a copy of the Assignment 2 +template notebook, then you’ll add to your copy with your original work. +The instructions which follow explain how to accomplish this.

+

NOTE: You already cloned the +DAR-Mars-F24 repository for Assignment 1; you do +not need to make another clone of the repo, but you must begin +by updating your copy as instructed below:

+
+

2.1 Updating your local +clone of the DAR-Mars-F24 repository

+
    +
  • Access RStudio Server on the IDEA Cluster at http://lp01.idea.rpi.edu/rstudio-ose/ +
      +
    • REMINDER: You must be on the RPI VPN!!
    • +
  • +
  • Access the Linux shell on the IDEA Cluster by clicking the +Terminal tab of RStudio Server (lower left panel). +
      +
    • You now see the Linux shell on the IDEA Cluster
    • +
    • cd (change directory) to enter your home directory +using: cd ~
    • +
    • Type pwd to confirm where you are
    • +
  • +
  • In the Linux shell, cd to DAR-Mars-F24 +
      +
    • Type git pull origin main to pull any updates
    • +
    • Always do this when you being work; we might have added or changed +something!
    • +
  • +
  • In the Linux shell, cd into Assignment02 +
      +
    • Type ls -al to list the current contents
    • +
    • Don’t be surprised if you see many files!
    • +
  • +
  • In the Linux shell, type git branch to verify your +current working branch +
      +
    • If it is not dar-yourrcs, type +git checkout dar-yourrcs (where yourrcs is +your RCS id)
    • +
    • Re-type git branch to confirm
    • +
  • +
  • Now in the RStudio Server UI, navigate to the +DAR-Mars-F24/StudentNotebooks/Assignment02 directory via +the Files panel (lower right panel) +
      +
    • Under the More menu, set this to be your R working +directory
    • +
    • Setting the correct working directory is essential for interactive R +use!
    • +
  • +
+

You’re now ready to start coding Assignment 2!

+
+
+

2.2 Creating your copy of +the Assignment 2 notebook

+
    +
  1. In RStudio, make a copy of +dar-f24-assignment2-template.Rmd file using a new, +original, descriptive filename that includes your RCS +ID! +
      +
    • Open dar-f24-assignment2-template.Rmd
    • +
    • Save As… using a new filename that includes your +RCS ID
    • +
    • Example filename for user erickj4: +erickj4-assignment2-f24.Rmd
    • +
    • POINTS OFF IF: +
        +
      • You don’t create a new filename!
      • +
      • You don’t include your RCS ID!
      • +
      • You include template in your new filename!
      • +
    • +
  2. +
  3. Edit your new notebook using RStudio and save +
      +
    • Change the title: and subtitle: headers +(at the top of the file)
    • +
    • Change the author:
    • +
    • Don’t bother changing the date:; it should update +automagically…
    • +
    • Save your changes
    • +
  4. +
  5. Use the RStudio Knit command to create an PDF file; +repeat as necessary +
      +
    • Use the down arrow next to the word Knit and select +Knit to PDF
    • +
    • You may also knit to HTML…
    • +
  6. +
  7. In the Linux terminal, use git add to add each new file +you want to add to the repository +
      +
    • Type: git add yourfilename.Rmd
    • +
    • Type: git add yourfilename.pdf (created when you +knitted)
    • +
    • Add your HTML if you also created one…
    • +
  8. +
  9. When you’re ready, in Linux commit your changes: +
      +
    • Type: git commit -m "some comment" where “some comment” +is a useful comment describing your changes
    • +
    • This commits your changes to your local repo, and sets the stage for +your next operation.
    • +
  10. +
  11. Finally, push your commits to the RPI github repo +
      +
    • Type: git push origin dar-yourrcs (where +dar-yourrcs is the branch you’ve been working in)
    • +
    • Your changes are now safely on the RPI github.
    • +
  12. +
  13. REQUIRED: On the RPI github, submit a pull +request. +
      +
    • In a web browser, navigate to https://github.rpi.edu/DataINCITE/DAR-Mars-F24
    • +
    • In the branch selector drop-down (by default says +master), select your branch
    • +
    • Submit a pull request for your branch
    • +
    • One of the DAR instructors will merge your branch, and your new +files will be added to the master branch of the repo. Do not merge +your branch yourself!
    • +
  14. +
+
+
+
+

3 DAR ASSIGNMENT 2 (Part +2): Loading the Mars 2020 (M20) Datasets

+

In this assignment there are four datasets from separate instruments +on the Mars Perserverance rover available for analysis:

+ +

Each dataset provides data about the mineralogy of the surface of +Mars. Based on the purpose and nature of the instrument, the data is +collected at different intervals along the path of Perseverance as it +makes it way across the Jezero crater. Some of the data (esp. LIBS) is +collected almost every Martian day, or sol. Some of the data +(PIXL and SHERLOC) is only collected at certain sample locations of +interest

+

Your objective is to perform an analysis of the your team’s assigned +dataset in order to learn all you can about these Mars samples.

+

NOTES:

+ +
+

3.1 Data Set A: Load the +Lithology Data

+

The first five features of the dataset describe twenty-four (24) +rover sample locations.

+

The remaining features provides a simple binary (1 or +0) summary of presence or absence of 35 minerals at the 24 +rover sample locations.

+

Only the first sixteen (16) samples are maintained, as the remaining +are missing the mineral descriptors.

+

The following code “cleans” the dataset to prepare for analysis. It +first creates a dataframe with metadata and measurements for samples, +and then creates a matrix containing only numeric measurements for later +analysis.

+
# Load the saved lithology data with locations added
+lithology.df<- readRDS("/academics/MATP-4910-F24/DAR-Mars-F24/Data/mineral_data_static.Rds")
+
+# Cast samples as numbers
+lithology.df$sample <- as.numeric(lithology.df$sample)
+
+# Convert rest into factors
+lithology.df[sapply(lithology.df, is.character)] <-
+  lapply(lithology.df[sapply(lithology.df, is.character)], 
+                                       as.factor)
+
+# Keep only first 16 samples because the data for the rest of the samples is not available yet
+lithology.df<-lithology.df[1:16,]
+
+# Look at summary of cleaned data frame
+summary(lithology.df)
+
##      sample              name          SampleType         campaign
+##  Min.   : 1.00   Atsah     : 1   atmospheric: 1   Crater Floor:9  
+##  1st Qu.: 4.75   Bearwallow: 1   regolith   : 0   Delta Front :7  
+##  Median : 8.50   Coulettes : 1   rock core  :15   Margin Unit :0  
+##  Mean   : 8.50   Hahonih   : 1                                    
+##  3rd Qu.:12.25   Hazeltop  : 1                                    
+##  Max.   :16.00   Kukaklek  : 1                                    
+##                  (Other)   :10                                    
+##          abrasion feldspar plagioclase pyroxene olivine quartz apatite
+##  Alfalfa     :2   0:14     0:13        0: 5     0: 6    0:14   0:13   
+##  Bellegarde  :2   1: 2     1: 3        1:11     1:10    1: 2   1: 3   
+##  Berry Hollow:2                                                       
+##  Dourbes     :2                                                       
+##  Novarupta   :2                                                       
+##  Quartier    :2                                                       
+##  (Other)     :4                                                       
+##  FeTi_Oxides Iron_Oxide Sulfate Perchlorates Phosphate Ca_Sulfate Carbonate
+##  0:13        0:9        0: 4    0:15         0:11      0:10       0: 1     
+##  1: 3        1:7        1:12    1: 1         1: 5      1: 6       1:15     
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##  Fe_Mg_clay Fe_Mg_carbonate Mg_sulfate Phyllosilicates Chlorite Halite
+##  0:13       0:14            0:13       0:12            0:14     0:13  
+##  1: 3       1: 2            1: 3       1: 4            1: 2     1: 3  
+##                                                                       
+##                                                                       
+##                                                                       
+##                                                                       
+##                                                                       
+##  Organic_matter Hydrated_Ca_Sulfate Hydrated_Sulfates Hydrated_Mg_Fe_Sulfate
+##  0: 5           0:14                0:14              0:13                  
+##  1:11           1: 2                1: 2              1: 3                  
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##  Na_Perchlorate Amorphous_Silicate Hydrated_Carbonates Disordered_Silicates
+##  0:15           0:9                0:16                0:14                
+##  1: 1           1:7                                    1: 2                
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##  Hydrated_Iron_Oxide Sulfate+Organic_Matter Other_hydrated_phases Kaolinite
+##  0:15                0:11                   0:8                   0:13     
+##  1: 1                1: 5                   1:8                   1: 3     
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##  Chromite Ilmenite Zircon/Baddeleyite Spinels
+##  0:14     0:14     0:14               0:14   
+##  1: 2     1: 2     1: 2               1: 2   
+##                                              
+##                                              
+##                                              
+##                                              
+## 
+
# Create a matrix containing only the numeric measurements.  The remaining features are metadata about the sample. 
+lithology.matrix <- sapply(lithology.df[,6:40],as.numeric)-1            
+
+# Review the structure of our matrix
+str(lithology.matrix)
+
##  num [1:16, 1:35] 0 0 0 0 0 0 0 1 1 0 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:35] "feldspar" "plagioclase" "pyroxene" "olivine" ...
+
+
+

3.2 Data Set B: Load the +PIXL Data

+

The PIXL data provides summaries of the mineral compositions measured +at selected sample sites by the PIXL instrument. Note that here we scale +pixl.mat so features have mean 0 and standard deviation so results will +be different than in Assignment 1.

+
# Load the saved PIXL data with locations added
+pixl.df <- readRDS("/academics/MATP-4910-F24/DAR-Mars-F24/Data/samples_pixl_wide.Rds")
+
+# Convert to factors
+pixl.df[sapply(pixl.df, is.character)] <- lapply(pixl.df[sapply(pixl.df, is.character)], 
+                                       as.factor)
+
+# Review our dataframe
+summary(pixl.df)
+
##      sample           Na20            Mgo             Al203       
+##  Min.   : 1.00   Min.   :1.000   Min.   : 0.730   Min.   : 1.700  
+##  1st Qu.: 4.75   1st Qu.:1.853   1st Qu.: 2.533   1st Qu.: 2.220  
+##  Median : 8.50   Median :1.900   Median :12.800   Median : 3.710  
+##  Mean   : 8.50   Mean   :2.672   Mean   :11.682   Mean   : 5.072  
+##  3rd Qu.:12.25   3rd Qu.:4.500   3rd Qu.:19.100   3rd Qu.: 7.117  
+##  Max.   :16.00   Max.   :5.550   Max.   :22.700   Max.   :11.600  
+##                                                                   
+##       Si02            P205             S03               Cl       
+##  Min.   :22.60   Min.   :0.1000   Min.   : 0.780   Min.   :0.400  
+##  1st Qu.:31.22   1st Qu.:0.2350   1st Qu.: 1.495   1st Qu.:0.940  
+##  Median :38.85   Median :0.5250   Median : 2.600   Median :1.740  
+##  Mean   :38.55   Mean   :0.6512   Mean   : 5.562   Mean   :1.846  
+##  3rd Qu.:41.17   3rd Qu.:0.8400   3rd Qu.: 3.800   3rd Qu.:2.080  
+##  Max.   :57.10   Max.   :2.7600   Max.   :21.530   Max.   :4.500  
+##                                                                   
+##       K20              Cao             Ti02            Cr203      
+##  Min.   :0.0000   Min.   :1.500   Min.   :0.2000   Min.   :0.000  
+##  1st Qu.:0.1600   1st Qu.:2.655   1st Qu.:0.5900   1st Qu.:0.025  
+##  Median :0.2000   Median :3.120   Median :0.7000   Median :0.155  
+##  Mean   :0.5800   Mean   :3.688   Mean   :0.8194   Mean   :0.355  
+##  3rd Qu.:0.8275   3rd Qu.:4.310   3rd Qu.:0.9900   3rd Qu.:0.290  
+##  Max.   :1.9000   Max.   :7.770   Max.   :2.4900   Max.   :1.900  
+##                                                                   
+##       Mno             FeO-T               name             type  
+##  Min.   :0.1000   Min.   :13.24   Atsah     : 1   Igneous    :8  
+##  1st Qu.:0.2800   1st Qu.:16.71   Bearwallow: 1   N/A        :1  
+##  Median :0.4000   Median :23.86   Coulettes : 1   Sedimentary:7  
+##  Mean   :0.3812   Mean   :21.45   Hahonih   : 1                  
+##  3rd Qu.:0.4900   3rd Qu.:25.70   Hazeltop  : 1                  
+##  Max.   :0.6900   Max.   :30.05   Kukaklek  : 1                  
+##                                   (Other)   :10                  
+##          campaign    location          abrasion
+##  Crater Floor:9   01     : 1   Alfalfa     :2  
+##  Delta Front :7   02     : 1   Bellegrade  :2  
+##                   03     : 1   Berry Hollow:2  
+##                   04     : 1   Dourbes     :2  
+##                   05     : 1   Novarupta   :2  
+##                   06     : 1   Quartier    :2  
+##                   (Other):10   (Other)     :4
+
# Make the matrix of just mineral percentage measurements
+pixl.matrix <- pixl.df[,2:14] %>% scale()
+
+# Review the structure
+str(pixl.matrix)
+
##  num [1:16, 1:13] 1.928 1.338 -0.498 -0.538 1.225 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:13] "Na20" "Mgo" "Al203" "Si02" ...
+##  - attr(*, "scaled:center")= Named num [1:13] 2.672 11.682 5.072 38.554 0.651 ...
+##   ..- attr(*, "names")= chr [1:13] "Na20" "Mgo" "Al203" "Si02" ...
+##  - attr(*, "scaled:scale")= Named num [1:13] 1.492 7.957 3.75 11.026 0.694 ...
+##   ..- attr(*, "names")= chr [1:13] "Na20" "Mgo" "Al203" "Si02" ...
+
+
+

3.3 Data Set C: Load the +LIBS Data

+

The LIBS data provides summaries of the mineral compositions measured +at selected sample sites by the LIBS instrument, part of the +Perseverance SuperCam.

+
# Load the saved LIBS data with locations added
+libs.df <- readRDS("/academics/MATP-4910-F24/DAR-Mars-F24/Data/supercam_libs_moc_loc.Rds")
+
+#Drop  features that are not to be used in the analysis for this notebook
+libs.df <- libs.df %>% 
+  select(!(c(distance_mm,Tot.Em.,SiO2_stdev,TiO2_stdev,Al2O3_stdev,FeOT_stdev,
+             MgO_stdev,Na2O_stdev,CaO_stdev,K2O_stdev,Total)))
+
+# Convert the points to numeric
+libs.df$point <- as.numeric(libs.df$point)
+
+# Review what we have
+summary(libs.df)
+
##       sol              lat             lon           target         
+##  Min.   :  15.0   Min.   :18.43   Min.   :77.34   Length:1932       
+##  1st Qu.: 281.0   1st Qu.:18.44   1st Qu.:77.36   Class :character  
+##  Median : 557.0   Median :18.46   Median :77.40   Mode  :character  
+##  Mean   : 565.1   Mean   :18.46   Mean   :77.40                     
+##  3rd Qu.: 872.0   3rd Qu.:18.48   3rd Qu.:77.44                     
+##  Max.   :1019.0   Max.   :18.50   Max.   :77.45                     
+##      point             SiO2            TiO2            Al2O3       
+##  Min.   : 1.000   Min.   : 0.00   Min.   :0.0000   Min.   : 0.000  
+##  1st Qu.: 3.000   1st Qu.:42.04   1st Qu.:0.0300   1st Qu.: 3.080  
+##  Median : 5.000   Median :45.80   Median :0.3200   Median : 4.925  
+##  Mean   : 5.776   Mean   :43.47   Mean   :0.3719   Mean   : 6.246  
+##  3rd Qu.: 8.000   3rd Qu.:49.23   3rd Qu.:0.6400   3rd Qu.: 8.533  
+##  Max.   :28.000   Max.   :76.12   Max.   :2.4000   Max.   :38.350  
+##       FeOT            MgO             CaO              Na2O       
+##  Min.   : 0.29   Min.   : 0.29   Min.   : 0.080   Min.   :0.0000  
+##  1st Qu.:13.27   1st Qu.: 5.72   1st Qu.: 1.830   1st Qu.:0.9775  
+##  Median :20.21   Median :12.78   Median : 3.625   Median :1.5200  
+##  Mean   :20.07   Mean   :16.47   Mean   : 4.726   Mean   :1.7600  
+##  3rd Qu.:25.45   3rd Qu.:27.83   3rd Qu.: 4.622   3rd Qu.:2.4000  
+##  Max.   :82.68   Max.   :45.21   Max.   :52.130   Max.   :7.5200  
+##       K2O         
+##  Min.   : 0.0000  
+##  1st Qu.: 0.0000  
+##  Median : 0.3000  
+##  Mean   : 0.5909  
+##  3rd Qu.: 0.7800  
+##  Max.   :34.8700
+
# Make the a matrix contain only the libs measurements for each mineral
+libs.matrix <- as.matrix(libs.df[,6:13]) 
+
+# Check to see scaling
+str(libs.matrix)
+
##  num [1:1932, 1:8] 49.7 55.8 61.2 51 48 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:8] "SiO2" "TiO2" "Al2O3" "FeOT" ...
+
+
+

3.4 Dataset D: Load the +SHERLOC Data

+

The SHERLOC data you will be using for this lab is the result of +scientists’ interpretations of extensive spectral analysis of abrasion +samples provided by the SHERLOC instrument.

+

NOTE: This dataset presents minerals as rows and +sample sites as columns. You’ll probably want to rotate the dataset for +easier analysis….

+
# Read in data as provided.  
+sherloc_abrasion_raw <- readRDS("/academics/MATP-4910-F24/DAR-Mars-F24/Data/abrasions_sherloc_samples.Rds")
+
+# Clean up data types
+sherloc_abrasion_raw$Mineral<-as.factor(sherloc_abrasion_raw$Mineral)
+sherloc_abrasion_raw[sapply(sherloc_abrasion_raw, is.character)] <- lapply(sherloc_abrasion_raw[sapply(sherloc_abrasion_raw, is.character)], 
+                                       as.numeric)
+# Transform NA's to 0
+sherloc_abrasion_raw <- sherloc_abrasion_raw %>% replace(is.na(.), 0)
+
+# Reformat data so that rows are "abrasions" and columns list the presence of minerals. 
+# Do this by "pivoting" to a long format, and then back to the desired wide format.  
+
+sherloc_long <- sherloc_abrasion_raw %>%
+  pivot_longer(!Mineral, names_to = "Name", values_to = "Presence")
+
+# Make abrasion a factor 
+sherloc_long$Name <- as.factor(sherloc_long$Name)
+
+# Make it a matrix
+sherloc.matrix <- sherloc_long %>%
+  pivot_wider(names_from = Mineral, values_from = Presence)
+
+# Get sample information from PIXL and add to measurements -- assumes order is the same
+
+sherloc.df <- cbind(pixl.df[,c("sample","type","campaign","abrasion")],sherloc.matrix)
+
+# Review what we have
+summary(sherloc.df)
+
##      sample               type           campaign         abrasion
+##  Min.   : 1.00   Igneous    :8   Crater Floor:9   Alfalfa     :2  
+##  1st Qu.: 4.75   N/A        :1   Delta Front :7   Bellegrade  :2  
+##  Median : 8.50   Sedimentary:7                    Berry Hollow:2  
+##  Mean   : 8.50                                    Dourbes     :2  
+##  3rd Qu.:12.25                                    Novarupta   :2  
+##  Max.   :16.00                                    Quartier    :2  
+##                                                   (Other)     :4  
+##          Name     Plagioclase        Sulfate         Ca-sulfate    
+##  Atsah     : 1   Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
+##  Bearwallow: 1   1st Qu.:0.0000   1st Qu.:0.1875   1st Qu.:0.0000  
+##  Coulettes : 1   Median :0.0000   Median :1.0000   Median :0.0000  
+##  Hahonih   : 1   Mean   :0.1875   Mean   :0.6562   Mean   :0.3438  
+##  Hazeltop  : 1   3rd Qu.:0.0000   3rd Qu.:1.0000   3rd Qu.:1.0000  
+##  Kukaklek  : 1   Max.   :1.0000   Max.   :1.0000   Max.   :1.0000  
+##  (Other)   :10                                                     
+##  Hydrated Ca-sulfate   Mg-sulfate     Hydrated Sulfates Hydrated Mg-Fe sulfate
+##  Min.   :0.000       Min.   :0.0000   Min.   :0.000     Min.   :0.0000        
+##  1st Qu.:0.000       1st Qu.:0.0000   1st Qu.:0.000     1st Qu.:0.0000        
+##  Median :0.000       Median :0.0000   Median :0.000     Median :0.0000        
+##  Mean   :0.125       Mean   :0.1875   Mean   :0.125     Mean   :0.1875        
+##  3rd Qu.:0.000       3rd Qu.:0.0000   3rd Qu.:0.000     3rd Qu.:0.0000        
+##  Max.   :1.000       Max.   :1.0000   Max.   :1.000     Max.   :1.0000        
+##                                                                               
+##   Perchlorates    Na-perchlorate    Amorphous Silicate   Phosphate     
+##  Min.   :0.0000   Min.   :0.00000   Min.   :0.0000     Min.   :0.0000  
+##  1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.0000     1st Qu.:0.0000  
+##  Median :0.0000   Median :0.00000   Median :0.0000     Median :0.0000  
+##  Mean   :0.0625   Mean   :0.03125   Mean   :0.1406     Mean   :0.2031  
+##  3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.2500     3rd Qu.:0.3125  
+##  Max.   :1.0000   Max.   :0.50000   Max.   :0.5000     Max.   :1.0000  
+##                                                                        
+##     Pyroxene         Olivine         Carbonate      Fe-Mg carbonate
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.0000   Min.   :0.000  
+##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.4375   1st Qu.:0.000  
+##  Median :1.0000   Median :0.6250   Median :1.0000   Median :0.000  
+##  Mean   :0.6875   Mean   :0.5312   Mean   :0.7344   Mean   :0.125  
+##  3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:0.000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :1.0000   Max.   :1.000  
+##                                                                    
+##  Hydrated Carbonates Disordered Silicates    Feldspar         Quartz       
+##  Min.   :0           Min.   :0.000        Min.   :0.000   Min.   :0.00000  
+##  1st Qu.:0           1st Qu.:0.000        1st Qu.:0.000   1st Qu.:0.00000  
+##  Median :0           Median :0.000        Median :0.000   Median :0.00000  
+##  Mean   :0           Mean   :0.125        Mean   :0.125   Mean   :0.03125  
+##  3rd Qu.:0           3rd Qu.:0.000        3rd Qu.:0.000   3rd Qu.:0.00000  
+##  Max.   :0           Max.   :1.000        Max.   :1.000   Max.   :0.25000  
+##                                                                            
+##     Apatite        FeTi oxides         Halite          Iron oxide    
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.00000   Min.   :0.0000  
+##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.0000  
+##  Median :0.0000   Median :0.0000   Median :0.00000   Median :0.0000  
+##  Mean   :0.1406   Mean   :0.1406   Mean   :0.04688   Mean   :0.2812  
+##  3rd Qu.:0.0000   3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.5000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :0.25000   Max.   :1.0000  
+##                                                                      
+##  Hydrated Iron oxide Organic matter   Sulfate+Organic matter
+##  Min.   :0.00000     Min.   :0.0000   Min.   :0.0000        
+##  1st Qu.:0.00000     1st Qu.:0.0000   1st Qu.:0.0000        
+##  Median :0.00000     Median :1.0000   Median :0.0000        
+##  Mean   :0.01562     Mean   :0.5938   Mean   :0.2188        
+##  3rd Qu.:0.00000     3rd Qu.:1.0000   3rd Qu.:0.2500        
+##  Max.   :0.25000     Max.   :1.0000   Max.   :1.0000        
+##                                                             
+##  Other hydrated phases Phyllosilicates      Chlorite     
+##  Min.   :0.0000        Min.   :0.00000   Min.   :0.0000  
+##  1st Qu.:0.0000        1st Qu.:0.00000   1st Qu.:0.0000  
+##  Median :0.2500        Median :0.00000   Median :0.0000  
+##  Mean   :0.4375        Mean   :0.09375   Mean   :0.0625  
+##  3rd Qu.:1.0000        3rd Qu.:0.06250   3rd Qu.:0.0000  
+##  Max.   :1.0000        Max.   :0.50000   Max.   :0.5000  
+##                                                          
+##  Kaolinite (hydrous Al-clay)    Chromite        Ilmenite     Zircon/Baddeleyite
+##  Min.   :0.0000              Min.   :0.000   Min.   :0.000   Min.   :0.000     
+##  1st Qu.:0.0000              1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0.000     
+##  Median :0.0000              Median :0.000   Median :0.000   Median :0.000     
+##  Mean   :0.1875              Mean   :0.125   Mean   :0.125   Mean   :0.125     
+##  3rd Qu.:0.0000              3rd Qu.:0.000   3rd Qu.:0.000   3rd Qu.:0.000     
+##  Max.   :1.0000              Max.   :1.000   Max.   :1.000   Max.   :1.000     
+##                                                                                
+##  Fe-Mg-clay minerals    Spinels      
+##  Min.   :0.0000      Min.   :0.0000  
+##  1st Qu.:0.0000      1st Qu.:0.0000  
+##  Median :0.0000      Median :0.0000  
+##  Mean   :0.1875      Mean   :0.0625  
+##  3rd Qu.:0.0000      3rd Qu.:0.0000  
+##  Max.   :1.0000      Max.   :0.5000  
+## 
+
# Measurements are everything except first column
+sherloc.matrix<-as.matrix(sherloc.matrix[,-1])
+
+# Sherlock measurement matrix
+# Review the structure 
+str(sherloc.matrix)
+
##  num [1:16, 1:35] 1 1 1 0 0 0 0 0 0 0 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:35] "Plagioclase" "Sulfate" "Ca-sulfate" "Hydrated Ca-sulfate" ...
+
+
+

3.5 Data Set E: PIXL + +Sherloc

+
# Combine PIXL and SHERLOC dataframes 
+pixl_sherloc.df <- cbind(pixl.df,sherloc.df )
+
+# Review what we have
+summary(pixl_sherloc.df)
+
##      sample           Na20            Mgo             Al203       
+##  Min.   : 1.00   Min.   :1.000   Min.   : 0.730   Min.   : 1.700  
+##  1st Qu.: 4.75   1st Qu.:1.853   1st Qu.: 2.533   1st Qu.: 2.220  
+##  Median : 8.50   Median :1.900   Median :12.800   Median : 3.710  
+##  Mean   : 8.50   Mean   :2.672   Mean   :11.682   Mean   : 5.072  
+##  3rd Qu.:12.25   3rd Qu.:4.500   3rd Qu.:19.100   3rd Qu.: 7.117  
+##  Max.   :16.00   Max.   :5.550   Max.   :22.700   Max.   :11.600  
+##                                                                   
+##       Si02            P205             S03               Cl       
+##  Min.   :22.60   Min.   :0.1000   Min.   : 0.780   Min.   :0.400  
+##  1st Qu.:31.22   1st Qu.:0.2350   1st Qu.: 1.495   1st Qu.:0.940  
+##  Median :38.85   Median :0.5250   Median : 2.600   Median :1.740  
+##  Mean   :38.55   Mean   :0.6512   Mean   : 5.562   Mean   :1.846  
+##  3rd Qu.:41.17   3rd Qu.:0.8400   3rd Qu.: 3.800   3rd Qu.:2.080  
+##  Max.   :57.10   Max.   :2.7600   Max.   :21.530   Max.   :4.500  
+##                                                                   
+##       K20              Cao             Ti02            Cr203      
+##  Min.   :0.0000   Min.   :1.500   Min.   :0.2000   Min.   :0.000  
+##  1st Qu.:0.1600   1st Qu.:2.655   1st Qu.:0.5900   1st Qu.:0.025  
+##  Median :0.2000   Median :3.120   Median :0.7000   Median :0.155  
+##  Mean   :0.5800   Mean   :3.688   Mean   :0.8194   Mean   :0.355  
+##  3rd Qu.:0.8275   3rd Qu.:4.310   3rd Qu.:0.9900   3rd Qu.:0.290  
+##  Max.   :1.9000   Max.   :7.770   Max.   :2.4900   Max.   :1.900  
+##                                                                   
+##       Mno             FeO-T               name             type  
+##  Min.   :0.1000   Min.   :13.24   Atsah     : 1   Igneous    :8  
+##  1st Qu.:0.2800   1st Qu.:16.71   Bearwallow: 1   N/A        :1  
+##  Median :0.4000   Median :23.86   Coulettes : 1   Sedimentary:7  
+##  Mean   :0.3812   Mean   :21.45   Hahonih   : 1                  
+##  3rd Qu.:0.4900   3rd Qu.:25.70   Hazeltop  : 1                  
+##  Max.   :0.6900   Max.   :30.05   Kukaklek  : 1                  
+##                                   (Other)   :10                  
+##          campaign    location          abrasion     sample               type  
+##  Crater Floor:9   01     : 1   Alfalfa     :2   Min.   : 1.00   Igneous    :8  
+##  Delta Front :7   02     : 1   Bellegrade  :2   1st Qu.: 4.75   N/A        :1  
+##                   03     : 1   Berry Hollow:2   Median : 8.50   Sedimentary:7  
+##                   04     : 1   Dourbes     :2   Mean   : 8.50                  
+##                   05     : 1   Novarupta   :2   3rd Qu.:12.25                  
+##                   06     : 1   Quartier    :2   Max.   :16.00                  
+##                   (Other):10   (Other)     :4                                  
+##          campaign         abrasion         Name     Plagioclase    
+##  Crater Floor:9   Alfalfa     :2   Atsah     : 1   Min.   :0.0000  
+##  Delta Front :7   Bellegrade  :2   Bearwallow: 1   1st Qu.:0.0000  
+##                   Berry Hollow:2   Coulettes : 1   Median :0.0000  
+##                   Dourbes     :2   Hahonih   : 1   Mean   :0.1875  
+##                   Novarupta   :2   Hazeltop  : 1   3rd Qu.:0.0000  
+##                   Quartier    :2   Kukaklek  : 1   Max.   :1.0000  
+##                   (Other)     :4   (Other)   :10                   
+##     Sulfate         Ca-sulfate     Hydrated Ca-sulfate   Mg-sulfate    
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.000       Min.   :0.0000  
+##  1st Qu.:0.1875   1st Qu.:0.0000   1st Qu.:0.000       1st Qu.:0.0000  
+##  Median :1.0000   Median :0.0000   Median :0.000       Median :0.0000  
+##  Mean   :0.6562   Mean   :0.3438   Mean   :0.125       Mean   :0.1875  
+##  3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:0.000       3rd Qu.:0.0000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :1.000       Max.   :1.0000  
+##                                                                        
+##  Hydrated Sulfates Hydrated Mg-Fe sulfate  Perchlorates    Na-perchlorate   
+##  Min.   :0.000     Min.   :0.0000         Min.   :0.0000   Min.   :0.00000  
+##  1st Qu.:0.000     1st Qu.:0.0000         1st Qu.:0.0000   1st Qu.:0.00000  
+##  Median :0.000     Median :0.0000         Median :0.0000   Median :0.00000  
+##  Mean   :0.125     Mean   :0.1875         Mean   :0.0625   Mean   :0.03125  
+##  3rd Qu.:0.000     3rd Qu.:0.0000         3rd Qu.:0.0000   3rd Qu.:0.00000  
+##  Max.   :1.000     Max.   :1.0000         Max.   :1.0000   Max.   :0.50000  
+##                                                                             
+##  Amorphous Silicate   Phosphate         Pyroxene         Olivine      
+##  Min.   :0.0000     Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
+##  1st Qu.:0.0000     1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.0000  
+##  Median :0.0000     Median :0.0000   Median :1.0000   Median :0.6250  
+##  Mean   :0.1406     Mean   :0.2031   Mean   :0.6875   Mean   :0.5312  
+##  3rd Qu.:0.2500     3rd Qu.:0.3125   3rd Qu.:1.0000   3rd Qu.:1.0000  
+##  Max.   :0.5000     Max.   :1.0000   Max.   :1.0000   Max.   :1.0000  
+##                                                                       
+##    Carbonate      Fe-Mg carbonate Hydrated Carbonates Disordered Silicates
+##  Min.   :0.0000   Min.   :0.000   Min.   :0           Min.   :0.000       
+##  1st Qu.:0.4375   1st Qu.:0.000   1st Qu.:0           1st Qu.:0.000       
+##  Median :1.0000   Median :0.000   Median :0           Median :0.000       
+##  Mean   :0.7344   Mean   :0.125   Mean   :0           Mean   :0.125       
+##  3rd Qu.:1.0000   3rd Qu.:0.000   3rd Qu.:0           3rd Qu.:0.000       
+##  Max.   :1.0000   Max.   :1.000   Max.   :0           Max.   :1.000       
+##                                                                           
+##     Feldspar         Quartz           Apatite        FeTi oxides    
+##  Min.   :0.000   Min.   :0.00000   Min.   :0.0000   Min.   :0.0000  
+##  1st Qu.:0.000   1st Qu.:0.00000   1st Qu.:0.0000   1st Qu.:0.0000  
+##  Median :0.000   Median :0.00000   Median :0.0000   Median :0.0000  
+##  Mean   :0.125   Mean   :0.03125   Mean   :0.1406   Mean   :0.1406  
+##  3rd Qu.:0.000   3rd Qu.:0.00000   3rd Qu.:0.0000   3rd Qu.:0.0000  
+##  Max.   :1.000   Max.   :0.25000   Max.   :1.0000   Max.   :1.0000  
+##                                                                     
+##      Halite          Iron oxide     Hydrated Iron oxide Organic matter  
+##  Min.   :0.00000   Min.   :0.0000   Min.   :0.00000     Min.   :0.0000  
+##  1st Qu.:0.00000   1st Qu.:0.0000   1st Qu.:0.00000     1st Qu.:0.0000  
+##  Median :0.00000   Median :0.0000   Median :0.00000     Median :1.0000  
+##  Mean   :0.04688   Mean   :0.2812   Mean   :0.01562     Mean   :0.5938  
+##  3rd Qu.:0.00000   3rd Qu.:0.5000   3rd Qu.:0.00000     3rd Qu.:1.0000  
+##  Max.   :0.25000   Max.   :1.0000   Max.   :0.25000     Max.   :1.0000  
+##                                                                         
+##  Sulfate+Organic matter Other hydrated phases Phyllosilicates  
+##  Min.   :0.0000         Min.   :0.0000        Min.   :0.00000  
+##  1st Qu.:0.0000         1st Qu.:0.0000        1st Qu.:0.00000  
+##  Median :0.0000         Median :0.2500        Median :0.00000  
+##  Mean   :0.2188         Mean   :0.4375        Mean   :0.09375  
+##  3rd Qu.:0.2500         3rd Qu.:1.0000        3rd Qu.:0.06250  
+##  Max.   :1.0000         Max.   :1.0000        Max.   :0.50000  
+##                                                                
+##     Chlorite      Kaolinite (hydrous Al-clay)    Chromite        Ilmenite    
+##  Min.   :0.0000   Min.   :0.0000              Min.   :0.000   Min.   :0.000  
+##  1st Qu.:0.0000   1st Qu.:0.0000              1st Qu.:0.000   1st Qu.:0.000  
+##  Median :0.0000   Median :0.0000              Median :0.000   Median :0.000  
+##  Mean   :0.0625   Mean   :0.1875              Mean   :0.125   Mean   :0.125  
+##  3rd Qu.:0.0000   3rd Qu.:0.0000              3rd Qu.:0.000   3rd Qu.:0.000  
+##  Max.   :0.5000   Max.   :1.0000              Max.   :1.000   Max.   :1.000  
+##                                                                              
+##  Zircon/Baddeleyite Fe-Mg-clay minerals    Spinels      
+##  Min.   :0.000      Min.   :0.0000      Min.   :0.0000  
+##  1st Qu.:0.000      1st Qu.:0.0000      1st Qu.:0.0000  
+##  Median :0.000      Median :0.0000      Median :0.0000  
+##  Mean   :0.125      Mean   :0.1875      Mean   :0.0625  
+##  3rd Qu.:0.000      3rd Qu.:0.0000      3rd Qu.:0.0000  
+##  Max.   :1.000      Max.   :1.0000      Max.   :0.5000  
+## 
+
# Combine PIXL and SHERLOC matrices
+pixl_sherloc.matrix<-cbind(pixl.matrix,sherloc.matrix)
+
+# Review the structure of our matrix
+str(pixl_sherloc.matrix)
+
##  num [1:16, 1:48] 1.928 1.338 -0.498 -0.538 1.225 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:48] "Na20" "Mgo" "Al203" "Si02" ...
+
+
+

3.6 Data Set F: PIXL + +Lithography

+

Create data and matrix from prior datasets

+
# Combine our PIXL and Lithology dataframes
+pixl_lithology.df <- cbind(pixl.df,lithology.df )
+
+# Review what we have
+summary(pixl_lithology.df)
+
##      sample           Na20            Mgo             Al203       
+##  Min.   : 1.00   Min.   :1.000   Min.   : 0.730   Min.   : 1.700  
+##  1st Qu.: 4.75   1st Qu.:1.853   1st Qu.: 2.533   1st Qu.: 2.220  
+##  Median : 8.50   Median :1.900   Median :12.800   Median : 3.710  
+##  Mean   : 8.50   Mean   :2.672   Mean   :11.682   Mean   : 5.072  
+##  3rd Qu.:12.25   3rd Qu.:4.500   3rd Qu.:19.100   3rd Qu.: 7.117  
+##  Max.   :16.00   Max.   :5.550   Max.   :22.700   Max.   :11.600  
+##                                                                   
+##       Si02            P205             S03               Cl       
+##  Min.   :22.60   Min.   :0.1000   Min.   : 0.780   Min.   :0.400  
+##  1st Qu.:31.22   1st Qu.:0.2350   1st Qu.: 1.495   1st Qu.:0.940  
+##  Median :38.85   Median :0.5250   Median : 2.600   Median :1.740  
+##  Mean   :38.55   Mean   :0.6512   Mean   : 5.562   Mean   :1.846  
+##  3rd Qu.:41.17   3rd Qu.:0.8400   3rd Qu.: 3.800   3rd Qu.:2.080  
+##  Max.   :57.10   Max.   :2.7600   Max.   :21.530   Max.   :4.500  
+##                                                                   
+##       K20              Cao             Ti02            Cr203      
+##  Min.   :0.0000   Min.   :1.500   Min.   :0.2000   Min.   :0.000  
+##  1st Qu.:0.1600   1st Qu.:2.655   1st Qu.:0.5900   1st Qu.:0.025  
+##  Median :0.2000   Median :3.120   Median :0.7000   Median :0.155  
+##  Mean   :0.5800   Mean   :3.688   Mean   :0.8194   Mean   :0.355  
+##  3rd Qu.:0.8275   3rd Qu.:4.310   3rd Qu.:0.9900   3rd Qu.:0.290  
+##  Max.   :1.9000   Max.   :7.770   Max.   :2.4900   Max.   :1.900  
+##                                                                   
+##       Mno             FeO-T               name             type  
+##  Min.   :0.1000   Min.   :13.24   Atsah     : 1   Igneous    :8  
+##  1st Qu.:0.2800   1st Qu.:16.71   Bearwallow: 1   N/A        :1  
+##  Median :0.4000   Median :23.86   Coulettes : 1   Sedimentary:7  
+##  Mean   :0.3812   Mean   :21.45   Hahonih   : 1                  
+##  3rd Qu.:0.4900   3rd Qu.:25.70   Hazeltop  : 1                  
+##  Max.   :0.6900   Max.   :30.05   Kukaklek  : 1                  
+##                                   (Other)   :10                  
+##          campaign    location          abrasion     sample              name   
+##  Crater Floor:9   01     : 1   Alfalfa     :2   Min.   : 1.00   Atsah     : 1  
+##  Delta Front :7   02     : 1   Bellegrade  :2   1st Qu.: 4.75   Bearwallow: 1  
+##                   03     : 1   Berry Hollow:2   Median : 8.50   Coulettes : 1  
+##                   04     : 1   Dourbes     :2   Mean   : 8.50   Hahonih   : 1  
+##                   05     : 1   Novarupta   :2   3rd Qu.:12.25   Hazeltop  : 1  
+##                   06     : 1   Quartier    :2   Max.   :16.00   Kukaklek  : 1  
+##                   (Other):10   (Other)     :4                   (Other)   :10  
+##        SampleType         campaign         abrasion feldspar plagioclase
+##  atmospheric: 1   Crater Floor:9   Alfalfa     :2   0:14     0:13       
+##  regolith   : 0   Delta Front :7   Bellegarde  :2   1: 2     1: 3       
+##  rock core  :15   Margin Unit :0   Berry Hollow:2                       
+##                                    Dourbes     :2                       
+##                                    Novarupta   :2                       
+##                                    Quartier    :2                       
+##                                    (Other)     :4                       
+##  pyroxene olivine quartz apatite FeTi_Oxides Iron_Oxide Sulfate Perchlorates
+##  0: 5     0: 6    0:14   0:13    0:13        0:9        0: 4    0:15        
+##  1:11     1:10    1: 2   1: 3    1: 3        1:7        1:12    1: 1        
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##  Phosphate Ca_Sulfate Carbonate Fe_Mg_clay Fe_Mg_carbonate Mg_sulfate
+##  0:11      0:10       0: 1      0:13       0:14            0:13      
+##  1: 5      1: 6       1:15      1: 3       1: 2            1: 3      
+##                                                                      
+##                                                                      
+##                                                                      
+##                                                                      
+##                                                                      
+##  Phyllosilicates Chlorite Halite Organic_matter Hydrated_Ca_Sulfate
+##  0:12            0:14     0:13   0: 5           0:14               
+##  1: 4            1: 2     1: 3   1:11           1: 2               
+##                                                                    
+##                                                                    
+##                                                                    
+##                                                                    
+##                                                                    
+##  Hydrated_Sulfates Hydrated_Mg_Fe_Sulfate Na_Perchlorate Amorphous_Silicate
+##  0:14              0:13                   0:15           0:9               
+##  1: 2              1: 3                   1: 1           1:7               
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##  Hydrated_Carbonates Disordered_Silicates Hydrated_Iron_Oxide
+##  0:16                0:14                 0:15               
+##                      1: 2                 1: 1               
+##                                                              
+##                                                              
+##                                                              
+##                                                              
+##                                                              
+##  Sulfate+Organic_Matter Other_hydrated_phases Kaolinite Chromite Ilmenite
+##  0:11                   0:8                   0:13      0:14     0:14    
+##  1: 5                   1:8                   1: 3      1: 2     1: 2    
+##                                                                          
+##                                                                          
+##                                                                          
+##                                                                          
+##                                                                          
+##  Zircon/Baddeleyite Spinels
+##  0:14               0:14   
+##  1: 2               1: 2   
+##                            
+##                            
+##                            
+##                            
+## 
+
# Combine PIXL and Lithology matrices
+pixl_lithology.matrix<-cbind(pixl.matrix,lithology.matrix)
+
+# Review the structure
+str(pixl_lithology.matrix)
+
##  num [1:16, 1:48] 1.928 1.338 -0.498 -0.538 1.225 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:48] "Na20" "Mgo" "Al203" "Si02" ...
+
+
+

3.7 Data Set G: Sherloc + +Lithology

+

Create Data and matrix from prior datasets by taking on appropriate +combinations.

+
# Combine the Lithology and SHERLOC dataframes
+sherloc_lithology.df <- cbind(sherloc.df,lithology.df )
+
+# Review what we have
+summary(sherloc_lithology.df)
+
##      sample               type           campaign         abrasion
+##  Min.   : 1.00   Igneous    :8   Crater Floor:9   Alfalfa     :2  
+##  1st Qu.: 4.75   N/A        :1   Delta Front :7   Bellegrade  :2  
+##  Median : 8.50   Sedimentary:7                    Berry Hollow:2  
+##  Mean   : 8.50                                    Dourbes     :2  
+##  3rd Qu.:12.25                                    Novarupta   :2  
+##  Max.   :16.00                                    Quartier    :2  
+##                                                   (Other)     :4  
+##          Name     Plagioclase        Sulfate         Ca-sulfate    
+##  Atsah     : 1   Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
+##  Bearwallow: 1   1st Qu.:0.0000   1st Qu.:0.1875   1st Qu.:0.0000  
+##  Coulettes : 1   Median :0.0000   Median :1.0000   Median :0.0000  
+##  Hahonih   : 1   Mean   :0.1875   Mean   :0.6562   Mean   :0.3438  
+##  Hazeltop  : 1   3rd Qu.:0.0000   3rd Qu.:1.0000   3rd Qu.:1.0000  
+##  Kukaklek  : 1   Max.   :1.0000   Max.   :1.0000   Max.   :1.0000  
+##  (Other)   :10                                                     
+##  Hydrated Ca-sulfate   Mg-sulfate     Hydrated Sulfates Hydrated Mg-Fe sulfate
+##  Min.   :0.000       Min.   :0.0000   Min.   :0.000     Min.   :0.0000        
+##  1st Qu.:0.000       1st Qu.:0.0000   1st Qu.:0.000     1st Qu.:0.0000        
+##  Median :0.000       Median :0.0000   Median :0.000     Median :0.0000        
+##  Mean   :0.125       Mean   :0.1875   Mean   :0.125     Mean   :0.1875        
+##  3rd Qu.:0.000       3rd Qu.:0.0000   3rd Qu.:0.000     3rd Qu.:0.0000        
+##  Max.   :1.000       Max.   :1.0000   Max.   :1.000     Max.   :1.0000        
+##                                                                               
+##   Perchlorates    Na-perchlorate    Amorphous Silicate   Phosphate     
+##  Min.   :0.0000   Min.   :0.00000   Min.   :0.0000     Min.   :0.0000  
+##  1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.0000     1st Qu.:0.0000  
+##  Median :0.0000   Median :0.00000   Median :0.0000     Median :0.0000  
+##  Mean   :0.0625   Mean   :0.03125   Mean   :0.1406     Mean   :0.2031  
+##  3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.2500     3rd Qu.:0.3125  
+##  Max.   :1.0000   Max.   :0.50000   Max.   :0.5000     Max.   :1.0000  
+##                                                                        
+##     Pyroxene         Olivine         Carbonate      Fe-Mg carbonate
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.0000   Min.   :0.000  
+##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.4375   1st Qu.:0.000  
+##  Median :1.0000   Median :0.6250   Median :1.0000   Median :0.000  
+##  Mean   :0.6875   Mean   :0.5312   Mean   :0.7344   Mean   :0.125  
+##  3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:0.000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :1.0000   Max.   :1.000  
+##                                                                    
+##  Hydrated Carbonates Disordered Silicates    Feldspar         Quartz       
+##  Min.   :0           Min.   :0.000        Min.   :0.000   Min.   :0.00000  
+##  1st Qu.:0           1st Qu.:0.000        1st Qu.:0.000   1st Qu.:0.00000  
+##  Median :0           Median :0.000        Median :0.000   Median :0.00000  
+##  Mean   :0           Mean   :0.125        Mean   :0.125   Mean   :0.03125  
+##  3rd Qu.:0           3rd Qu.:0.000        3rd Qu.:0.000   3rd Qu.:0.00000  
+##  Max.   :0           Max.   :1.000        Max.   :1.000   Max.   :0.25000  
+##                                                                            
+##     Apatite        FeTi oxides         Halite          Iron oxide    
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.00000   Min.   :0.0000  
+##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.0000  
+##  Median :0.0000   Median :0.0000   Median :0.00000   Median :0.0000  
+##  Mean   :0.1406   Mean   :0.1406   Mean   :0.04688   Mean   :0.2812  
+##  3rd Qu.:0.0000   3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.5000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :0.25000   Max.   :1.0000  
+##                                                                      
+##  Hydrated Iron oxide Organic matter   Sulfate+Organic matter
+##  Min.   :0.00000     Min.   :0.0000   Min.   :0.0000        
+##  1st Qu.:0.00000     1st Qu.:0.0000   1st Qu.:0.0000        
+##  Median :0.00000     Median :1.0000   Median :0.0000        
+##  Mean   :0.01562     Mean   :0.5938   Mean   :0.2188        
+##  3rd Qu.:0.00000     3rd Qu.:1.0000   3rd Qu.:0.2500        
+##  Max.   :0.25000     Max.   :1.0000   Max.   :1.0000        
+##                                                             
+##  Other hydrated phases Phyllosilicates      Chlorite     
+##  Min.   :0.0000        Min.   :0.00000   Min.   :0.0000  
+##  1st Qu.:0.0000        1st Qu.:0.00000   1st Qu.:0.0000  
+##  Median :0.2500        Median :0.00000   Median :0.0000  
+##  Mean   :0.4375        Mean   :0.09375   Mean   :0.0625  
+##  3rd Qu.:1.0000        3rd Qu.:0.06250   3rd Qu.:0.0000  
+##  Max.   :1.0000        Max.   :0.50000   Max.   :0.5000  
+##                                                          
+##  Kaolinite (hydrous Al-clay)    Chromite        Ilmenite     Zircon/Baddeleyite
+##  Min.   :0.0000              Min.   :0.000   Min.   :0.000   Min.   :0.000     
+##  1st Qu.:0.0000              1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0.000     
+##  Median :0.0000              Median :0.000   Median :0.000   Median :0.000     
+##  Mean   :0.1875              Mean   :0.125   Mean   :0.125   Mean   :0.125     
+##  3rd Qu.:0.0000              3rd Qu.:0.000   3rd Qu.:0.000   3rd Qu.:0.000     
+##  Max.   :1.0000              Max.   :1.000   Max.   :1.000   Max.   :1.000     
+##                                                                                
+##  Fe-Mg-clay minerals    Spinels           sample              name   
+##  Min.   :0.0000      Min.   :0.0000   Min.   : 1.00   Atsah     : 1  
+##  1st Qu.:0.0000      1st Qu.:0.0000   1st Qu.: 4.75   Bearwallow: 1  
+##  Median :0.0000      Median :0.0000   Median : 8.50   Coulettes : 1  
+##  Mean   :0.1875      Mean   :0.0625   Mean   : 8.50   Hahonih   : 1  
+##  3rd Qu.:0.0000      3rd Qu.:0.0000   3rd Qu.:12.25   Hazeltop  : 1  
+##  Max.   :1.0000      Max.   :0.5000   Max.   :16.00   Kukaklek  : 1  
+##                                                       (Other)   :10  
+##        SampleType         campaign         abrasion feldspar plagioclase
+##  atmospheric: 1   Crater Floor:9   Alfalfa     :2   0:14     0:13       
+##  regolith   : 0   Delta Front :7   Bellegarde  :2   1: 2     1: 3       
+##  rock core  :15   Margin Unit :0   Berry Hollow:2                       
+##                                    Dourbes     :2                       
+##                                    Novarupta   :2                       
+##                                    Quartier    :2                       
+##                                    (Other)     :4                       
+##  pyroxene olivine quartz apatite FeTi_Oxides Iron_Oxide Sulfate Perchlorates
+##  0: 5     0: 6    0:14   0:13    0:13        0:9        0: 4    0:15        
+##  1:11     1:10    1: 2   1: 3    1: 3        1:7        1:12    1: 1        
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##  Phosphate Ca_Sulfate Carbonate Fe_Mg_clay Fe_Mg_carbonate Mg_sulfate
+##  0:11      0:10       0: 1      0:13       0:14            0:13      
+##  1: 5      1: 6       1:15      1: 3       1: 2            1: 3      
+##                                                                      
+##                                                                      
+##                                                                      
+##                                                                      
+##                                                                      
+##  Phyllosilicates Chlorite Halite Organic_matter Hydrated_Ca_Sulfate
+##  0:12            0:14     0:13   0: 5           0:14               
+##  1: 4            1: 2     1: 3   1:11           1: 2               
+##                                                                    
+##                                                                    
+##                                                                    
+##                                                                    
+##                                                                    
+##  Hydrated_Sulfates Hydrated_Mg_Fe_Sulfate Na_Perchlorate Amorphous_Silicate
+##  0:14              0:13                   0:15           0:9               
+##  1: 2              1: 3                   1: 1           1:7               
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##  Hydrated_Carbonates Disordered_Silicates Hydrated_Iron_Oxide
+##  0:16                0:14                 0:15               
+##                      1: 2                 1: 1               
+##                                                              
+##                                                              
+##                                                              
+##                                                              
+##                                                              
+##  Sulfate+Organic_Matter Other_hydrated_phases Kaolinite Chromite Ilmenite
+##  0:11                   0:8                   0:13      0:14     0:14    
+##  1: 5                   1:8                   1: 3      1: 2     1: 2    
+##                                                                          
+##                                                                          
+##                                                                          
+##                                                                          
+##                                                                          
+##  Zircon/Baddeleyite Spinels
+##  0:14               0:14   
+##  1: 2               1: 2   
+##                            
+##                            
+##                            
+##                            
+## 
+
# Combine the Lithology and SHERLOC matrices
+sherloc_lithology.matrix<-cbind(sherloc.matrix,lithology.matrix)
+
+# Review the resulting matrix
+str(sherloc_lithology.matrix)
+
##  num [1:16, 1:70] 1 1 1 0 0 0 0 0 0 0 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:70] "Plagioclase" "Sulfate" "Ca-sulfate" "Hydrated Ca-sulfate" ...
+
+
+

3.8 Data Set H: Sherloc + +Lithology + PIXL

+

Create data frame and matrix from prior datasets by making on +appropriate combinations.

+
# Combine the Lithology and SHERLOC dataframes
+sherloc_lithology_pixl.df <- cbind(sherloc.df,lithology.df, pixl.df )
+
+# Review what we have
+summary(sherloc_lithology_pixl.df)
+
##      sample               type           campaign         abrasion
+##  Min.   : 1.00   Igneous    :8   Crater Floor:9   Alfalfa     :2  
+##  1st Qu.: 4.75   N/A        :1   Delta Front :7   Bellegrade  :2  
+##  Median : 8.50   Sedimentary:7                    Berry Hollow:2  
+##  Mean   : 8.50                                    Dourbes     :2  
+##  3rd Qu.:12.25                                    Novarupta   :2  
+##  Max.   :16.00                                    Quartier    :2  
+##                                                   (Other)     :4  
+##          Name     Plagioclase        Sulfate         Ca-sulfate    
+##  Atsah     : 1   Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
+##  Bearwallow: 1   1st Qu.:0.0000   1st Qu.:0.1875   1st Qu.:0.0000  
+##  Coulettes : 1   Median :0.0000   Median :1.0000   Median :0.0000  
+##  Hahonih   : 1   Mean   :0.1875   Mean   :0.6562   Mean   :0.3438  
+##  Hazeltop  : 1   3rd Qu.:0.0000   3rd Qu.:1.0000   3rd Qu.:1.0000  
+##  Kukaklek  : 1   Max.   :1.0000   Max.   :1.0000   Max.   :1.0000  
+##  (Other)   :10                                                     
+##  Hydrated Ca-sulfate   Mg-sulfate     Hydrated Sulfates Hydrated Mg-Fe sulfate
+##  Min.   :0.000       Min.   :0.0000   Min.   :0.000     Min.   :0.0000        
+##  1st Qu.:0.000       1st Qu.:0.0000   1st Qu.:0.000     1st Qu.:0.0000        
+##  Median :0.000       Median :0.0000   Median :0.000     Median :0.0000        
+##  Mean   :0.125       Mean   :0.1875   Mean   :0.125     Mean   :0.1875        
+##  3rd Qu.:0.000       3rd Qu.:0.0000   3rd Qu.:0.000     3rd Qu.:0.0000        
+##  Max.   :1.000       Max.   :1.0000   Max.   :1.000     Max.   :1.0000        
+##                                                                               
+##   Perchlorates    Na-perchlorate    Amorphous Silicate   Phosphate     
+##  Min.   :0.0000   Min.   :0.00000   Min.   :0.0000     Min.   :0.0000  
+##  1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.0000     1st Qu.:0.0000  
+##  Median :0.0000   Median :0.00000   Median :0.0000     Median :0.0000  
+##  Mean   :0.0625   Mean   :0.03125   Mean   :0.1406     Mean   :0.2031  
+##  3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.2500     3rd Qu.:0.3125  
+##  Max.   :1.0000   Max.   :0.50000   Max.   :0.5000     Max.   :1.0000  
+##                                                                        
+##     Pyroxene         Olivine         Carbonate      Fe-Mg carbonate
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.0000   Min.   :0.000  
+##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.4375   1st Qu.:0.000  
+##  Median :1.0000   Median :0.6250   Median :1.0000   Median :0.000  
+##  Mean   :0.6875   Mean   :0.5312   Mean   :0.7344   Mean   :0.125  
+##  3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:0.000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :1.0000   Max.   :1.000  
+##                                                                    
+##  Hydrated Carbonates Disordered Silicates    Feldspar         Quartz       
+##  Min.   :0           Min.   :0.000        Min.   :0.000   Min.   :0.00000  
+##  1st Qu.:0           1st Qu.:0.000        1st Qu.:0.000   1st Qu.:0.00000  
+##  Median :0           Median :0.000        Median :0.000   Median :0.00000  
+##  Mean   :0           Mean   :0.125        Mean   :0.125   Mean   :0.03125  
+##  3rd Qu.:0           3rd Qu.:0.000        3rd Qu.:0.000   3rd Qu.:0.00000  
+##  Max.   :0           Max.   :1.000        Max.   :1.000   Max.   :0.25000  
+##                                                                            
+##     Apatite        FeTi oxides         Halite          Iron oxide    
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.00000   Min.   :0.0000  
+##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.0000  
+##  Median :0.0000   Median :0.0000   Median :0.00000   Median :0.0000  
+##  Mean   :0.1406   Mean   :0.1406   Mean   :0.04688   Mean   :0.2812  
+##  3rd Qu.:0.0000   3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.5000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :0.25000   Max.   :1.0000  
+##                                                                      
+##  Hydrated Iron oxide Organic matter   Sulfate+Organic matter
+##  Min.   :0.00000     Min.   :0.0000   Min.   :0.0000        
+##  1st Qu.:0.00000     1st Qu.:0.0000   1st Qu.:0.0000        
+##  Median :0.00000     Median :1.0000   Median :0.0000        
+##  Mean   :0.01562     Mean   :0.5938   Mean   :0.2188        
+##  3rd Qu.:0.00000     3rd Qu.:1.0000   3rd Qu.:0.2500        
+##  Max.   :0.25000     Max.   :1.0000   Max.   :1.0000        
+##                                                             
+##  Other hydrated phases Phyllosilicates      Chlorite     
+##  Min.   :0.0000        Min.   :0.00000   Min.   :0.0000  
+##  1st Qu.:0.0000        1st Qu.:0.00000   1st Qu.:0.0000  
+##  Median :0.2500        Median :0.00000   Median :0.0000  
+##  Mean   :0.4375        Mean   :0.09375   Mean   :0.0625  
+##  3rd Qu.:1.0000        3rd Qu.:0.06250   3rd Qu.:0.0000  
+##  Max.   :1.0000        Max.   :0.50000   Max.   :0.5000  
+##                                                          
+##  Kaolinite (hydrous Al-clay)    Chromite        Ilmenite     Zircon/Baddeleyite
+##  Min.   :0.0000              Min.   :0.000   Min.   :0.000   Min.   :0.000     
+##  1st Qu.:0.0000              1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0.000     
+##  Median :0.0000              Median :0.000   Median :0.000   Median :0.000     
+##  Mean   :0.1875              Mean   :0.125   Mean   :0.125   Mean   :0.125     
+##  3rd Qu.:0.0000              3rd Qu.:0.000   3rd Qu.:0.000   3rd Qu.:0.000     
+##  Max.   :1.0000              Max.   :1.000   Max.   :1.000   Max.   :1.000     
+##                                                                                
+##  Fe-Mg-clay minerals    Spinels           sample              name   
+##  Min.   :0.0000      Min.   :0.0000   Min.   : 1.00   Atsah     : 1  
+##  1st Qu.:0.0000      1st Qu.:0.0000   1st Qu.: 4.75   Bearwallow: 1  
+##  Median :0.0000      Median :0.0000   Median : 8.50   Coulettes : 1  
+##  Mean   :0.1875      Mean   :0.0625   Mean   : 8.50   Hahonih   : 1  
+##  3rd Qu.:0.0000      3rd Qu.:0.0000   3rd Qu.:12.25   Hazeltop  : 1  
+##  Max.   :1.0000      Max.   :0.5000   Max.   :16.00   Kukaklek  : 1  
+##                                                       (Other)   :10  
+##        SampleType         campaign         abrasion feldspar plagioclase
+##  atmospheric: 1   Crater Floor:9   Alfalfa     :2   0:14     0:13       
+##  regolith   : 0   Delta Front :7   Bellegarde  :2   1: 2     1: 3       
+##  rock core  :15   Margin Unit :0   Berry Hollow:2                       
+##                                    Dourbes     :2                       
+##                                    Novarupta   :2                       
+##                                    Quartier    :2                       
+##                                    (Other)     :4                       
+##  pyroxene olivine quartz apatite FeTi_Oxides Iron_Oxide Sulfate Perchlorates
+##  0: 5     0: 6    0:14   0:13    0:13        0:9        0: 4    0:15        
+##  1:11     1:10    1: 2   1: 3    1: 3        1:7        1:12    1: 1        
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##  Phosphate Ca_Sulfate Carbonate Fe_Mg_clay Fe_Mg_carbonate Mg_sulfate
+##  0:11      0:10       0: 1      0:13       0:14            0:13      
+##  1: 5      1: 6       1:15      1: 3       1: 2            1: 3      
+##                                                                      
+##                                                                      
+##                                                                      
+##                                                                      
+##                                                                      
+##  Phyllosilicates Chlorite Halite Organic_matter Hydrated_Ca_Sulfate
+##  0:12            0:14     0:13   0: 5           0:14               
+##  1: 4            1: 2     1: 3   1:11           1: 2               
+##                                                                    
+##                                                                    
+##                                                                    
+##                                                                    
+##                                                                    
+##  Hydrated_Sulfates Hydrated_Mg_Fe_Sulfate Na_Perchlorate Amorphous_Silicate
+##  0:14              0:13                   0:15           0:9               
+##  1: 2              1: 3                   1: 1           1:7               
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##  Hydrated_Carbonates Disordered_Silicates Hydrated_Iron_Oxide
+##  0:16                0:14                 0:15               
+##                      1: 2                 1: 1               
+##                                                              
+##                                                              
+##                                                              
+##                                                              
+##                                                              
+##  Sulfate+Organic_Matter Other_hydrated_phases Kaolinite Chromite Ilmenite
+##  0:11                   0:8                   0:13      0:14     0:14    
+##  1: 5                   1:8                   1: 3      1: 2     1: 2    
+##                                                                          
+##                                                                          
+##                                                                          
+##                                                                          
+##                                                                          
+##  Zircon/Baddeleyite Spinels     sample           Na20            Mgo        
+##  0:14               0:14    Min.   : 1.00   Min.   :1.000   Min.   : 0.730  
+##  1: 2               1: 2    1st Qu.: 4.75   1st Qu.:1.853   1st Qu.: 2.533  
+##                             Median : 8.50   Median :1.900   Median :12.800  
+##                             Mean   : 8.50   Mean   :2.672   Mean   :11.682  
+##                             3rd Qu.:12.25   3rd Qu.:4.500   3rd Qu.:19.100  
+##                             Max.   :16.00   Max.   :5.550   Max.   :22.700  
+##                                                                             
+##      Al203             Si02            P205             S03        
+##  Min.   : 1.700   Min.   :22.60   Min.   :0.1000   Min.   : 0.780  
+##  1st Qu.: 2.220   1st Qu.:31.22   1st Qu.:0.2350   1st Qu.: 1.495  
+##  Median : 3.710   Median :38.85   Median :0.5250   Median : 2.600  
+##  Mean   : 5.072   Mean   :38.55   Mean   :0.6512   Mean   : 5.562  
+##  3rd Qu.: 7.117   3rd Qu.:41.17   3rd Qu.:0.8400   3rd Qu.: 3.800  
+##  Max.   :11.600   Max.   :57.10   Max.   :2.7600   Max.   :21.530  
+##                                                                    
+##        Cl             K20              Cao             Ti02       
+##  Min.   :0.400   Min.   :0.0000   Min.   :1.500   Min.   :0.2000  
+##  1st Qu.:0.940   1st Qu.:0.1600   1st Qu.:2.655   1st Qu.:0.5900  
+##  Median :1.740   Median :0.2000   Median :3.120   Median :0.7000  
+##  Mean   :1.846   Mean   :0.5800   Mean   :3.688   Mean   :0.8194  
+##  3rd Qu.:2.080   3rd Qu.:0.8275   3rd Qu.:4.310   3rd Qu.:0.9900  
+##  Max.   :4.500   Max.   :1.9000   Max.   :7.770   Max.   :2.4900  
+##                                                                   
+##      Cr203            Mno             FeO-T               name   
+##  Min.   :0.000   Min.   :0.1000   Min.   :13.24   Atsah     : 1  
+##  1st Qu.:0.025   1st Qu.:0.2800   1st Qu.:16.71   Bearwallow: 1  
+##  Median :0.155   Median :0.4000   Median :23.86   Coulettes : 1  
+##  Mean   :0.355   Mean   :0.3812   Mean   :21.45   Hahonih   : 1  
+##  3rd Qu.:0.290   3rd Qu.:0.4900   3rd Qu.:25.70   Hazeltop  : 1  
+##  Max.   :1.900   Max.   :0.6900   Max.   :30.05   Kukaklek  : 1  
+##                                                   (Other)   :10  
+##           type           campaign    location          abrasion
+##  Igneous    :8   Crater Floor:9   01     : 1   Alfalfa     :2  
+##  N/A        :1   Delta Front :7   02     : 1   Bellegrade  :2  
+##  Sedimentary:7                    03     : 1   Berry Hollow:2  
+##                                   04     : 1   Dourbes     :2  
+##                                   05     : 1   Novarupta   :2  
+##                                   06     : 1   Quartier    :2  
+##                                   (Other):10   (Other)     :4
+
# Combine the Lithology, SHERLOC and PIXLmatrices
+sherloc_lithology_pixl.matrix<-cbind(sherloc.matrix,lithology.matrix,pixl.matrix)
+
+# Review the resulting matrix
+str(sherloc_lithology_pixl.matrix)
+
##  num [1:16, 1:83] 1 1 1 0 0 0 0 0 0 0 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:83] "Plagioclase" "Sulfate" "Ca-sulfate" "Hydrated Ca-sulfate" ...
+
+
+
+

4 Analysis of Data (Part +3)

+

Each team has been assigned one of six datasets:

+
    +
  1. Dataset B: PIXL: The PIXL team’s goal is to understand and +explain how scaling changes results from Assignment 1. The matrix +version was scaled above but not in Assignment 1.

  2. +
  3. Dataset C: LIBS (with appropriate scaling as necessary. Not +scaled yet.)

  4. +
  5. Dataset D: Sherloc (with appropriate scaling as necessary. Not +scaled yet.)

  6. +
  7. Dataset E: PIXL + Sherloc (with appropriate scaling as necessary. +Not scaled yet.)

  8. +
  9. Dataset F: PIXL + Lithography (with appropriate scaling as +necessary. Not scaled yet.)

  10. +
  11. Dataset G: Sherloc + Lithograpy (with appropriate scaling as +necessary. Not scaled yet.)

  12. +
  13. Dataset H: PIXL + Sherloc + Lithograpy (with appropriate scaling +as necessary. Not scaled yet.)

  14. +
+

For the data set assigned to your team, perform the following +steps. Feel free to use the methods/code from Assignment 1 as +desired. Communicate with your teammates. Make sure that you are doing +different variations of below analysis so that no team member does the +exact same analysis. If you want to use the same clustering for your +team (which is okay but then vary rest), make sure you use the same +random seeds.

+
    +
  1. Describe the data set contained in the data frame and +matrix: How many rows does it have and how many features? Which +features are measurements and which features are metadata about the +samples? (3 pts) There is 16 rows and 99 features. measurements are +comprised with all chemical compound such as sulfate, Ca-sulfate and +Hydrated Ca-sulfate, and metadata about the samples are as the +following: sample, name, type, campaign, abrasion.
  2. +
+
summary(sherloc_lithology.df)
+
##      sample               type           campaign         abrasion
+##  Min.   : 1.00   Igneous    :8   Crater Floor:9   Alfalfa     :2  
+##  1st Qu.: 4.75   N/A        :1   Delta Front :7   Bellegrade  :2  
+##  Median : 8.50   Sedimentary:7                    Berry Hollow:2  
+##  Mean   : 8.50                                    Dourbes     :2  
+##  3rd Qu.:12.25                                    Novarupta   :2  
+##  Max.   :16.00                                    Quartier    :2  
+##                                                   (Other)     :4  
+##          Name     Plagioclase        Sulfate         Ca-sulfate    
+##  Atsah     : 1   Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
+##  Bearwallow: 1   1st Qu.:0.0000   1st Qu.:0.1875   1st Qu.:0.0000  
+##  Coulettes : 1   Median :0.0000   Median :1.0000   Median :0.0000  
+##  Hahonih   : 1   Mean   :0.1875   Mean   :0.6562   Mean   :0.3438  
+##  Hazeltop  : 1   3rd Qu.:0.0000   3rd Qu.:1.0000   3rd Qu.:1.0000  
+##  Kukaklek  : 1   Max.   :1.0000   Max.   :1.0000   Max.   :1.0000  
+##  (Other)   :10                                                     
+##  Hydrated Ca-sulfate   Mg-sulfate     Hydrated Sulfates Hydrated Mg-Fe sulfate
+##  Min.   :0.000       Min.   :0.0000   Min.   :0.000     Min.   :0.0000        
+##  1st Qu.:0.000       1st Qu.:0.0000   1st Qu.:0.000     1st Qu.:0.0000        
+##  Median :0.000       Median :0.0000   Median :0.000     Median :0.0000        
+##  Mean   :0.125       Mean   :0.1875   Mean   :0.125     Mean   :0.1875        
+##  3rd Qu.:0.000       3rd Qu.:0.0000   3rd Qu.:0.000     3rd Qu.:0.0000        
+##  Max.   :1.000       Max.   :1.0000   Max.   :1.000     Max.   :1.0000        
+##                                                                               
+##   Perchlorates    Na-perchlorate    Amorphous Silicate   Phosphate     
+##  Min.   :0.0000   Min.   :0.00000   Min.   :0.0000     Min.   :0.0000  
+##  1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.0000     1st Qu.:0.0000  
+##  Median :0.0000   Median :0.00000   Median :0.0000     Median :0.0000  
+##  Mean   :0.0625   Mean   :0.03125   Mean   :0.1406     Mean   :0.2031  
+##  3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.2500     3rd Qu.:0.3125  
+##  Max.   :1.0000   Max.   :0.50000   Max.   :0.5000     Max.   :1.0000  
+##                                                                        
+##     Pyroxene         Olivine         Carbonate      Fe-Mg carbonate
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.0000   Min.   :0.000  
+##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.4375   1st Qu.:0.000  
+##  Median :1.0000   Median :0.6250   Median :1.0000   Median :0.000  
+##  Mean   :0.6875   Mean   :0.5312   Mean   :0.7344   Mean   :0.125  
+##  3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:0.000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :1.0000   Max.   :1.000  
+##                                                                    
+##  Hydrated Carbonates Disordered Silicates    Feldspar         Quartz       
+##  Min.   :0           Min.   :0.000        Min.   :0.000   Min.   :0.00000  
+##  1st Qu.:0           1st Qu.:0.000        1st Qu.:0.000   1st Qu.:0.00000  
+##  Median :0           Median :0.000        Median :0.000   Median :0.00000  
+##  Mean   :0           Mean   :0.125        Mean   :0.125   Mean   :0.03125  
+##  3rd Qu.:0           3rd Qu.:0.000        3rd Qu.:0.000   3rd Qu.:0.00000  
+##  Max.   :0           Max.   :1.000        Max.   :1.000   Max.   :0.25000  
+##                                                                            
+##     Apatite        FeTi oxides         Halite          Iron oxide    
+##  Min.   :0.0000   Min.   :0.0000   Min.   :0.00000   Min.   :0.0000  
+##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.0000  
+##  Median :0.0000   Median :0.0000   Median :0.00000   Median :0.0000  
+##  Mean   :0.1406   Mean   :0.1406   Mean   :0.04688   Mean   :0.2812  
+##  3rd Qu.:0.0000   3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.5000  
+##  Max.   :1.0000   Max.   :1.0000   Max.   :0.25000   Max.   :1.0000  
+##                                                                      
+##  Hydrated Iron oxide Organic matter   Sulfate+Organic matter
+##  Min.   :0.00000     Min.   :0.0000   Min.   :0.0000        
+##  1st Qu.:0.00000     1st Qu.:0.0000   1st Qu.:0.0000        
+##  Median :0.00000     Median :1.0000   Median :0.0000        
+##  Mean   :0.01562     Mean   :0.5938   Mean   :0.2188        
+##  3rd Qu.:0.00000     3rd Qu.:1.0000   3rd Qu.:0.2500        
+##  Max.   :0.25000     Max.   :1.0000   Max.   :1.0000        
+##                                                             
+##  Other hydrated phases Phyllosilicates      Chlorite     
+##  Min.   :0.0000        Min.   :0.00000   Min.   :0.0000  
+##  1st Qu.:0.0000        1st Qu.:0.00000   1st Qu.:0.0000  
+##  Median :0.2500        Median :0.00000   Median :0.0000  
+##  Mean   :0.4375        Mean   :0.09375   Mean   :0.0625  
+##  3rd Qu.:1.0000        3rd Qu.:0.06250   3rd Qu.:0.0000  
+##  Max.   :1.0000        Max.   :0.50000   Max.   :0.5000  
+##                                                          
+##  Kaolinite (hydrous Al-clay)    Chromite        Ilmenite     Zircon/Baddeleyite
+##  Min.   :0.0000              Min.   :0.000   Min.   :0.000   Min.   :0.000     
+##  1st Qu.:0.0000              1st Qu.:0.000   1st Qu.:0.000   1st Qu.:0.000     
+##  Median :0.0000              Median :0.000   Median :0.000   Median :0.000     
+##  Mean   :0.1875              Mean   :0.125   Mean   :0.125   Mean   :0.125     
+##  3rd Qu.:0.0000              3rd Qu.:0.000   3rd Qu.:0.000   3rd Qu.:0.000     
+##  Max.   :1.0000              Max.   :1.000   Max.   :1.000   Max.   :1.000     
+##                                                                                
+##  Fe-Mg-clay minerals    Spinels           sample              name   
+##  Min.   :0.0000      Min.   :0.0000   Min.   : 1.00   Atsah     : 1  
+##  1st Qu.:0.0000      1st Qu.:0.0000   1st Qu.: 4.75   Bearwallow: 1  
+##  Median :0.0000      Median :0.0000   Median : 8.50   Coulettes : 1  
+##  Mean   :0.1875      Mean   :0.0625   Mean   : 8.50   Hahonih   : 1  
+##  3rd Qu.:0.0000      3rd Qu.:0.0000   3rd Qu.:12.25   Hazeltop  : 1  
+##  Max.   :1.0000      Max.   :0.5000   Max.   :16.00   Kukaklek  : 1  
+##                                                       (Other)   :10  
+##        SampleType         campaign         abrasion feldspar plagioclase
+##  atmospheric: 1   Crater Floor:9   Alfalfa     :2   0:14     0:13       
+##  regolith   : 0   Delta Front :7   Bellegarde  :2   1: 2     1: 3       
+##  rock core  :15   Margin Unit :0   Berry Hollow:2                       
+##                                    Dourbes     :2                       
+##                                    Novarupta   :2                       
+##                                    Quartier    :2                       
+##                                    (Other)     :4                       
+##  pyroxene olivine quartz apatite FeTi_Oxides Iron_Oxide Sulfate Perchlorates
+##  0: 5     0: 6    0:14   0:13    0:13        0:9        0: 4    0:15        
+##  1:11     1:10    1: 2   1: 3    1: 3        1:7        1:12    1: 1        
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##                                                                             
+##  Phosphate Ca_Sulfate Carbonate Fe_Mg_clay Fe_Mg_carbonate Mg_sulfate
+##  0:11      0:10       0: 1      0:13       0:14            0:13      
+##  1: 5      1: 6       1:15      1: 3       1: 2            1: 3      
+##                                                                      
+##                                                                      
+##                                                                      
+##                                                                      
+##                                                                      
+##  Phyllosilicates Chlorite Halite Organic_matter Hydrated_Ca_Sulfate
+##  0:12            0:14     0:13   0: 5           0:14               
+##  1: 4            1: 2     1: 3   1:11           1: 2               
+##                                                                    
+##                                                                    
+##                                                                    
+##                                                                    
+##                                                                    
+##  Hydrated_Sulfates Hydrated_Mg_Fe_Sulfate Na_Perchlorate Amorphous_Silicate
+##  0:14              0:13                   0:15           0:9               
+##  1: 2              1: 3                   1: 1           1:7               
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##                                                                            
+##  Hydrated_Carbonates Disordered_Silicates Hydrated_Iron_Oxide
+##  0:16                0:14                 0:15               
+##                      1: 2                 1: 1               
+##                                                              
+##                                                              
+##                                                              
+##                                                              
+##                                                              
+##  Sulfate+Organic_Matter Other_hydrated_phases Kaolinite Chromite Ilmenite
+##  0:11                   0:8                   0:13      0:14     0:14    
+##  1: 5                   1:8                   1: 3      1: 2     1: 2    
+##                                                                          
+##                                                                          
+##                                                                          
+##                                                                          
+##                                                                          
+##  Zircon/Baddeleyite Spinels
+##  0:14               0:14   
+##  1: 2               1: 2   
+##                            
+##                            
+##                            
+##                            
+## 
+
str(sherloc_lithology.matrix)
+
##  num [1:16, 1:70] 1 1 1 0 0 0 0 0 0 0 ...
+##  - attr(*, "dimnames")=List of 2
+##   ..$ : NULL
+##   ..$ : chr [1:70] "Plagioclase" "Sulfate" "Ca-sulfate" "Hydrated Ca-sulfate" ...
+
    +
  1. Scale this data appropriately (you can choose the scaling +method or decide to not scale data): Explain why you chose a +scaling method or to not scale. (3 pts) Since the dataset contains both +numerical and categorical features, I decide to not scale the data since +scaling categorical variables can result in meaningless +transformations.

  2. +
  3. Cluster the data using k-means or your favorite clustering +method (like hierarchical clustering): Describe how you picked the +best number of clusters. Indicate the number of points in each clusters. +Coordinate with your team so you try different approaches. If you want +to share results with your team mates, make sure to use the same random +seeds. (6 pts) After darwing the wss plot of the matrix, I use elbow +method plot to decide the best number of clusters. In this case, The +elbow appears to form around 3 or 4 clusters. The sharp drop in the WCSS +from 2 clusters to 3 clusters suggests that adding a third cluster +significantly improves the clustering quality. Therefore, I choose 3 +clusters. The first cluster has 7 points, the second cluster has 2 +points and the third cluster has 7 points.

  4. +
+

CLustering

+
# A user-defined function to examine clusters and plot the results
+wssplot <- function(data, nc=15, seed=10){
+  wss <- data.frame(cluster=1:nc, quality=c(0))
+  for (i in 1:nc){
+    set.seed(seed)
+    wss[i,2] <- kmeans(data, centers=i)$tot.withinss}
+  ggplot(data=wss,aes(x=cluster,y=quality)) + 
+    geom_line() + 
+    ggtitle("Quality of k-means by Cluster")
+}
+
+wssplot(sherloc_lithology.matrix, nc=8, seed=2)
+

+

Create final clusters

+
# Use our chosen 'k' to perform k-means clustering
+set.seed(2)
+k <- 3
+km <- kmeans(sherloc_lithology.matrix,k)
+

At first, we keep the scale as the origin, and create a heat map of +the cluster centers with rows and columns clustered.

+
pheatmap(km$centers,scale="none")
+

+According to this heat map, the features at left have a high mean than +the features at right. Moreover, cluster 2 has an over all more high +mean than cluster 1 and cluster 3.

+

Next, indicating how many samples are in each cluster

+
library(knitr)
+# clusters sizes are in the km object produced by kmeans
+clusters.df<-data.frame(cluster= 1:3, size=km$size)
+kable(clusters.df,caption="Samples per cluster")
+ + + + + + + + + + + + + + + + + + + + + + +
Samples per cluster
clustersize
17
22
37
+
    +
  1. _Perform a creative analysis that provides insights +into what one or more of the clusters are and what they tell you about +the MARS data: Alternatively do another creative analysis of your +datasets that leads to one of more findings. Make sure to explain what +your analysis and discuss your the results.
    +Now, performing PCA.
  2. +
+
# Perform the PCA on the matrix we created earlier
+
+sherloc_lithology.pca <- prcomp(sherloc_lithology.matrix, scale=FALSE)
+
+# generate the Scree plot
+ggscreeplot(sherloc_lithology.pca)
+

+

Creative analysis:

+
summary(sherloc_lithology.pca)
+
## Importance of components:
+##                           PC1    PC2    PC3    PC4     PC5     PC6     PC7
+## Standard deviation     1.6370 1.5095 1.3427 1.1118 0.88099 0.70792 0.52226
+## Proportion of Variance 0.2793 0.2375 0.1879 0.1289 0.08091 0.05224 0.02843
+## Cumulative Proportion  0.2793 0.5169 0.7048 0.8337 0.91458 0.96682 0.99526
+##                            PC8       PC9     PC10      PC11     PC12      PC13
+## Standard deviation     0.21330 2.894e-16 1.79e-16 1.175e-16 9.92e-17 6.478e-17
+## Proportion of Variance 0.00474 0.000e+00 0.00e+00 0.000e+00 0.00e+00 0.000e+00
+## Cumulative Proportion  1.00000 1.000e+00 1.00e+00 1.000e+00 1.00e+00 1.000e+00
+##                             PC14      PC15      PC16
+## Standard deviation     4.869e-17 1.972e-17 2.379e-18
+## Proportion of Variance 0.000e+00 0.000e+00 0.000e+00
+## Cumulative Proportion  1.000e+00 1.000e+00 1.000e+00
+
# Plotting the variance explained by each principal component
+plot(sherloc_lithology.pca, type="l")
+

+Together, the first three components explain about 70.48% of the +variance.This means that using the first three components might provide +a good approximation of the dataset, significantly reducing its +dimensionality while retaining most of the important information. Elbow +Rule: The plot shows a clear “elbow” around the 3rd or 4th component. +After this point, the variance explained by each additional component +drops off significantly. Based on this scree plot, the first 3-4 +principal components should be considered for further analysis, as they +explain the majority of the variance in the dataset. After the 4th +component, the additional variance explained becomes minimal.

+
loadings <- abs(sherloc_lithology.pca$rotation[, 1:3])
+print(loadings)
+
##                                     PC1         PC2         PC3
+## Plagioclase                 0.064336916 0.253285711 0.034736225
+## Sulfate                     0.175146396 0.057235074 0.031239837
+## Ca-sulfate                  0.232159520 0.167134575 0.064154734
+## Hydrated Ca-sulfate         0.042131612 0.170024387 0.021970393
+## Mg-sulfate                  0.200670557 0.107436782 0.114769312
+## Hydrated Sulfates           0.046640374 0.046533930 0.004709232
+## Hydrated Mg-Fe sulfate      0.200670557 0.107436782 0.114769312
+## Perchlorates                0.022205304 0.083261324 0.012765831
+## Na-perchlorate              0.011102652 0.041630662 0.006382916
+## Amorphous Silicate          0.017782440 0.039123645 0.003335076
+## Phosphate                   0.050067834 0.156937069 0.139435041
+## Pyroxene                    0.205440349 0.175242080 0.113777068
+## Olivine                     0.199073864 0.131670868 0.156241523
+## Carbonate                   0.128752482 0.006768303 0.124116776
+## Fe-Mg carbonate             0.090812262 0.012522980 0.038558702
+## Hydrated Carbonates         0.000000000 0.000000000 0.000000000
+## Disordered Silicates        0.087911478 0.018904080 0.101611247
+## Feldspar                    0.087911478 0.018904080 0.101611247
+## Quartz                      0.021977870 0.004726020 0.025402812
+## Apatite                     0.010321118 0.046989967 0.231737838
+## FeTi oxides                 0.047682938 0.190839718 0.025161851
+## Halite                      0.017151739 0.023946076 0.006448218
+## Iron oxide                  0.002321888 0.246964416 0.025709074
+## Hydrated Iron oxide         0.005551326 0.020815331 0.003191458
+## Organic matter              0.022898001 0.214954717 0.167587308
+## Sulfate+Organic matter      0.020247980 0.106056547 0.030089121
+## Other hydrated phases       0.225821526 0.068591591 0.097707669
+## Phyllosilicates             0.066658805 0.006321295 0.060445299
+## Chlorite                    0.043955739 0.009452040 0.050805623
+## Kaolinite (hydrous Al-clay) 0.200670557 0.107436782 0.114769312
+## Chromite                    0.004769792 0.067805298 0.228546380
+## Ilmenite                    0.004769792 0.067805298 0.228546380
+## Zircon/Baddeleyite          0.004769792 0.067805298 0.228546380
+## Fe-Mg-clay minerals         0.200670557 0.107436782 0.114769312
+## Spinels                     0.002384896 0.033902649 0.114273190
+## feldspar                    0.087911478 0.018904080 0.101611247
+## plagioclase                 0.064336916 0.253285711 0.034736225
+## pyroxene                    0.205440349 0.175242080 0.113777068
+## olivine                     0.265007473 0.145848928 0.080033088
+## quartz                      0.087911478 0.018904080 0.101611247
+## apatite                     0.026975096 0.015456026 0.241312212
+## FeTi_Oxides                 0.064336916 0.253285711 0.034736225
+## Iron_Oxide                  0.114386824 0.246904610 0.105433723
+## Sulfate                     0.178723740 0.006381100 0.140169948
+## Perchlorates                0.022205304 0.083261324 0.012765831
+## Phosphate                   0.069106708 0.185480413 0.263282605
+## Ca_Sulfate                  0.265007473 0.145848928 0.080033088
+## Carbonate                   0.022205304 0.083261324 0.012765831
+## Fe_Mg_clay                  0.200670557 0.107436782 0.114769312
+## Fe_Mg_carbonate             0.090812262 0.012522980 0.038558702
+## Mg_sulfate                  0.200670557 0.107436782 0.114769312
+## Phyllosilicates             0.178723740 0.006381100 0.140169948
+## Chlorite                    0.087911478 0.018904080 0.101611247
+## Halite                      0.068606958 0.095784304 0.025792870
+## Organic_matter              0.026475345 0.265808691 0.003822477
+## Hydrated_Ca_Sulfate         0.042131612 0.170024387 0.021970393
+## Hydrated_Sulfates           0.046640374 0.046533930 0.004709232
+## Hydrated_Mg_Fe_Sulfate      0.200670557 0.107436782 0.114769312
+## Na_Perchlorate              0.022205304 0.083261324 0.012765831
+## Amorphous_Silicate          0.026716609 0.181623180 0.026392880
+## Hydrated_Carbonates         0.000000000 0.000000000 0.000000000
+## Disordered_Silicates        0.087911478 0.018904080 0.101611247
+## Hydrated_Iron_Oxide         0.022205304 0.083261324 0.012765831
+## Sulfate+Organic_Matter      0.023825324 0.156910520 0.201498906
+## Other_hydrated_phases       0.269777265 0.078043631 0.148513293
+## Kaolinite                   0.200670557 0.107436782 0.114769312
+## Chromite                    0.004769792 0.067805298 0.228546380
+## Ilmenite                    0.004769792 0.067805298 0.228546380
+## Zircon/Baddeleyite          0.004769792 0.067805298 0.228546380
+## Spinels                     0.004769792 0.067805298 0.228546380
+
threshold <- 0.2
+important_vars <- apply(loadings, 1, function(x) any(x > threshold))
+sherloc_lithology_filtered <- sherloc_lithology.pca
+sherloc_lithology_filtered$rotation <- sherloc_lithology_filtered$rotation[important_vars, ]
+

Using loading to show how much each variable contributes to the +principal components. Then, I filtered the variables which only keep the +variables that has a contribution greater than 0.2. The high positive or +negative values in the loading are most important to each component +Based on the result, SHERLOC measurements dominate PC1 and lithology +measurements dominate PC2, we could infer that PC1 captures the primary +chemical or spectroscopic composition of the Martian surface, while PC2 +relates to the geological context.

+

Create a PCA biplot to visualize the clusters

+
sherloc_lithology.df$cluster <- factor(km$cluster, 
+                                       levels = c(1, 2, 3), 
+                                       labels = c("Cluster 1", "Cluster 2", "Cluster 3"))
+# For this lab we'll create a PCA biplot the easy way using ggbiplot!
+ggbiplot::ggbiplot(sherloc_lithology_filtered,
+                   choices = c(1, 2),
+                   labels = sherloc_lithology.df$type,
+                   groups = sherloc_lithology.df$cluster) +
+  xlim(-2, 2) + ylim(-2, 2) +
+  ggtitle("Filtered Biplot: PC1 vs PC2") 
+

+Iron Oxide, Amorphous Silicate, Pyroxene, Olivine, Hydrated Sulfates: +These variables contribute the most to PC1, suggesting that PC1 +continues to represent a contrast between igneous materials (e.g., +pyroxene, olivine) and sedimentary or hydrated minerals (e.g., hydrated +sulfates). Moreover, as these variables group closely together, which +indicates a common geological origin. This likely corresponds to igneous +regions on Mars Phyllosilicates and Iron Oxide: These variables are also +significant contributors to PC2, meaning PC2 is likely to represent +variations within sedimentary environments which separate different +types of hydrated minerals and phyllosilicates. This could reflect +differences in the extent or type of chemical alteration due to +water.

+

make another PCA biplot to create a comparison between PC1 and +PC3

+
ggbiplot::ggbiplot(sherloc_lithology_filtered,
+                   choices = c(1, 3),
+                   labels = sherloc_lithology.df$type,
+                   groups = sherloc_lithology.df$cluster) +
+  xlim(-2, 2) + ylim(-2, 2) +
+  ggtitle("Filtered Biplot: PC1 vs PC3") 
+
## Warning: Removed 2 rows containing missing values or values outside the scale range
+## (`geom_text()`).
+

+Organic Matter and Phosphate: These variables are much more important in +PC3 than PC2, suggesting that PC3 may capture some trend related to the +presence of organic compounds or chemical processes that differ from +those driving the first two PCs, distinguishing areas where organic +compounds or specific chemical interactions are more prevalent.

+
+
+

5 Preparation of Team +Presentation (Part 4)

+

Prepare a presentation of your teams result to present in class on +September 11 starting at 9am in AE217 (20 pts) The +presentation should include the following elements

+

0.Your teams names and members 1. A Description of +the data set that you analyzed including how many observations and how +many features. (<= 1.5 mins) 2. Each team member gets three +minutes to explain their analysis: * what analysis they +performed * the results of that analysis * a brief discussion of their +interpretation of these results * <= 18 mins total! 3. A +Conclusion slide indicating major findings of the teams +(<= 1.5 mins) 4. Thoughts on potential next steps +for the MARS team (<= 1.5 mins)

+ +

https://docs.google.com/document/d/1-4o1O4h2r8aMjAplmE-ItblQnyDAKZwNs5XCnmwacjs/pub

+ +
+
+

6 When you’re done: SAVE, +COMMIT and PUSH YOUR CHANGES!

+

When you are satisfied with your edits and your notebook knits +successfully, remember to push your changes to the repo using the +following steps:

+ +
+
+

7 APPENDIX: Accessing +RStudio Server on the IDEA Cluster

+

The IDEA Cluster provides seven compute nodes (4x 48 cores, 3x 80 +cores, 1x storage server)

+ +
+
+

8 More info about Rstudio +on our Cluster

+
+

8.1 RStudio GUI +Access:

+ +
+
+ + + + +
+ + + + + + + + + + + + + + + diff --git a/StudentNotebooks/Assignment02/zhaot4-f24-assignment2.pdf b/StudentNotebooks/Assignment02/zhaot4-f24-assignment2.pdf new file mode 100644 index 0000000..27e289d Binary files /dev/null and b/StudentNotebooks/Assignment02/zhaot4-f24-assignment2.pdf differ