PhenoCam ROI Summary Files With R

Here's a jupyter notebook demonstrating how to read in and plot an ROI (Region of Interest) summary using R. In this case I'm using the 3-day summary file from the alligatorriver site. The summary files are in CSV format and can be read directly from the site using a URL.



In [1]:

    
library(ggplot2)
library(lubridate)

baseurl = 'http://klima.sr.unh.edu/data/archive'
sitename = 'alligatorriver'
roiname1 = 'DB_0001'

csvfile = sprintf("%s_%s_3day.csv",sitename,roiname1)
csvurl = sprintf("%s/%s/ROI/%s",baseurl,sitename,csvfile)
df = read.csv(url(csvurl),comment.char="#",header=TRUE)
df$date = as.Date(df$date)
df$year = year(df$date)
ystart = min(df$year)
yend = max(df$year)
df$year = factor(df$year,levels=seq(ystart,yend))
head(df)









    



Attaching package: ‘lubridate’

The following object is masked from ‘package:base’:

    date







    





date year doy image_count midday_filename midday_r midday_g midday_b midday_gcc midday_rcc ⋯ rcc_std rcc_50 rcc_75 rcc_90 max_solar_elev snow_flag outlierflag_gcc_mean outlierflag_gcc_50 outlierflag_gcc_75 outlierflag_gcc_90

	2012-05-04                          2012                                125                                  2                                  alligatorriver_2012_05_03_120110.jpg 106.30031                           115.7373                            55.34694                            0.41724                             0.38322                             ⋯                                   0.00038                             0.38285                             0.38304                             0.38315                             70.15241                            NA                                  NA                                  NA                                  NA                                  NA                                  
	2012-05-07                          2012                                128                                 56                                  alligatorriver_2012_05_07_120109.jpg 104.66830                           114.4270                            57.99294                            0.41296                             0.37774                             ⋯                                   0.00839                             0.37729                             0.38064                             0.38655                             71.54443                            NA                                  NA                                  NA                                  NA                                  NA                                  
	2012-05-10                          2012                                131                                 62                                  alligatorriver_2012_05_10_113109.jpg  94.53853                           114.4593                            68.72398                            0.41214                             0.34041                             ⋯                                   0.01312                             0.38170                             0.38501                             0.38677                             72.32268                            NA                                  NA                                  NA                                  NA                                  NA                                  
	2012-05-13                          2012                                134                                 62                                  alligatorriver_2012_05_13_120110.jpg 104.59880                           113.6020                            57.22023                            0.41247                             0.37978                             ⋯                                   0.00911                             0.37968                             0.38395                             0.38772                             73.05576                            NA                                  NA                                  NA                                  NA                                  NA                                  
	2012-05-16                          2012                                137                                 57                                  alligatorriver_2012_05_16_113128.jpg 102.15546                           111.6633                            53.31193                            0.41801                             0.38242                             ⋯                                   0.00946                             0.36699                             0.37010                             0.37619                             73.74132                            NA                                  NA                                  NA                                  NA                                  NA                                  
	2012-05-19                          2012                                140                                 56                                  alligatorriver_2012_05_19_120110.jpg 104.56388                           114.9894                            58.09885                            0.41415                             0.37660                             ⋯                                   0.00739                             0.37182                             0.37666                             0.38113                             74.37753                            NA                                  NA                                  NA                                  NA                                  NA



In [2]:

    
options(repr.plot.width = 8)
options(repr.plot.height = 2.5)
p = ggplot(df,aes(x=date,y=gcc_90)) + geom_line(col='green') + geom_point(size=.5, na.rm=TRUE)
p



In [4]:

    
## plot gcc_90 vs doy for each year
options(repr.plot.width = 8)
options(repr.plot.height = 3.0)
df$year = factor(df$year,levels=seq(ystart,yend))
p = ggplot(df,aes(x=doy,y=gcc_90,col=year)) + geom_line(alpha=.5, na.rm=TRUE) 
p = p + geom_point(alpha=.5, na.rm=TRUE)
p



In [ ]:

date	year	doy	image_count	midday_filename	midday_r	midday_g	midday_b	midday_gcc	midday_rcc	⋯	rcc_std	rcc_50	rcc_75	rcc_90	max_solar_elev	snow_flag	outlierflag_gcc_mean	outlierflag_gcc_50	outlierflag_gcc_75	outlierflag_gcc_90
2012-05-04	2012	125	2	alligatorriver_2012_05_03_120110.jpg	106.30031	115.7373	55.34694	0.41724	0.38322	⋯	0.00038	0.38285	0.38304	0.38315	70.15241	NA	NA	NA	NA	NA
2012-05-07	2012	128	56	alligatorriver_2012_05_07_120109.jpg	104.66830	114.4270	57.99294	0.41296	0.37774	⋯	0.00839	0.37729	0.38064	0.38655	71.54443	NA	NA	NA	NA	NA
2012-05-10	2012	131	62	alligatorriver_2012_05_10_113109.jpg	94.53853	114.4593	68.72398	0.41214	0.34041	⋯	0.01312	0.38170	0.38501	0.38677	72.32268	NA	NA	NA	NA	NA
2012-05-13	2012	134	62	alligatorriver_2012_05_13_120110.jpg	104.59880	113.6020	57.22023	0.41247	0.37978	⋯	0.00911	0.37968	0.38395	0.38772	73.05576	NA	NA	NA	NA	NA
2012-05-16	2012	137	57	alligatorriver_2012_05_16_113128.jpg	102.15546	111.6633	53.31193	0.41801	0.38242	⋯	0.00946	0.36699	0.37010	0.37619	73.74132	NA	NA	NA	NA	NA
2012-05-19	2012	140	56	alligatorriver_2012_05_19_120110.jpg	104.56388	114.9894	58.09885	0.41415	0.37660	⋯	0.00739	0.37182	0.37666	0.38113	74.37753	NA	NA	NA	NA	NA