if (!require("pacman")) install.packages("pacman")
## Loading required package: pacman
library(readxl)


SilverSagebrushData2024 <- read_excel("C:/Users/tlittmann/USDA/Rangeland responses to fire - Sagebrush/A_cana/Data/SilverSagebrushData2024.xlsx")
## New names:
## • `` -> `...10`
## • `` -> `...11`
View(SilverSagebrushData2024)


summary(SilverSagebrushData2024)
##       Plot          Shrub ID       Height (cm)        D1 (cm)      
##  Min.   :501.0   Min.   :  1.00   Min.   :  0.00   Min.   :  0.00  
##  1st Qu.:507.0   1st Qu.: 19.75   1st Qu.:  0.00   1st Qu.:  0.00  
##  Median :513.5   Median : 38.50   Median : 52.00   Median : 45.00  
##  Mean   :513.2   Mean   : 74.14   Mean   : 44.14   Mean   : 54.76  
##  3rd Qu.:519.2   3rd Qu.:131.50   3rd Qu.: 69.25   3rd Qu.: 95.00  
##  Max.   :525.0   Max.   :215.00   Max.   :130.00   Max.   :181.00  
##     D2 (cm)         # of Stems   # of Resprouts     Length of Resprouts
##  Min.   :  0.00   Min.   : 0.0   Length:80          Length:80          
##  1st Qu.:  0.00   1st Qu.: 0.0   Class :character   Class :character   
##  Median : 35.00   Median : 2.0   Mode  :character   Mode  :character   
##  Mean   : 40.61   Mean   : 3.8                                         
##  3rd Qu.: 65.50   3rd Qu.: 5.0                                         
##  Max.   :136.00   Max.   :23.0                                         
##    Gall Index     ...10            ...11          
##  Min.   :0.000   Mode:logical   Length:80         
##  1st Qu.:0.000   NA's:80        Class :character  
##  Median :0.000                  Mode  :character  
##  Mean   :0.125                                    
##  3rd Qu.:0.000                                    
##  Max.   :1.000
str(SilverSagebrushData2024)
## tibble [80 × 11] (S3: tbl_df/tbl/data.frame)
##  $ Plot               : num [1:80] 501 501 501 502 502 502 503 503 503 504 ...
##  $ Shrub ID           : num [1:80] 1 2 3 102 104 106 4 5 6 7 ...
##  $ Height (cm)        : num [1:80] 0 0 0 0 0 0 124 94 100 0 ...
##  $ D1 (cm)            : num [1:80] 0 0 0 0 0 0 181 116 160 0 ...
##  $ D2 (cm)            : num [1:80] 0 0 0 0 0 0 112 107 124 0 ...
##  $ # of Stems         : num [1:80] 0 0 0 0 0 0 5 2 1 0 ...
##  $ # of Resprouts     : chr [1:80] "0" "0" "0" "0" ...
##  $ Length of Resprouts: chr [1:80] "0" "0" "0" "0" ...
##  $ Gall Index         : num [1:80] 0 0 0 0 0 0 1 0 0 0 ...
##  $ ...10              : logi [1:80] NA NA NA NA NA NA ...
##  $ ...11              : chr [1:80] NA NA NA NA ...
data1 <- c(SilverSagebrushData2024$`Height (cm)`)

data1
##  [1]   0   0   0   0   0   0 124  94 100   0   0   0  72  49   0  58  89 130 130
## [20]   0  54   0  52   0   0  68  59  58  53  38   0  79  71  71   0  58  58   0
## [39]  92  38   0  50  99  99  52  52  76  76  52  58  76   0   0   0  63   0  33
## [58]   0  48  63  77  77  57 110  57  36  36  57  66  48   0  69  62   0  70  52
## [77]  27   0   0  38
mean(data1)
## [1] 44.1375
dim(SilverSagebrushData2024)
## [1] 80 11
names(SilverSagebrushData2024)
##  [1] "Plot"                "Shrub ID"            "Height (cm)"        
##  [4] "D1 (cm)"             "D2 (cm)"             "# of Stems"         
##  [7] "# of Resprouts"      "Length of Resprouts" "Gall Index"         
## [10] "...10"               "...11"
head(SilverSagebrushData2024$`Shrub ID`[4])
## [1] 102

##Manipulation

columns <- names(SilverSagebrushData2024)
columns
##  [1] "Plot"                "Shrub ID"            "Height (cm)"        
##  [4] "D1 (cm)"             "D2 (cm)"             "# of Stems"         
##  [7] "# of Resprouts"      "Length of Resprouts" "Gall Index"         
## [10] "...10"               "...11"
for( i in 1:length(columns)) {
  column = columns[i]
  print(head(SilverSagebrushData2024[[column]]))  
}
## [1] 501 501 501 502 502 502
## [1]   1   2   3 102 104 106
## [1] 0 0 0 0 0 0
## [1] 0 0 0 0 0 0
## [1] 0 0 0 0 0 0
## [1] 0 0 0 0 0 0
## [1] "0" "0" "0" "0" "0" "0"
## [1] "0" "0" "0" "0" "0" "0"
## [1] 0 0 0 0 0 0
## [1] NA NA NA NA NA NA
## [1] NA  NA  NA  NA  "." NA
i
## [1] 11
# Sample vector
values <- c(data1)

# Initialize an empty vector to store non-zero values
non_zero_values <- c()

# Loop through each value in the vector
for (value in values) {
  # Check if the value is not zero
  if (value != 0) {
    # Append the non-zero value to the new vector
    non_zero_values <- c(non_zero_values, value)
  }
}

# Print the result
print(non_zero_values)
##  [1] 124  94 100  72  49  58  89 130 130  54  52  68  59  58  53  38  79  71  71
## [20]  58  58  92  38  50  99  99  52  52  76  76  52  58  76  63  33  48  63  77
## [39]  77  57 110  57  36  36  57  66  48  69  62  70  52  27  38
###Histo it foo

hist(non_zero_values, 
     main="Histogram of Sage Height", 
     xlab="Height cm",
     ylab = "Number of Plants", 
     col="red", 
     border="black")