Merge pull request #6 from hlwander/master

updating directories

scripts/Extract_Delaware_P_T_data.R

@@ -22,14 +22,14 @@ library(data.table)
 
 
 #  Read realsat data
-lakes_realsat <- read.csv('data/all_groups.csv') 
+lakes_realsat <- read.csv('data/Code_data/all_groups.csv') 
 
 lakes_realsat <- lakes_realsat %>%
   select(ID,long,lat) %>%
   rename(Lon=long,Lat=lat)
 
 
-mynetcdf <- 'data/us_average_P_1985_2015.nc'
+mynetcdf <- 'data/Code_data/us_average_P_1985_2015.nc'
 ncFile <- nc_open(mynetcdf)
 ilongitude <- ncvar_get(ncFile,"lon")
 ilatitude <- ncvar_get(ncFile,"lat")
@@ -38,7 +38,7 @@ Lon <- ilongitude
 Lat <- ilatitude
 image.plot(pr_mean)
 
-mynetcdf_t <- 'data/us_average_T_1985_2015.nc'
+mynetcdf_t <- 'data/Code_data/us_average_T_1985_2015.nc'
 ncFile_t <- nc_open(mynetcdf_t)
 ilongitude <- ncvar_get(ncFile_t,"lon")
 ilatitude <- ncvar_get(ncFile_t,"lat")
@@ -114,7 +114,7 @@ data_pr_temp <- data_pr_temp[, c(1,3,4,2,5)]
 
 #  Read elevation file
 
-file <- 'data/us_elevation.nc'
+file <- 'data/Code_data/us_elevation.nc'
 ncFile_alt <- nc_open(file)
 ilongitude <- ncvar_get(ncFile_t,"lon")
 ilatitude <- ncvar_get(ncFile_t,"lat")
@@ -155,4 +155,4 @@ data_elevation <- data_elevation %>%
 
 data_final <- left_join(data_pr_temp,data_elevation,by=c('ID','Lon','Lat'))
 
-write.csv(data_final,'data/pr_temp_elev_us_1985_2015.csv')
+write.csv(data_final,'data/Code_data/pr_temp_elev_us_1985_2015.csv')

scripts/FigureManuscript_SpatialDistributionClusters.R

@@ -4,22 +4,22 @@ rm(list = ls())
 Sys.setenv(TZ='UTC')
 
 if (!require("pacman"))install.packages("pacman")
-pacman::p_load(rgdal, sf)
+pacman::p_load(rgdal, sf, tidyverse)
 
 #  Get density plot by latitude
 
-data <- read.csv('data/all_groups.csv')
+data <- read.csv('data/Code_data/all_groups.csv')
 
 data <- data %>% 
   mutate(cluster = case_when(
 
-    Group_num %in%  1 ~ "Cluster 1: No change over time",
-    Group_num %in%  2 ~ "Cluster 2: Substantial increase and then maintain",
-    Group_num %in%  3 ~ "Cluster 3: Steady increase over time",
-    Group_num %in%  4 ~ "Cluster 4: Steady decrease over time",
-    Group_num %in%  5 ~ "Cluster 5: Peaks",
-    Group_num %in%  6 ~ "Cluster 6: Troughs",
-    Group_num %in%  7 ~ "Cluster 7: Outliers"
+    Group_num %in%  1 ~ "Group 1: No change over time",
+    Group_num %in%  2 ~ "Group 2: Substantial increase and then maintain",
+    Group_num %in%  3 ~ "Group 3: Steady increase over time",
+    Group_num %in%  4 ~ "Group 4: Steady decrease over time",
+    Group_num %in%  5 ~ "Group 5: Peaks",
+    Group_num %in%  6 ~ "Group 6: Troughs",
+    Group_num %in%  7 ~ "Group 7: Outliers"
     ))
 
 
@@ -53,7 +53,7 @@ p2 <- ggplot(data, mapping = aes(x = lat, color = cluster))+
   theme_figure()
 
 #  read shape file for map
-shp <- readOGR(dsn = file.path(paste0(getwd(),'/data/s_22mr22.shp')), stringsAsFactors = F)
+shp <- readOGR(dsn = file.path(paste0(getwd(),'/data/Code_data/s_22mr22.shp')), stringsAsFactors = F)
 
 data <- na.omit(data)
 

scripts/SupFigure_MapClusters.R

@@ -8,17 +8,17 @@ if (!require("pacman"))install.packages("pacman")
 pacman::p_load(tidyverse, sf, rgdal)
 
 # Read data
-data <- read.csv('data/all_groups.csv')
+data <- read.csv('data/Code_data/all_groups.csv')
 
 data <- data %>% 
   mutate(cluster = case_when(
-    Group_num %in%  1 ~ "Cluster 1: No change over time",
-    Group_num %in%  2 ~ "Cluster 2: Substantial increase and then maintain",
-    Group_num %in%  3 ~ "Cluster 3: Steady increase over time",
-    Group_num %in%  4 ~ "Cluster 4: Steady decrease over time",
-    Group_num %in%  5 ~ "Cluster 5: Peaks",
-    Group_num %in%  6 ~ "Cluster 6: Troughs",
-    Group_num %in%  7 ~ "Cluster 7: Outliers"
+    Group_num %in%  1 ~ "Group 1: No change over time",
+    Group_num %in%  2 ~ "Group 2: Substantial increase and then maintain",
+    Group_num %in%  3 ~ "Group 3: Steady increase over time",
+    Group_num %in%  4 ~ "Group 4: Steady decrease over time",
+    Group_num %in%  5 ~ "Group 5: Peaks",
+    Group_num %in%  6 ~ "Group 6: Troughs",
+    Group_num %in%  7 ~ "Group 7: Outliers"
   ))