Working with data
Last updated on 2024-05-24 | Edit this page
Overview
Questions
- How do you manipulate tabular data in R?
Objectives
- Import CSV data into R.
- Use pipes to link steps together into pipelines.
- Export data to a CSV file.
R Packages
R packages are extensions to the R language. R packages contain code, data, and documentation that people can download and install to add more functionality to R.
To download and install packages onto your computer, type
install.packages("package_name") in the R console. Must use
quotes. This function will connect to the internet and download packages
from servers that have R packages. The Comprehensive R Archive Network
(cran.r-project.org) is a network of web servers around the world that
store R packages.
To use the package, use library(package_name) to load
it. Do not use quotes. You want to install the package to your computer
once, and then load it with library() in each script where
you need to use it. Generally its a good idea to list all the libraries
at the beginning of the script.
Importing data
File paths
When we reference other files from an R script, we need to give R precise instructions on where those files are. We do that using something called a file path.
There are two kinds of paths: absolute and relative. Absolute paths are specific to a particular computer, whereas relative paths are relative to a certain folder. For instance an absolute path is “/Users/wyk/Documents/code_stuff/CNC_coding_intro_lesson”, and relative path is “CNC_coding_intro_lesson”.
Read a file
Use library to load the needed packages.
R
library(readr)
library(lubridate)
library(dplyr)
We will use the read_csv function from
readr package to read a csv of CNC iNaturalist
observations, and the argument we give will be the path to the CSV file.
We will store the observations in an object named
inat_raw.
R
inat_raw <- read_csv('data/raw/observations-397280.csv')
OUTPUT
Rows: 171155 Columns: 39
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (23): observed_on_string, time_observed_at, time_zone, user_login, user...
dbl (10): id, user_id, num_identification_agreements, num_identification_di...
lgl (5): captive_cultivated, private_place_guess, private_latitude, privat...
date (1): observed_on
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.inat_raw is stored in memory. It appears in
Environment tab. Double click on inat_raw
in Environment to see all the data.
read_csv provides some info about the CSV.
- the number of rows and columns
- the delimiter of the file, which is how values are
separated, a comma
"," - the data types for the columns
Use glimpse() to see a information about a dataframe.
Number of rows and columns. For each column, we see the name, data type
(dbl for number, chr for character,
lgl for logical. date is a data type
from data.frame), and the first few values.
R
glimpse(inat_raw)
OUTPUT
Rows: 171,155
Columns: 39
$ id <dbl> 2931940, 2934641, 2934854, 2934961, 2…
$ observed_on_string <chr> "2016-04-14 12:25:00 AM PDT", "Thu Ap…
$ observed_on <date> 2016-04-14, 2016-04-14, 2016-04-14, …
$ time_observed_at <chr> "2016-04-14 19:25:00 UTC", "2016-04-1…
$ time_zone <chr> "Pacific Time (US & Canada)", "Pacifi…
$ user_id <dbl> 151043, 10814, 8510, 80445, 80445, 80…
$ user_login <chr> "msmorales", "smartrf", "stonebird", …
$ user_name <chr> "Michael Morales", "Richard Smart (he…
$ created_at <chr> "2016-04-14 07:28:36 UTC", "2016-04-1…
$ updated_at <chr> "2021-12-26 06:58:04 UTC", "2018-05-2…
$ quality_grade <chr> "research", "needs_id", "needs_id", "…
$ license <chr> "CC-BY", "CC-BY-NC", NA, NA, NA, NA, …
$ url <chr> "http://www.inaturalist.org/observati…
$ image_url <chr> "https://inaturalist-open-data.s3.ama…
$ sound_url <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ tag_list <chr> NA, NA, "\"Allen's Hummingbird\" \"Se…
$ description <chr> "Spotted on a the wall of a planter, …
$ num_identification_agreements <dbl> 5, 2, 0, 1, 2, 2, 1, 0, 1, 2, 1, 1, 1…
$ num_identification_disagreements <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ captive_cultivated <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FA…
$ oauth_application_id <dbl> 2, 3, NA, NA, NA, NA, 3, 3, NA, NA, N…
$ place_guess <chr> "Olive Lane Walk Pomona, CA 91768", "…
$ latitude <dbl> 34.05829, 34.01742, NA, 34.13020, 34.…
$ longitude <dbl> -117.8219, -118.2892, NA, -118.8226, …
$ positional_accuracy <dbl> 4, 5, 220, NA, NA, NA, NA, 17, 55, 55…
$ private_place_guess <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ private_latitude <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ private_longitude <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ public_positional_accuracy <dbl> 4, 5, 28888, NA, NA, NA, NA, 17, 55, …
$ geoprivacy <chr> NA, NA, "private", NA, NA, NA, NA, NA…
$ taxon_geoprivacy <chr> NA, NA, "open", NA, "open", "open", N…
$ coordinates_obscured <lgl> FALSE, FALSE, TRUE, FALSE, FALSE, FAL…
$ positioning_method <chr> "gps", NA, NA, NA, NA, NA, NA, NA, NA…
$ positioning_device <chr> "gps", NA, NA, NA, NA, NA, NA, NA, NA…
$ species_guess <chr> "Garden Snail", "Oestroidea", "Allen'…
$ scientific_name <chr> "Cornu aspersum", "Oestroidea", "Sela…
$ common_name <chr> "Garden Snail", "Bot Flies, Blow Flie…
$ iconic_taxon_name <chr> "Mollusca", "Insecta", "Aves", "Insec…
$ taxon_id <dbl> 480298, 356157, 6359, 54247, 36100, 3…nrow() returns the number of rows. ncol()
returns the number of columns dim() returns the number of
rows and columns.
R
nrow(inat_raw)
OUTPUT
[1] 171155R
ncol(inat_raw)
OUTPUT
[1] 39R
dim(inat_raw)
OUTPUT
[1] 171155 39names() shows the column names
R
names(inat_raw)
OUTPUT
[1] "id" "observed_on_string"
[3] "observed_on" "time_observed_at"
[5] "time_zone" "user_id"
[7] "user_login" "user_name"
[9] "created_at" "updated_at"
[11] "quality_grade" "license"
[13] "url" "image_url"
[15] "sound_url" "tag_list"
[17] "description" "num_identification_agreements"
[19] "num_identification_disagreements" "captive_cultivated"
[21] "oauth_application_id" "place_guess"
[23] "latitude" "longitude"
[25] "positional_accuracy" "private_place_guess"
[27] "private_latitude" "private_longitude"
[29] "public_positional_accuracy" "geoprivacy"
[31] "taxon_geoprivacy" "coordinates_obscured"
[33] "positioning_method" "positioning_device"
[35] "species_guess" "scientific_name"
[37] "common_name" "iconic_taxon_name"
[39] "taxon_id" To access one column, use $ and name of the column
R
inat_raw$quality_grade
OUTPUT
[1] "research" "needs_id" "needs_id" "research" "research" "research"
[7] "needs_id" "needs_id" "casual" "research" "research" "research"
[13] "needs_id" "research" "research" "research" "research" "research"
[19] "research" "research" "needs_id" "research" "research" "casual"
[25] "casual" "casual" "casual" "research" "casual" "casual"
[31] "casual" "research" "research" "casual" "research" "needs_id"
[37] "needs_id" "research" "research" "research" "research" "research"
[43] "casual" "needs_id" "research" "research" "research" "needs_id"
[49] "research" "casual" "casual" "casual" "research" "research"
[55] "needs_id" "research" "research" "research" "needs_id" "needs_id"
[61] "research" "needs_id" "research" "research" "casual" "needs_id"
[67] "research" "research" "needs_id" "research" "research" "research"
[73] "needs_id" "needs_id" "research" "research" "casual" "research"
[79] "research" "research" "needs_id" "research" "casual" "needs_id"
[85] "research" "research" "research" "research" "research" "research"
[91] "needs_id" "research" "research" "casual" "research" "needs_id"
[97] "needs_id" "research" "research" "needs_id"
[ reached getOption("max.print") -- omitted 171055 entries ]To view all the unique values in a column, use
unique()
R
unique(inat_raw$quality_grade)
OUTPUT
[1] "research" "needs_id" "casual" Manipulating data
One of the most important skills for working with data in R is the
ability to manipulate, modify, and reshape data. The dplyr
package provide a series of powerful functions for many common data
manipulation tasks.
select() filter() mutate() arrange() count()
select()
select() picks certain columns of a data.frame. To use
the select() function, the first argument is the name of
the data.frame, and the rest of the arguments are unquoted
names of the columns you want.
iNaturalist has 39 columns. We want four columns. The columns are
arranged in the order we specified inside select().
R
select(inat_raw, user_login, common_name, scientific_name, observed_on)
OUTPUT
# A tibble: 171,155 × 4
user_login common_name scientific_name observed_on
<chr> <chr> <chr> <date>
1 msmorales Garden Snail Cornu aspersum 2016-04-14
2 smartrf Bot Flies, Blow Flies, and Allies Oestroidea 2016-04-14
3 stonebird Allen's Hummingbird Selasphorus sa… 2016-04-14
4 cdegroof California Orange-winged Grasshopp… Arphia ramona 2016-04-14
5 cdegroof Western Side-blotched Lizard Uta stansburia… 2016-04-14
6 cdegroof Western Fence Lizard Sceloporus occ… 2016-04-14
7 ttempel <NA> Coelocnemis 2016-04-14
8 bradrumble House Sparrow Passer domesti… 2016-04-15
9 deedeeflower5 Amur Carp Cyprinus rubro… 2016-04-14
10 deedeeflower5 Red-eared Slider Trachemys scri… 2016-04-14
# ℹ 171,145 more rowsfilter()
The filter() function is used to select rows that meet
certain criteria. To get all the rows where the value of
common_name is equal to Western Fence Lizard,
we would run the following:
R
filter(inat_raw, common_name == 'Western Fence Lizard')
OUTPUT
# A tibble: 2,970 × 39
id observed_on_string observed_on time_observed_at time_zone user_id
<dbl> <chr> <date> <chr> <chr> <dbl>
1 2934994 2016-04-14 12:19:09 2016-04-14 2016-04-14 19:1… Pacific … 80445
2 2935263 2016-04-14 2016-04-14 <NA> Pacific … 216108
3 2935420 2016-04-14 2016-04-14 <NA> Pacific … 216108
4 2935748 2016-04-14 14:01:29 2016-04-14 2016-04-14 21:0… Pacific … 80445
5 2935965 Thu Apr 14 2016 12:44… 2016-04-14 2016-04-14 19:4… Pacific … 171443
6 2938607 Thu Apr 14 2016 16:33… 2016-04-14 2016-04-14 23:3… Pacific … 146517
7 2940103 2016-04-15 9:31:39 AM… 2016-04-15 2016-04-15 16:3… Pacific … 80984
8 2940838 Fri Apr 15 2016 10:11… 2016-04-15 2016-04-15 17:1… Pacific … 201119
9 2940848 Fri Apr 15 2016 10:17… 2016-04-15 2016-04-15 17:1… Pacific … 201119
10 2940855 Fri Apr 15 2016 10:42… 2016-04-15 2016-04-15 17:4… Pacific … 201119
# ℹ 2,960 more rows
# ℹ 33 more variables: user_login <chr>, user_name <chr>, created_at <chr>,
# updated_at <chr>, quality_grade <chr>, license <chr>, url <chr>,
# image_url <chr>, sound_url <chr>, tag_list <chr>, description <chr>,
# num_identification_agreements <dbl>,
# num_identification_disagreements <dbl>, captive_cultivated <lgl>,
# oauth_application_id <dbl>, place_guess <chr>, latitude <dbl>, …The == sign means “is equal to”. There are several other
operators we can use: >, >=, <, <=, and != (not equal
to).
The pipe: %>%
What happens if we want to both select() and
filter() our data?
We use the pipe operator (%>%) to call multiple
functions. You can insert it by using the keyboard shortcut
Shift+Cmd+M (Mac) or Shift+Ctrl+M (Windows).
Get user_login, common_name, scientific_name, observed_on for all observations where common_name is ‘Western Fence Lizard’. Use filter to select rows, then use select to select columns.
R
inat_raw %>%
filter(common_name == 'Western Fence Lizard') %>%
select(user_login, common_name, scientific_name, observed_on)
OUTPUT
# A tibble: 2,970 × 4
user_login common_name scientific_name observed_on
<chr> <chr> <chr> <date>
1 cdegroof Western Fence Lizard Sceloporus occidentalis 2016-04-14
2 deedeeflower5 Western Fence Lizard Sceloporus occidentalis 2016-04-14
3 deedeeflower5 Western Fence Lizard Sceloporus occidentalis 2016-04-14
4 cdegroof Western Fence Lizard Sceloporus occidentalis 2016-04-14
5 lchroman Western Fence Lizard Sceloporus occidentalis 2016-04-14
6 maiz Western Fence Lizard Sceloporus occidentalis 2016-04-14
7 kimssight Western Fence Lizard Sceloporus occidentalis 2016-04-15
8 sarahwenner Western Fence Lizard Sceloporus occidentalis 2016-04-15
9 sarahwenner Western Fence Lizard Sceloporus occidentalis 2016-04-15
10 sarahwenner Western Fence Lizard Sceloporus occidentalis 2016-04-15
# ℹ 2,960 more rowsPipe operator take the thing on the lefthand side and insert it as
the first argument of the function on the righthand side. By putting
each of our functions onto a new line, we can build a nice, readable
pipeline. It can be useful to think of this as a little assembly line
for our data. It starts at the top and gets piped into a
filter() function, and it comes out modified somewhat. It
then gets sent into the select() function, where it is
further modified, and then the final product gets printed out to our
console. It can also be helpful to think of %>% as
meaning “and then”.
If you want to see all the records, assign the data.frame to an object.
R
temp <- inat_raw %>%
filter(common_name == 'Western Fence Lizard') %>%
select(user_login, common_name, scientific_name, observed_on)
We can also use multiple conditions in one filter()
statement.
When researchers use iNaturalist data, the normally use research
grade observations. Here we will get all observations that research
grade and common_name is Western Fence Lizard. use &
for and.
R
inat_raw %>%
filter( common_name == 'Western Fence Lizard'
& quality_grade == 'research') %>%
select(user_login, common_name, scientific_name, observed_on)
OUTPUT
# A tibble: 2,942 × 4
user_login common_name scientific_name observed_on
<chr> <chr> <chr> <date>
1 cdegroof Western Fence Lizard Sceloporus occidentalis 2016-04-14
2 deedeeflower5 Western Fence Lizard Sceloporus occidentalis 2016-04-14
3 deedeeflower5 Western Fence Lizard Sceloporus occidentalis 2016-04-14
4 cdegroof Western Fence Lizard Sceloporus occidentalis 2016-04-14
5 lchroman Western Fence Lizard Sceloporus occidentalis 2016-04-14
6 maiz Western Fence Lizard Sceloporus occidentalis 2016-04-14
7 kimssight Western Fence Lizard Sceloporus occidentalis 2016-04-15
8 sarahwenner Western Fence Lizard Sceloporus occidentalis 2016-04-15
9 sarahwenner Western Fence Lizard Sceloporus occidentalis 2016-04-15
10 sarahwenner Western Fence Lizard Sceloporus occidentalis 2016-04-15
# ℹ 2,932 more rowsHere we will get observations where user_login is
‘natureinla’ and common_name is ‘Western Fence Lizard’.
R
inat_raw %>%
filter(user_login == 'natureinla' & common_name == 'Western Fence Lizard') %>%
select(user_login, common_name, scientific_name, observed_on)
OUTPUT
# A tibble: 79 × 4
user_login common_name scientific_name observed_on
<chr> <chr> <chr> <date>
1 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-16
2 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-16
3 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-17
4 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-16
5 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-17
6 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-17
7 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-19
8 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-16
9 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-18
10 natureinla Western Fence Lizard Sceloporus occidentalis 2016-04-16
# ℹ 69 more rowsHere we will get observations where common_name is
‘Western Fence Lizard’ or ‘Western Honey Bee’. use | for
or.
R
inat_raw %>%
filter(common_name == 'Western Honey Bee' | common_name == 'Western Fence Lizard') %>%
select(user_login, observed_on, common_name)
OUTPUT
# A tibble: 4,788 × 3
user_login observed_on common_name
<chr> <date> <chr>
1 cdegroof 2016-04-14 Western Fence Lizard
2 deedeeflower5 2016-04-14 Western Fence Lizard
3 deedeeflower5 2016-04-14 Western Fence Lizard
4 cdegroof 2016-04-14 Western Fence Lizard
5 lchroman 2016-04-14 Western Fence Lizard
6 smartrf 2016-04-14 Western Honey Bee
7 maiz 2016-04-14 Western Fence Lizard
8 smartrf 2016-04-15 Western Honey Bee
9 kimssight 2016-04-15 Western Fence Lizard
10 catherineh 2016-04-15 Western Honey Bee
# ℹ 4,778 more rowsSometimes we want to combine and or. We want observations from
‘cdegroof’ or ‘deedeeflower5’ for ‘Western Fence Lizard’. You can use
both & and | together in a single
filter.
R
temp <- inat_raw %>%
filter(user_login == 'cdegroof'
| user_login == 'deedeeflower5'
& common_name == 'Western Fence Lizard') %>%
select(user_login, common_name, scientific_name, observed_on)
You can also use multiple filter statememts.
R
temp <- inat_raw %>%
filter(user_login == 'cdegroof'
| user_login == 'deedeeflower5') %>%
filter(common_name == 'Western Fence Lizard') %>%
select(user_login, observed_on, common_name)
Cleaning up raw data, exporting dataframe
A common step during data analysis is to clean up the raw data. We fix any obvious errors, edit column names, exclude rows we do not want, and save the cleaned up data set. We do the analysis on the cleaned data set.
We want observation that match these criteria - have a species information. - have latitude or longitude. - have ‘research’ for quality_grade
Use colSums(is.na()) to count the number of rows that
have NA values for each column.
R
colSums(is.na(inat_raw))
OUTPUT
id observed_on_string
0 0
observed_on time_observed_at
0 5819
time_zone user_id
0 0
user_login user_name
0 63304
created_at updated_at
0 0
quality_grade license
0 42937
url image_url
0 2214
sound_url tag_list
170645 164464
description num_identification_agreements
149235 0
num_identification_disagreements captive_cultivated
0 0
oauth_application_id place_guess
66613 440
latitude longitude
438 438
positional_accuracy private_place_guess
38319 171155
private_latitude private_longitude
171155 171155
public_positional_accuracy geoprivacy
34911 158521
taxon_geoprivacy coordinates_obscured
129409 0
positioning_method positioning_device
156084 154467
species_guess scientific_name
25721 1685
common_name iconic_taxon_name
11164 1846
taxon_id
1685 All rows have id, observed_on, and user_id.
1685 rows don’t have scientific_name. 438 rows don’t have latitude or longitude.
table is a function from base R that can count the
number of unique values in a column. Get a count for
quality_grade.
R
table(inat_raw$quality_grade)
OUTPUT
casual needs_id research
23194 53875 94086 94086 rows are research grade.
use filter to select the observations we want.
!is.na will select rows that have are not NA, meaning
rows that have a value. quality_grade == 'research' will
select rows that are ‘research’ grade.
save the cleaned up data in a new object inat.
R
inat <- inat_raw %>%
filter(!is.na(latitude) &
!is.na(longitude) &
!is.na(scientific_name)) %>%
filter(quality_grade == 'research')
The original dataframe ‘inat_raw’ had 171K rows, the cleaned dataframe ‘inat’ has 93K rows.
We can double check our work.
latitude, longitude, scientific_name have zero NA.
R
colSums(is.na(inat))
OUTPUT
id observed_on_string
0 0
observed_on time_observed_at
0 3167
time_zone user_id
0 0
user_login user_name
0 30889
created_at updated_at
0 0
quality_grade license
0 21944
url image_url
0 334
sound_url tag_list
93561 89612
description num_identification_agreements
82364 0
num_identification_disagreements captive_cultivated
0 0
oauth_application_id place_guess
41638 1
latitude longitude
0 0
positional_accuracy private_place_guess
22494 93950
private_latitude private_longitude
93950 93950
public_positional_accuracy geoprivacy
20663 87462
taxon_geoprivacy coordinates_obscured
59216 0
positioning_method positioning_device
84974 84450
species_guess scientific_name
138 0
common_name iconic_taxon_name
1626 4
taxon_id
0 quality_grade only has research.
R
table(inat$quality_grade)
OUTPUT
research
93950 We want to save the cleaned up data set so we can use it later. We
can save data.frame to a CSV using the write_csv() function
from the readr package. The first argument is the name of
the data.frame, and the second is the path to the new file we want to
create, including the file extension .csv.
R
write_csv(inat, file= 'data/cleaned/observations.csv')
If we go look into our cleaned_data folder, we will see
this new CSV file.
Errors in code
We are writing instructions for the computer. If there is typos, mispelling, pass in wrong arguments into functions, etc, code will not work and we will see errors. R will display the errors in red.
typo for %>
R
inat %>%
select(user_login, observed_on, common_name) %>%
filter(user_login == 'natureinla')
OUTPUT
# A tibble: 1,528 × 3
user_login observed_on common_name
<chr> <date> <chr>
1 natureinla 2016-04-14 Red-eared Slider
2 natureinla 2016-04-14 Monarch
3 natureinla 2016-04-14 San Diego Gopher Snake
4 natureinla 2016-04-14 California Towhee
5 natureinla 2016-04-14 Cooper's Hawk
6 natureinla 2016-04-14 Monarch
7 natureinla 2016-04-14 Allen's Hummingbird
8 natureinla 2016-04-15 Northern Mockingbird
9 natureinla 2016-04-15 House Sparrow
10 natureinla 2016-04-15 Indian Peafowl
# ℹ 1,518 more rowsMisspelled user_logi
R
inat %>%
select(user_login, observed_on, common_name) %>%
filter(user_login == 'natureinla')
OUTPUT
# A tibble: 1,528 × 3
user_login observed_on common_name
<chr> <date> <chr>
1 natureinla 2016-04-14 Red-eared Slider
2 natureinla 2016-04-14 Monarch
3 natureinla 2016-04-14 San Diego Gopher Snake
4 natureinla 2016-04-14 California Towhee
5 natureinla 2016-04-14 Cooper's Hawk
6 natureinla 2016-04-14 Monarch
7 natureinla 2016-04-14 Allen's Hummingbird
8 natureinla 2016-04-15 Northern Mockingbird
9 natureinla 2016-04-15 House Sparrow
10 natureinla 2016-04-15 Indian Peafowl
# ℹ 1,518 more rowstypo for =
R
inat %>%
select(user_login, observed_on, common_name) %>%
filter(user_login == 'natureinla')
OUTPUT
# A tibble: 1,528 × 3
user_login observed_on common_name
<chr> <date> <chr>
1 natureinla 2016-04-14 Red-eared Slider
2 natureinla 2016-04-14 Monarch
3 natureinla 2016-04-14 San Diego Gopher Snake
4 natureinla 2016-04-14 California Towhee
5 natureinla 2016-04-14 Cooper's Hawk
6 natureinla 2016-04-14 Monarch
7 natureinla 2016-04-14 Allen's Hummingbird
8 natureinla 2016-04-15 Northern Mockingbird
9 natureinla 2016-04-15 House Sparrow
10 natureinla 2016-04-15 Indian Peafowl
# ℹ 1,518 more rowsextra )
R
inat %>%
select(user_login, observed_on, common_name) %>%
filter (user_login == 'natureinla')
OUTPUT
# A tibble: 1,528 × 3
user_login observed_on common_name
<chr> <date> <chr>
1 natureinla 2016-04-14 Red-eared Slider
2 natureinla 2016-04-14 Monarch
3 natureinla 2016-04-14 San Diego Gopher Snake
4 natureinla 2016-04-14 California Towhee
5 natureinla 2016-04-14 Cooper's Hawk
6 natureinla 2016-04-14 Monarch
7 natureinla 2016-04-14 Allen's Hummingbird
8 natureinla 2016-04-15 Northern Mockingbird
9 natureinla 2016-04-15 House Sparrow
10 natureinla 2016-04-15 Indian Peafowl
# ℹ 1,518 more rowsR
inat %>%
filter(user_login == 'natureinla' & common_name == 'Red-eared Slider') %>%
select(user_login, observed_on, common_name)
OUTPUT
# A tibble: 13 × 3
user_login observed_on common_name
<chr> <date> <chr>
1 natureinla 2016-04-14 Red-eared Slider
2 natureinla 2016-04-14 Red-eared Slider
3 natureinla 2017-04-15 Red-eared Slider
4 natureinla 2017-04-15 Red-eared Slider
5 natureinla 2017-04-16 Red-eared Slider
6 natureinla 2017-04-14 Red-eared Slider
7 natureinla 2017-04-17 Red-eared Slider
8 natureinla 2017-04-18 Red-eared Slider
9 natureinla 2017-04-18 Red-eared Slider
10 natureinla 2017-04-14 Red-eared Slider
11 natureinla 2018-04-30 Red-eared Slider
12 natureinla 2018-04-30 Red-eared Slider
13 natureinla 2019-04-27 Red-eared SliderMaking new columns with mutate()
Another common task is creating a new column based on values in existing columns. For example, we could add a new column for year.
Use mutate() to a column. We pass in the name of the new
column, and the value of the column.
Use year() from lubridate on a date column
to get the year.
This code will get the year from ‘observed_on’, and create a ‘year’ column.
R
temp <- inat %>%
mutate(year = year(observed_on))
Get observations for 2020.
R
inat %>%
mutate(year = year(observed_on)) %>%
filter(year == 2020)
OUTPUT
# A tibble: 10,659 × 40
id observed_on_string observed_on time_observed_at time_zone user_id
<dbl> <chr> <date> <chr> <chr> <dbl>
1 43036534 Fri Apr 24 2020 00:0… 2020-04-24 2020-04-24 07:0… Pacific … 146517
2 43036989 Fri Apr 24 2020 00:0… 2020-04-24 2020-04-24 07:0… Pacific … 74669
3 43037631 Fri Apr 24 2020 00:1… 2020-04-24 2020-04-24 07:1… Pacific … 403949
4 43037703 Fri Apr 24 2020 00:1… 2020-04-24 2020-04-24 07:1… Pacific … 403949
5 43037736 Fri Apr 24 2020 00:0… 2020-04-24 2020-04-24 07:0… Pacific … 403949
6 43037745 Fri Apr 24 2020 00:1… 2020-04-24 2020-04-24 07:1… Pacific … 2556338
7 43037824 2020-04-24 12:05:06 … 2020-04-24 2020-04-24 07:0… Pacific … 1628946
8 43037956 Fri Apr 24 2020 00:1… 2020-04-24 2020-04-24 07:1… Pacific … 74669
9 43037961 Fri Apr 24 2020 00:2… 2020-04-24 2020-04-24 07:2… Pacific … 2556338
10 43038195 Fri Apr 24 2020 00:2… 2020-04-24 2020-04-24 07:2… Pacific … 2556338
# ℹ 10,649 more rows
# ℹ 34 more variables: user_login <chr>, user_name <chr>, created_at <chr>,
# updated_at <chr>, quality_grade <chr>, license <chr>, url <chr>,
# image_url <chr>, sound_url <chr>, tag_list <chr>, description <chr>,
# num_identification_agreements <dbl>,
# num_identification_disagreements <dbl>, captive_cultivated <lgl>,
# oauth_application_id <dbl>, place_guess <chr>, latitude <dbl>, …R
inat %>%
mutate(year = year(observed_on)) %>%
filter(user_login == 'natureinla' & year == 2023) %>%
select(user_login, observed_on, common_name)
OUTPUT
# A tibble: 3 × 3
user_login observed_on common_name
<chr> <date> <chr>
1 natureinla 2023-04-29 Thick-leaved Yerba Santa
2 natureinla 2023-04-29 Big Berry Manzanita
3 natureinla 2023-04-29 chamise Count the number of rows with count()
Use count() from dplyr to count the number of values for
one or more columns.
Let’s try counting of all our observations by year. Use
mutate to add a year column. Use count to
count the number of observations for each year. By default, count will
add a new column caled n.
R
inat %>%
mutate(year = year(observed_on)) %>%
count(year)
OUTPUT
# A tibble: 8 × 2
year n
<dbl> <int>
1 2016 5791
2 2017 9354
3 2018 10855
4 2019 17950
5 2020 10659
6 2021 13051
7 2022 11924
8 2023 14366We can specify the name of the count column by passing in
name to count()
R
inat %>%
mutate(year = year(observed_on)) %>%
count(year, name='obs_count')
OUTPUT
# A tibble: 8 × 2
year obs_count
<dbl> <int>
1 2016 5791
2 2017 9354
3 2018 10855
4 2019 17950
5 2020 10659
6 2021 13051
7 2022 11924
8 2023 14366Let’s count the number of observations for each species. We will pass in both ‘common_name’ and ‘scientific_name’ because some species don’t have a common_name.
R
inat %>%
count(common_name, scientific_name, name='obs_count')
OUTPUT
# A tibble: 3,675 × 3
common_name scientific_name obs_count
<chr> <chr> <int>
1 Abert's Thread-waisted Wasp Ammophila aberti 1
2 Accipiters Accipiter 2
3 Acmon Blue Icaricia acmon 35
4 Acorn Woodpecker Melanerpes formicivorus 256
5 Acton's Brittlebush Encelia actoni 11
6 Acute Bladder Snail Physella acuta 8
7 Adams Mussel Brachidontes adamsianus 4
8 African Asparagus Asparagus aethiopicus 22
9 African Clawed Frog Xenopus laevis 1
10 African Cluster Bug Agonoscelis puberula 13
# ℹ 3,665 more rowsIt’s often useful to take a look at the results in some order, like
the lowest count to highest. We can use the arrange()
function for that. By default, arrange will return values from lowest to
highest.
R
inat %>%
count(common_name, scientific_name, name='obs_count') %>%
arrange(obs_count)
OUTPUT
# A tibble: 3,675 × 3
common_name scientific_name obs_count
<chr> <chr> <int>
1 Abert's Thread-waisted Wasp Ammophila aberti 1
2 African Clawed Frog Xenopus laevis 1
3 African boxthorn Lycium ferocissimum 1
4 Almond Prunus amygdalus 1
5 Alpine Brown Sunken Disk Lichen Bellemerea alpina 1
6 American Black-crowned Night Heron Nycticorax nycticorax hoactli 1
7 American Dewdrop Spider Argyrodes elevatus 1
8 American Dipper Cinclus mexicanus 1
9 American Softshells Apalone 1
10 American Sunflower Moth Homoeosoma electella 1
# ℹ 3,665 more rowsIf we want to reverse the order, we can wrap the column name in
desc():
R
inat %>%
count(common_name, scientific_name, name='obs_count') %>%
arrange(desc(obs_count))
OUTPUT
# A tibble: 3,675 × 3
common_name scientific_name obs_count
<chr> <chr> <int>
1 Western Fence Lizard Sceloporus occidentalis 2936
2 Western Honey Bee Apis mellifera 1803
3 Fox Squirrel Sciurus niger 1285
4 House Finch Haemorhous mexicanus 1067
5 Mourning Dove Zenaida macroura 1034
6 Mallard Anas platyrhynchos 810
7 House Sparrow Passer domesticus 800
8 Convergent Lady Beetle Hippodamia convergens 788
9 California Towhee Melozone crissalis 747
10 Northern Mockingbird Mimus polyglottos 719
# ℹ 3,665 more rowsuse slice() to return only certain number of records
slice(start:end)
Top ten species with the most observations.
R
inat %>%
count(common_name, scientific_name, name='obs_count') %>%
arrange(desc(obs_count)) %>%
slice(1:10)
OUTPUT
# A tibble: 10 × 3
common_name scientific_name obs_count
<chr> <chr> <int>
1 Western Fence Lizard Sceloporus occidentalis 2936
2 Western Honey Bee Apis mellifera 1803
3 Fox Squirrel Sciurus niger 1285
4 House Finch Haemorhous mexicanus 1067
5 Mourning Dove Zenaida macroura 1034
6 Mallard Anas platyrhynchos 810
7 House Sparrow Passer domesticus 800
8 Convergent Lady Beetle Hippodamia convergens 788
9 California Towhee Melozone crissalis 747
10 Northern Mockingbird Mimus polyglottos 719R
inat %>%
mutate(year = year(observed_on)) %>%
filter(user_login == 'natureinla') %>%
count(year, name='obs_count')
OUTPUT
# A tibble: 7 × 2
year obs_count
<dbl> <int>
1 2016 490
2 2017 606
3 2018 223
4 2019 195
5 2020 9
6 2021 2
7 2023 3