This tutorial explores working with date and time field in R. We will overview
the differences between
POSIXlt as used to convert
a date / time field in character (string) format to a date-time format that is
recognized by R. This conversion supports efficient plotting, subsetting and
analysis of time series data.
After completing this tutorial, you will be able to:
- Describe various date-time classes and data structure in R.
- Explain the difference between
POSIXltdata classes are and why POSIXct may be preferred for some tasks.
- Convert a column containing date-time information in character format to a date-time R class.
- Convert a date-time column to different date-time classes.
- Write out a date-time class object in different ways (month-day, month-day-year, etc).
Things You’ll Need To Complete This Tutorials
You will need the most current version of R and, preferably, RStudio loaded on your computer to complete this tutorial.
Install R Packages
More on Packages in R – Adapted from Software Carpentry.
The data used in this lesson were collected at the National Ecological Observatory Network's Harvard Forest field site. These data are proxy data for what will be available for 30 years on the NEON data portal for the Harvard Forest and other field sites located across the United States.
Set Working Directory: This lesson assumes that you have set your working directory to the location of the downloaded and unzipped data subsets.
R Script & Challenge Code: NEON data lessons often contain challenges that reinforce learned skills. If available, the code for challenge solutions is found in the downloadable R script of the entire lesson, available in the footer of each lesson page.
The Data Approach
Intro to Time Series Data in R tutorial
we imported a time series dataset in
.csv format into R. We learned how to
quickly plot these data by converting the date column to an R
In this tutorial we will explore how to work with a column that contains both a
date AND a time stamp.
We will use functions from both base R and the
lubridate package to work
with date-time data classes.
# Load packages required for entire script library(lubridate) #work with dates #Set the working directory and place your downloaded data there wd <- "~/Documents/"
Import CSV File
First, let's import our time series data. We are interested in temperature,
precipitation and photosynthetically active radiation (PAR) - metrics that are
strongly associated with vegetation green-up and brown down (phenology or
phenophase timing). We will use the
that contains atmospheric data for the NEON Harvard Forest field site,
aggregated at 15-minute intervals. Download the dataset for these exercises here.
# Load csv file of 15 min meteorological data from Harvard Forest # https://harvardforest.fas.harvard.edu/data/p00/hf001/hf001-10-15min-m.csv # Factors=FALSE so strings, series of letters/words/numerals, remain characters harMet_15Min <- read.csv( file=paste0(wd,"hf001-10-15min-m.csv"), stringsAsFactors = FALSE) ## Warning in file(file, "rt"): cannot open file '/Users/olearyd/Documents/ ## hf001-10-15min-m.csv': No such file or directory ## Error in file(file, "rt"): cannot open the connection
Date and Time Data
Let's revisit the data structure of our
harMet_15Min object. What is the class
# view column data class class(harMet_15Min$datetime) ## Error in eval(expr, envir, enclos): object 'harMet_15Min' not found # view sample data head(harMet_15Min$datetime) ## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'head': object 'harMet_15Min' not found
datetime column is stored as a
character class. We need to convert it to
date-time class. What happens when we use the
as.Date method that we learned
about in the
Intro to Time Series Data in R tutorial?
# convert column to date class dateOnly_HARV <- as.Date(harMet_15Min$datetime) ## Error in as.Date(harMet_15Min$datetime): object 'harMet_15Min' not found # view data head(dateOnly_HARV) ## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'head': object 'dateOnly_HARV' not found
When we use
as.Date, we lose the time stamp.
Explore Date and Time Classes
R - Date Class - as.Date
As we just saw, the
as.Date format doesn't store any time information. When we
as.Date method to convert a date stored as a character class to an R
date class, it will ignore all values after the date string.
# Convert character data to date (no time) myDate <- as.Date("2015-10-19 10:15") str(myDate) ## Date[1:1], format: "2015-10-19" # what happens if the date has text at the end? myDate2 <- as.Date("2015-10-19Hello") str(myDate2) ## Date[1:1], format: "2015-10-19"
As we can see above the
as.Date() function will convert the characters that it
recognizes to be part of a date into a date class and ignore all other
characters in the string.
R - Date-Time - The POSIX classes
If we have a column containing both date and time we need to use a class that
stores both date AND time. Base R offers two closely related classes for date
as.POSIXct method converts a date-time string into a
# Convert character data to date and time. timeDate <- as.POSIXct("2015-10-19 10:15") str(timeDate) ## POSIXct[1:1], format: "2015-10-19 10:15:00" timeDate ##  "2015-10-19 10:15:00 MDT"
as.POSIXct stores both a date and time with an associated time zone. The
default time zone selected, is the time zone that your computer is set to which
is most often your local time zone.
POSIXct stores date and time in seconds with the number of seconds beginning
at 1 January 1970. Negative numbers are used to store dates prior to 1970.
POSIXct format stores each date and time a single value in units of
seconds. Storing the data this way, optimizes use in
data.frames and speeds up
computation, processing and conversion to other formats.
# to see the data in this 'raw' format, i.e., not formatted according to the # class type to show us a date we recognize, use the `unclass()` function. unclass(timeDate) ##  1445271300 ## attr(,"tzone") ##  ""
Here we see the number of seconds from 1 January 1970 to 9 October 2015
1445271300). Also, we see that a time zone (
tzone) is associated with the value in seconds.
Data Tip: The
unclass method in R allows you
to view how a particular R object is stored.
POSIXct format is optimized for storage and computation. However, humans
aren't quite as computationally efficient as computers! Also, we often want to
quickly extract some portion of the data (e.g., months). The
stores date and time information in a format that we are used to seeing (e.g.,
second, min, hour, day of month, month, year, numeric day of year, etc).
# Convert character data to POSIXlt date and time timeDatelt<- as.POSIXlt("2015-10-19 10:15") str(timeDatelt) ## POSIXlt[1:1], format: "2015-10-19 10:15:00" timeDatelt ##  "2015-10-19 10:15:00 MDT" unclass(timeDatelt) ## $sec ##  0 ## ## $min ##  15 ## ## $hour ##  10 ## ## $mday ##  19 ## ## $mon ##  9 ## ## $year ##  115 ## ## $wday ##  1 ## ## $yday ##  291 ## ## $isdst ##  1 ## ## $zone ##  "MDT" ## ## $gmtoff ##  NA
When we convert a string to
POSIXlt, and view it in R, it still looks
similar to the
POSIXct format. However,
unclass() shows us that the data are
stored differently. The
POSIXlt class stores the hour, minute, second, day,
month, and year separately.
Months in POSIXlt
POSIXlt has a few quirks. First, the month values stored in the
zero-based indexing. This means that month #1 (January) is stored
as 0, and month #2 (February) is stored as 1. Notice in the output above,
October is stored as the 9th month (
$mon = 9).
Years in POSIXlt
Years are also stored differently in the
POSIXlt class. Year values are stored
using a base index value of 1900. Thus, 2015 is stored as 115 (
$year = 115
- 115 years since 1900).
Data Tip: To learn more about how R stores
information within date-time and other objects check out the R documentation
?POSIXlt). NOTE: you can use this same syntax to learn
about particular functions (e.g.,
Having dates classified as separate components makes
more resource intensive to use in
data.frames. This slows things down! We will
POSIXct for this tutorial.
Data Tip: There are other R packages that
support date-time data classes, including
Convert to Date-time Class
When we convert from a character to a date-time class we need to tell R how
the date and time information are stored in each string. To do this, we can use
format=. Let's have a look at one of our date-time strings to determine it's
# view one date-time field harMet_15Min$datetime ## Error in eval(expr, envir, enclos): object 'harMet_15Min' not found
Looking at the results above, we see that our data are stored in the format:
Year-Month-Day "T" Hour:Minute (
2005-01-01T00:15). We can use this information
to populate our
format string using the following designations for the
components of the date-time data:
- %Y - year
- %m - month
- %d - day
- %H:%M - hours:minutes
Data Tip: A list of options for date-time format
is available in the
strptime function help:
help(strptime). Check it out!
The "T" inserted into the middle of
datetime isn't a standard character for
date and time, however we can tell R where the character is so it can ignore
it and interpret the correct date and time as follows:
# convert single instance of date/time in format year-month-day hour:min:sec as.POSIXct(harMet_15Min$datetime,format="%Y-%m-%dT%H:%M") ## Error in as.POSIXct(harMet_15Min$datetime, format = "%Y-%m-%dT%H:%M"): object 'harMet_15Min' not found ## The format of date-time MUST match the specified format or the data will not # convert; see what happens when you try it a different way or without the "T" # specified as.POSIXct(harMet_15Min$datetime,format="%d-%m-%Y%H:%M") ## Error in as.POSIXct(harMet_15Min$datetime, format = "%d-%m-%Y%H:%M"): object 'harMet_15Min' not found as.POSIXct(harMet_15Min$datetime,format="%Y-%m-%d%H:%M") ## Error in as.POSIXct(harMet_15Min$datetime, format = "%Y-%m-%d%H:%M"): object 'harMet_15Min' not found
Using the syntax we've learned, we can convert the entire
datetime column into
new.date.time <- as.POSIXct(harMet_15Min$datetime, format="%Y-%m-%dT%H:%M" #format time ) ## Error in as.POSIXct(harMet_15Min$datetime, format = "%Y-%m-%dT%H:%M"): object 'harMet_15Min' not found # view output head(new.date.time) ## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'head': object 'new.date.time' not found # what class is the output class(new.date.time) ## Error in eval(expr, envir, enclos): object 'new.date.time' not found
About Time Zones
Above, we successfully converted our data into a date-time class. However, what
timezone is the output
new.date.time object that we created using?
2005-04-15 03:30:00 MDT
It appears as if our data were assigned MDT (which is the timezone of the computer where these tutorials were processed originally - in Colorado - Mountain Time). However, we know from the metadata, explored in the Why Metadata Are Important: How to Work with Metadata in Text & EML Format tutorial, that these data were stored in Eastern Standard Time.
Assign Time Zone
When we convert a date-time formatted column to
POSIXct format, we need to
assign an associated time zone. If we don't assign a time zone,R will
default to the local time zone that is defined on your computer.
There are individual designations for different time zones and time zone
variants (e.g., does the time occur during daylight savings time).
Data Tip: Codes for time zones can be found in this time zone table.
The code for the Eastern time zone that is the closest match to the NEON Harvard
Forest field site is
America/New_York. Let's convert our
one more time, and define the associated timezone (
# assign time zone to just the first entry as.POSIXct(harMet_15Min$datetime, format = "%Y-%m-%dT%H:%M", tz = "America/New_York") ## Error in as.POSIXct(harMet_15Min$datetime, format = "%Y-%m-%dT%H:%M", : object 'harMet_15Min' not found
The output above, shows us that the time zone is now correctly set as EST.
Convert to Date-time Data Class
Now, using the syntax that we learned above, we can convert the entire
datetime column to a
# convert to POSIXct date-time class harMet_15Min$datetime <- as.POSIXct(harMet_15Min$datetime, format = "%Y-%m-%dT%H:%M", tz = "America/New_York") ## Error in as.POSIXct(harMet_15Min$datetime, format = "%Y-%m-%dT%H:%M", : object 'harMet_15Min' not found # view structure and time zone of the newly defined datetime column str(harMet_15Min$datetime) ## Error in str(harMet_15Min$datetime): object 'harMet_15Min' not found tz(harMet_15Min$datetime) ## Error in tz(harMet_15Min$datetime): object 'harMet_15Min' not found
Now that our
datetime data are properly identified as a
data class we can continue on and look at the patterns of precipitation,
temperature, and PAR through time.
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