Updates

README.html

@@ -354,15 +354,20 @@
 
 <div id="forensicisotissues" class="section level1">
 <h1>ForensicIsoTissues</h1>
-<p>Data and scripts for forensic body tissue isotope literature
-review.</p>
+<p>Data and scripts for forensic body tissue isotope compilation and
+data review titled “Human Tissue Oxygen and Strontium Isotope Values in
+North America: A Data Compilation and Assessment for Forensic
+Geolocation.”</p>
 <div id="data" class="section level2">
 <h2>data/</h2>
 <p>Data used in analyses.</p>
 <ul>
 <li><strong>FIT_Dataset.xlsx</strong> Compiled Dataset of
 δ<sup>18</sup>O data and <sup>87</sup>Sr/<sup>86</sup>Sr isotopic data
 from human tissues in North America.</li>
+<li><strong>RefIDsRefNo.xlsx</strong> Spreadsheet to used to integrate
+references citations numbers with Reference.IDs in the complied
+dataset.</li>
 </ul>
 </div>
 <div id="code" class="section level2">
@@ -384,7 +389,8 @@ <h2>shapefiles/</h2>
 </div>
 <div id="figures" class="section level2">
 <h2>figures/</h2>
-<p>Figures and figure components included in the main manuscript.</p>
+<p>Out bound folder for figures and figure components generated in the
+script.</p>
 </div>
 </div>
 

README.md

@@ -1,20 +1,21 @@
 # ForensicIsoTissues
-Data and scripts for forensic body tissue isotope literature review.
+Data and scripts for forensic body tissue isotope compilation and data review titled "Human Tissue Oxygen and Strontium Isotope Values in North America: A Data Compilation and Assessment for Forensic Geolocation."
 
 ## data/
 Data used in analyses.
 
 - **FIT_Dataset.xlsx** Compiled Dataset of &delta;<sup>18</sup>O data and <sup>87</sup>Sr/<sup>86</sup>Sr isotopic data from human tissues in North America.
+- **RefIDsRefNo.xlsx** Spreadsheet to used to integrate references citations numbers with Reference.IDs in the complied dataset. 
 
 ## code/
 Scripts used for data analysis and plotting.
 
 - **FITDataSetup.R** Load data and set up for analysis. Includes some descriptive statistics.
-- **FITMapping.R** Create maps of spatial distribution of data.
-- **FITTapiso.R** Analyze data using isoscapes and statisics. Includes code for generation of figures. 
+- **FITMapping.R** Create maps of spatial distribution of data for hair and tooth enamel isotopic values.
+- **FITTapiso.R** Analyze data using isoscapes and statistics. Includes code for generation of figures. 
 
 ## shapefiles/
-Includes all shapefiles and geospatial data required for running analyses. 
+Includes all shapefiles and geospatial data required for running analyses that are not pulled from other R packages. 
 
 ## figures/
 Out bound folder for figures and figure components generated in the script.

code/FITDataSetup.R

@@ -1,6 +1,6 @@
 library(readxl);library(dplyr)
 
-#Read in dataset from data file from Github and merge sheets together
+#Read in dataset xlsx from data file from GitHub and merge sheets together
 FData1 <-read_excel("data/FIT_Dataset.xlsx", sheet = "Individual")
 FData2 <-read_excel("data/FIT_Dataset.xlsx", sheet = "Site")
 FData3 <-read_excel("data/FIT_Dataset.xlsx", sheet = "Sample")
@@ -11,10 +11,10 @@ Comp3 <-merge(Comp2,FData4,by= "Sample.ID")
 #convert lat and long to numeric
 Comp3$Lat= as.numeric(Comp3$Lat)
 Comp3$Lon= as.numeric(Comp3$Lon)
-#Select needed data columns
+#Select needed data columns, this makes data easier to read and visualize
 ForensicTisIsoData <-select(Comp3,1:3,5:15,17:21,24:29,30,32:34) 
 rm( FData1, FData2, FData3, FData4, Comp1, Comp2, Comp3)
-#Get rid of NA in Lat and Lon
+#Get rid of NAs in Lat and Lon
 ForensicTisIsoData =ForensicTisIsoData[!is.na(ForensicTisIsoData$Lat),]
 FTID <-ForensicTisIsoData
 
@@ -53,10 +53,10 @@ summstats4 <- FTID %>%
 
 #Remove cities routinely dropped from isoscapes
 FTID<- subset(FTID, City!="Tofino" & City!="Honolulu")
-#subset and remove fingernail and bone data
+#Subset data and remove fingernail and bone data
 FTID <- subset(FTID, Element=="hair"|Element=="teeth")
-#Make sure not duplicates have snuck in
+#Make sure there are no duplicates
 FTID<- FTID[!duplicated(FTID$Data.ID), ]
-#Write data to csv to run FITMapping and FITTapiso
+#Write data to csv to run FITMapping and FITTapiso, or run it from the FTID dataframe
 write.csv(FTID, file="data/ForensicTissue.csv")
 

code/FITMapping.R

@@ -13,89 +13,85 @@ NorAmericamap <-vect("shapefiles/Namap_aea.shp")
 FTID2 = vect(FTID, geom = c("Lon", "Lat"), crs = "WGS84")
 FTID2 = terra::project(FTID2, crs(NorAmericamap))
 
-#Map, distribution of oxygen hair (known and assumed)
+#Create Map, distribution of oxygen hair (known and assumed)
 ggplot() + 
   geom_sf(data = NorAmericamap) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="d18O" & FTID2$Element=="hair" & FTID2$Data.Origin == "known"), 
                   aes(color = "Known")) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="d18O" & FTID2$Element=="hair" & FTID2$Data.Origin == "known"), 
-                  color = "black", shape = 1, size = 2) +
+                  color = "black", shape = 1, size = 2.5) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="d18O" & FTID2$Element=="hair" & FTID2$Data.Origin == "assumed"), 
                   aes(color = "Assumed")) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="d18O" & FTID2$Element=="hair" & FTID2$Data.Origin == "assumed"), 
-                  color= "black", shape = 1, size = 2) +
+                  color= "black", shape = 1, size = 2.5) +
   scale_color_manual(name = "Legend", 
                      values = c(Known ="#7AD151FF", Assumed = "#414788FF")) +
-  labs(title = ("Oxygen Hair Samples"))+
   theme_void() + 
   theme(legend.box.background = element_rect(),legend.text = element_text(color = 'black'),
         legend.title = element_text(color = 'black'),
         legend.box.margin=margin(5,5,5,5), 
         legend.position = c(0.15, 0), legend.justification = c(0, 0)) 
-ggsave("figures/Map_hairoxygen.png")
+ggsave("figures/Figure1B.png")
 
 
-#Map, distribution of strontium hair (known and assumed)
+#Create Map, distribution of strontium hair (known and assumed)
 ggplot() + 
   geom_sf(data = NorAmericamap) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="87Sr/86Sr" & FTID2$Element=="hair" & FTID2$Data.Origin == "known"), 
              aes(color = "Known"), shape = 15, size=2) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="87Sr/86Sr" & FTID2$Element=="hair" & FTID2$Data.Origin == "known"), 
-             color = "black", shape = 0, size = 2)+
+             color = "black", shape = 0, size = 2.5)+
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="87Sr/86Sr" & FTID2$Element=="hair" & FTID2$Data.Origin == "assumed"), 
-             aes( color = "Assumed"), shape = 15, size=2) +
+             aes( color = "Assumed"), shape = 15, size=2.5) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="87Sr/86Sr" & FTID2$Element=="hair" & FTID2$Data.Origin == "assumed"), 
              color = "black", shape = 0, size = 2)+
   scale_color_manual(name = "Legend", 
                      values = c(Known= "#7AD151FF", Assumed = "#414788FF")) +
-  labs(title = "Strontium Hair Samples") +
   theme_void() + 
   theme(legend.box.background=element_rect(),legend.text = element_text(color = 'black'),
         legend.title = element_text(color = 'black'),
         legend.box.margin=margin(5,5,5,5), 
         legend.position = c(0.15, 0),legend.justification = c(0, 0))
-ggsave("figures/Map_KASrhair.png")
+ggsave("figures/Figure1A.png")
 
 
-#Map, distribution of oxygen tooth enamel (known and assumed)
+#Create Map, distribution of oxygen tooth enamel (known and assumed)
 ggplot() + 
   geom_sf(data = NorAmericamap)+
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="d18O" & FTID2$Element=="teeth" & FTID2$Data.Origin == "known"), 
              aes( color = "Known")) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="d18O" & FTID2$Element=="teeth" & FTID2$Data.Origin == "known"), 
-             color = "black", shape = 1, size = 2) +
+             color = "black", shape = 1, size = 2.5) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="d18O" & FTID2$Element=="teeth" & FTID2$Data.Origin == "assumed"), 
              aes( color = "Assumed")) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="d18O" & FTID2$Element=="teeth" & FTID2$Data.Origin == "assumed"), 
-             color= "black", shape = 1, size = 2) +
+             color= "black", shape = 1, size = 2.5) +
   scale_color_manual(name = "Legend", 
                      values = c(Known= "#7AD151FF", Assumed = "#414788FF")) +
-  labs(title = "Oxygen Teeth Samples") +
   theme_void() + 
   theme(legend.box.background=element_rect(),
         legend.box.margin=margin(5,5,5,5),
         legend.position = c(0.15, 0),legend.justification = c(0, 0))
-ggsave("figures/Map_KAoxygenteeth.png")
+ggsave("figures/Figure1D.png")
 
-#Map, distribution of strontium tooth enamel (known and assumed)
+#CreateMap, distribution of strontium tooth enamel (known and assumed)
 ggplot() + 
   geom_sf(data = NorAmericamap)+
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="87Sr/86Sr" & FTID2$Element=="teeth" & FTID2$Data.Origin == "known"), 
-             aes(color = "Known"), shape = 15, size=2) +
+             aes(color = "Known"), shape = 15, size=2.5) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="87Sr/86Sr" & FTID2$Element=="teeth" & FTID2$Data.Origin == "known"), 
-             color = "black", shape = 0, size = 2)+
+             color = "black", shape = 0, size = 2.5)+
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="87Sr/86Sr" & FTID2$Element=="teeth" & FTID2$Data.Origin == "assumed"), 
-             aes( color = "Assumed"), shape = 15, size=2) +
+             aes( color = "Assumed"), shape = 15, size=2.5) +
   geom_spatvector(data = subset(FTID2, FTID2$Isotope=="87Sr/86Sr" & FTID2$Element=="teeth" & FTID2$Data.Origin == "assumed"), 
-             color = "black", shape = 0, size = 2)+
+             color = "black", shape = 0, size = 2.5)+
   scale_color_manual(name = "Legend", 
                      values = c(Known= "#7AD151FF", Assumed = "#414788FF")) +
-  labs(title = "Strontium Teeth Samples") +
   theme_void() + 
   theme(legend.box.background=element_rect(),
         legend.box.margin=margin(5,5,5,5),
         legend.position = c(0.15, 0),legend.justification = c(0, 0))
-ggsave("figures/Map_KASrteeth.png")
+ggsave("figures/Figure1C.png")