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DAR-Mars-F24/StudentData/v1_consistent_data_naming.Rmd
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| This notebook takes our four main data sets (PIXL, LIBS, SHERLOC, & LITHOLOGY) and gives them a consistent naming scheme for their columns. | |
| ```{r setup, include=FALSE} | |
| # Set the default CRAN repository | |
| local({r <- getOption("repos") | |
| r["CRAN"] <- "http://cran.r-project.org" | |
| options(repos=r) | |
| }) | |
| if (!require("tidyr")) { | |
| install.packages("tidyr") | |
| library(qpcR) | |
| } | |
| if (!require("dplyr")) { | |
| install.packages("dplyr") | |
| library(qpcR) | |
| } | |
| if (!require("qpcR")) { | |
| install.packages("qpcR") | |
| library(qpcR) | |
| } | |
| ``` | |
| # Importing data frames | |
| ```{r} | |
| # Importing PIXL | |
| #pixl.df <- readRDS("~/DAR-Mars-F24/Data/samples_pixl_wide.Rds") #Old PIXL, missing Lat and Lon | |
| pixl.df <- readRDS("~/DAR-Mars-F24/StudentData/pixl_sol_coordinates.Rds") | |
| # Importing LIBS | |
| libs.df <- readRDS("~/DAR-Mars-F24/Data/supercam_libs_moc_loc.Rds") | |
| libs_type.df <- readRDS("~/DAR-Mars-F24/StudentData/libs_typed.Rds") | |
| # Importing Lithology | |
| lithology.df<- readRDS("~/DAR-Mars-F24/Data/mineral_data_static.Rds") | |
| # Importing and reformating Sherloc | |
| sherloc.df <- readRDS("~/DAR-Mars-F24/Data/abrasions_sherloc_samples.Rds") | |
| ## Clean up data types | |
| sherloc.df$Mineral <- as.factor(sherloc.df$Mineral) | |
| sherloc.df[sapply(sherloc.df, is.character)] <- lapply(sherloc.df[sapply(sherloc.df, is.character)],as.numeric) | |
| ## Change N/A's to "0" | |
| sherloc.df <- sherloc.df %>% 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.df <- sherloc.df %>% pivot_longer(!Mineral, names_to = "Name", values_to = "Presence") | |
| ## Make abrasion a factor | |
| sherloc.df$Name <- as.factor(sherloc.df$Name) | |
| ## Make it a matrix | |
| sherloc.matrix <- sherloc.df %>% pivot_wider(names_from = Mineral, values_from = Presence) | |
| sherloc.df <- cbind(sherloc.matrix,pixl.df[,"sample"]) | |
| # pixl and libs combined data frame | |
| pixl_libs.df <- readRDS("PIXL_LIBS_Combined.Rds") | |
| ``` | |
| # Renaming Columns | |
| ```{r} | |
| # Renaming PIXL names | |
| colnames(pixl.df) <- c("Lat","Lon","Sol","Sample", | |
| "Na2O","MgO","Al2O3","SiO2","P2O5","SO3","Cl","K2O","CaO","TiO2","Cr2O3","MnO","FeOT", | |
| "Name","Type","Campaign","Location","Abrasion") | |
| # Renaming LIBS | |
| libs.df <- cbind(libs.df,libs_type.df$"type") | |
| colnames(libs.df) <- c("Sol","Lat","Lon","Target","Point", | |
| "SiO2","SiO2_stdev","TiO2","TiO2_stdev","Al2O3","Al2O3_stdev","FeOT","FeOT_stdev","MgO","MgO_stdev","CaO","CaO_stdev","Na2O","Na2O_stdev","K2O","K2O_stdev", | |
| "Total","distance_mm","Tot.Em.", | |
| "Type") | |
| libs_type <- libs_type.df$"earthsample?" | |
| libs_type <- as.logical(libs_type) # Was originally "numeric" | |
| # Renaming Lithology | |
| colnames(lithology.df) <- c("Sample","Name","SampleType","Campaign","Abrasion", | |
| "Feldspar","Plagioclase","Pyroxene","Olivine","Quartz", | |
| "Apatite","FeTi oxides","Iron oxide","Sulfate","Perchlorates", | |
| "Phosphate","Ca-sulfate","Carbonate","Fe-Mg-clay minerals","Fe-Mg carbonate", | |
| "Mg-sulfate","Phyllosilicates","Chlorite","Halite","Organic matter", | |
| "Hydrated Ca-sulfate","Hydrated Sulfates","Hydrated Mg-Fe sulfate","Na-perchlorate","Amorphous Silicate", | |
| "Hydrated Carbonates","Disordered Silicates","Hydrated Iron oxide","Sulfate+Organic matter","Other hydrated phases", | |
| "Kaolinite (hydrous Al-clay)","Chromite","Ilmenite","Zircon/Baddeleyite","Spinels") | |
| # Renaming Sherloc | |
| colnames(sherloc.df) <- c("Name", | |
| "Plagioclase","Sulfate","Ca-sulfate","Hydrated Ca-sulfate", | |
| "Mg-sulfate","Hydrated Sulfates","Hydrated Mg-Fe sulfate","Perchlorates", | |
| "Na-perchlorate","Amorphous Silicate","Phosphate","Pyroxene", | |
| "Olivine","Carbonate","Fe-Mg carbonate","Hydrated Carbonates", | |
| "Disordered Silicates","Feldspar","Quartz","Apatite", | |
| "FeTi oxides","Halite","Iron oxide","Hydrated Iron oxide", | |
| "Organic matter","Sulfate+Organic matter","Other hydrated phases","Phyllosilicates", | |
| "Chlorite","Kaolinite (hydrous Al-clay)","Chromite","Ilmenite", | |
| "Zircon/Baddeleyite","Fe-Mg-clay minerals","Spinels","Sample") | |
| # Renaming Pixl and Libs combined data set | |
| colnames(pixl_libs.df) <- c("Target.libs","Lat.libs","Lon.libs","Sol.libs","Point.libs", | |
| "Distance", | |
| "Abrasion.pixl","Lat.pixl","Lon.pixl","Campaign.pixl", | |
| "SiO2.libs","TiO2.libs","Al2O3.libs","FeOT.libs","MgO.libs","CaO.libs","Na2O.libs","K2O.libs") | |
| ``` | |
| # Creating Sample metadata data frame | |
| ```{r} | |
| # Creating meta data data frame | |
| sample_meta.df <- qpcR:::cbind.na(pixl.df[,c("Sol","Lat","Lon","Type","Campaign","Abrasion","Name","Location")], lithology.df[,c("Sample","SampleType")]) | |
| # Reordering it | |
| sample_meta.df <- sample_meta.df[,c("Sample","Name","Sol","Lat","Lon","Abrasion","Campaign","Type","SampleType")] | |
| # Changing atmospherics type from "N/A" to "Atmospheric" | |
| sample_meta.df[1,"Type"] <- "Atmospheric" | |
| ``` | |
| # Seperating Libs | |
| Separating out earth reference Libs from normal Libs | |
| ```{r} | |
| # Creating a data frame with only the Scct Libs data | |
| libs_earth_references.df <- libs.df[libs_type,] | |
| # Removing the Scct Libs data from Libs.df | |
| libs.df <- libs.df[!libs_type,] | |
| ``` | |
| # Adding LIBS clusters | |
| Performs k-means and saves clusters | |
| ```{r} | |
| libs_ternary <- libs.df %>% select(c(SiO2, Al2O3, FeOT, MgO, CaO, Na2O, K2O))%>% | |
| mutate(x=(SiO2+Al2O3)/100,y=(FeOT+MgO)/100,z=(CaO+Na2O+K2O)/100) %>% | |
| select(-c(SiO2,Al2O3,FeOT,MgO,CaO,Na2O,K2O)) %>% | |
| drop_na() | |
| set.seed(10) | |
| k <- 4 | |
| tern.km <- kmeans(libs_ternary, k) | |
| Cluster <- as.factor(tern.km$cluster) | |
| libs.df <- cbind(libs.df, Cluster) | |
| ``` | |
| # Reordering Columns and removing meta data from PIXL, Lithology, LIBS, & Sherloc | |
| ```{r} | |
| # Resorting PIXL columns | |
| pixl.df <- pixl.df[,c("Sample", | |
| "SiO2","TiO2","Al2O3","FeOT","MgO","CaO","Na2O","K2O", #These show up in LIBS | |
| "P2O5","SO3","Cl","Cr2O3","MnO" #These ones don't show up in LIBS | |
| )] | |
| # Resorting LIBS columns | |
| libs.df <- libs.df[,c("Target","Point","Sol","Lat","Lon","Type","Cluster", | |
| "SiO2","SiO2_stdev","TiO2","TiO2_stdev","Al2O3","Al2O3_stdev","FeOT","FeOT_stdev","MgO","MgO_stdev","CaO","CaO_stdev","Na2O","Na2O_stdev","K2O","K2O_stdev", | |
| "Total","distance_mm","Tot.Em.")] | |
| # Resorting LIBS columns | |
| libs_earth_references.df <- libs_earth_references.df[,c("Target","Point","Sol","Lat","Lon","Type", | |
| "SiO2","SiO2_stdev","TiO2","TiO2_stdev","Al2O3","Al2O3_stdev","FeOT","FeOT_stdev","MgO","MgO_stdev","CaO","CaO_stdev","Na2O","Na2O_stdev","K2O","K2O_stdev", | |
| "Total","distance_mm","Tot.Em.")] | |
| # Resorting Lithology columns | |
| lithology.df <- lithology.df[1:16,c("Sample", | |
| "Plagioclase","Sulfate","Ca-sulfate","Hydrated Ca-sulfate", | |
| "Mg-sulfate","Hydrated Sulfates","Hydrated Mg-Fe sulfate","Perchlorates", | |
| "Na-perchlorate","Amorphous Silicate","Phosphate","Pyroxene", | |
| "Olivine","Carbonate","Fe-Mg carbonate","Hydrated Carbonates", | |
| "Disordered Silicates","Feldspar","Quartz","Apatite", | |
| "FeTi oxides","Halite","Iron oxide","Hydrated Iron oxide", | |
| "Organic matter","Sulfate+Organic matter","Other hydrated phases","Phyllosilicates", | |
| "Chlorite","Kaolinite (hydrous Al-clay)","Chromite","Ilmenite", | |
| "Zircon/Baddeleyite","Fe-Mg-clay minerals","Spinels")] | |
| # Resorting Sherloc columns | |
| sherloc.df <- sherloc.df[,c("Sample", | |
| "Plagioclase","Sulfate","Ca-sulfate","Hydrated Ca-sulfate", | |
| "Mg-sulfate","Hydrated Sulfates","Hydrated Mg-Fe sulfate","Perchlorates", | |
| "Na-perchlorate","Amorphous Silicate","Phosphate","Pyroxene", | |
| "Olivine","Carbonate","Fe-Mg carbonate","Hydrated Carbonates", | |
| "Disordered Silicates","Feldspar","Quartz","Apatite", | |
| "FeTi oxides","Halite","Iron oxide","Hydrated Iron oxide", | |
| "Organic matter","Sulfate+Organic matter","Other hydrated phases","Phyllosilicates", | |
| "Chlorite","Kaolinite (hydrous Al-clay)","Chromite","Ilmenite", | |
| "Zircon/Baddeleyite","Fe-Mg-clay minerals","Spinels")] | |
| # Resorting Pixl and Libs combined data set | |
| pixl_libs.df <- pixl_libs.df[,c("Target.libs","Point.libs","Sol.libs","Lat.libs","Lon.libs", | |
| "Distance", | |
| "Abrasion.pixl","Campaign.pixl","Lat.pixl","Lon.pixl", | |
| "SiO2.libs","TiO2.libs","Al2O3.libs","FeOT.libs","MgO.libs","CaO.libs","Na2O.libs","K2O.libs")] | |
| ``` | |
| # Fixing data types | |
| Check types and fix them (ex Sample, Sol, Lat, Lon -> numeric, Name -> character, Abrasion, Campaign, Type, SampleType -> Factor) | |
| ```{r} | |
| # Pixl | |
| ## Already good! | |
| ## Sample is integer and concentrations are numeric! | |
| # Libs | |
| libs.df$Point <- as.factor(libs.df$Point) # Was originally "character" | |
| # Lithology | |
| lithology.df[,2:36] <- lapply(lithology.df[,2:36],as.factor) # Was originally "character" | |
| lithology.df$Sample <- as.integer(lithology.df$Sample) #To match Pixl | |
| # Sherloc | |
| sherloc.df[] <- data.frame(lapply(sherloc.df[],as.factor)) # Was originally "character" | |
| sherloc.df$Sample <- as.integer(sherloc.df$Sample) # Back to original, since prior line changed it | |
| # Sample Meta | |
| sample_meta.df$Sample <- as.integer(sample_meta.df$Sample) | |
| # sample_meta.df$Name <- as.character(sample_meta.df$Name) # Already in the format! | |
| sample_meta.df$Sol <- as.numeric(sample_meta.df$Sol) | |
| sample_meta.df$Lat <- as.numeric(sample_meta.df$Lat) | |
| sample_meta.df$Lon <- as.numeric(sample_meta.df$Lon) | |
| sample_meta.df$Abrasion <- as.factor(sample_meta.df$Abrasion) | |
| sample_meta.df$Campaign <- as.factor(sample_meta.df$Campaign) | |
| sample_meta.df$Type <- as.factor(sample_meta.df$Type) | |
| sample_meta.df$SampleType <- as.factor(sample_meta.df$SampleType) | |
| # Pixl and Libs combined | |
| ## Already good! | |
| ``` | |
| # Saving New data frames | |
| ```{r} | |
| saveRDS(sample_meta.df, "v1_sample_meta.Rds") | |
| saveRDS(libs.df, "v1_libs.Rds") | |
| saveRDS(libs_earth_references.df, "v1_libs_earth_references.Rds") | |
| saveRDS(lithology.df, "v1_lithology.Rds") | |
| saveRDS(sherloc.df, "v1_sherloc.Rds") | |
| saveRDS(pixl.df, "v1_pixl.Rds") | |
| saveRDS(pixl_libs.df, "v1_libs_to_sample.Rds") | |
| ``` |