fixed detection time

YBC_scripts/detecttime_surveydate.R

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+#Lindsey Bell
+#5/16/2023, 13:03
+#Using yellow billed cuckoo survey data to complete R lab exercises
+
+#Libraries used:
+    library(lubridate)
+
+
+#Load data into R in a usable format
+#Use relative directory to tell R where to look (use 'getwd()'
+#to see where in the directory you are and what you need to specify. 
+#Here, I had to specify the folder 'YBCU_data/' before the csv file)
+
+#second time loading up, had to specify full location:
+
+ybc=read.csv("C:/Users/Asus PC/Documents/R_Projects/R_Exercises/YBCU_data/AESO_YBCU_Pre2022DataExport_WorkingCopy_20230118.csv", header=TRUE, na.strings=c("NR","RN","-","?", "NA"))
+
+#Change misread types of data to their proper class, e.g.:
+
+t_h=as.numeric(ybc$TotalHours)
+typeof(t_h)
+
+#Must remove NAs from var when calculating stats manually: 
+
+mean(t_h, na.rm=TRUE)
+sd(t_h, na.rm=TRUE)
+mean_t_h=mean(t_h, na.rm=TRUE)
+sd_t_h=sd(t_h, na.rm=TRUE)
+    #use scale to make a standardized plot:
+        plot(scale(t_h))
+
+
+#finding best survey time with survey date and detection time
+   #Problem: multi-day surveys.
+      #convert the dates to a usable form; use sub-string to extract important values
+      #limit mutli-day surveys to only reflect starting date
+          m_d_survdat=substr(survdt, 1, 9)
+
+      #change class from character to date
+          mdy_survdat=as.Date(m_d_survdat, format = "MM/DD/YYYY") 
+
+      #convert to a usable format for R using lubridate
+          mdy_survdat=mdy(m_d_survdat)
+
+  #extract survey dates
+    dayofyear_survdat=format(mdy_survdat, "%j")
+    ybc$Month=months(mdy_survdat)
+
+  #formatting number obs (with detection time)
+    #plot doesn't display correctly: there should certainly be more points on it!
+    plot(dayofyear_survdat, ybc$TimeDetect)
+
+    #we can double check that there should be more points by plotting another variable
+    #that could represent detections. Here, we chose to plot number of calls,
+    #since NumCalls is only recorded if a detection is made
+    #new plot 
+    plot(dayofyear_survdat, ybc$NumCalls,
+         main = "Suvery Date vs. Number of Calls",
+         xlab = "Survey Date",
+         ylab = "Num of Calls",
+         xlim = c(150,268)
+    )
+    grid()
+
+  #can likely fix this plot by converting detection times from char to num (using lubridate)
+
+    library(lubridate)
+    dt=ybc$TimeDetect
+      #many detection times also include AM, so use substring to pull out only numeric values
+        dt_clean=substr(dt, 1,5)
+      #use lubridate to pull out numeric hour and minute (all observations are in the morning, 
+      #so no need to convert to 24hr clock)
+         dt_clean=hm(dt_clean)
+         typeof(dt_clean)
+
+  #plot should look much more reasonable now:
+   plot(dayofyear_survdat, dt_clean,
+        main = "Suvery Date vs. YBC Detection Time",
+        xlab = "Survey Date",
+        ylab = "Detection Time",
+        xlim = c(150,270),
+        yaxt="n"
+        )
+    grid()
+
+
+    plot(ybc$Month, dt_clean,
+         main = "Suvery Date vs. YBC Detection Time",
+         xlab = "Survey Date",
+         ylab = "Detection Time",
+    )
+    grid()
+
+
+