Working my way through a tutorial named Data Carpentry
(https://datacarpentry.org/R-ecology-lesson/). for the most part it is
excellent but I’m stuck on the very last section
(https://datacarpentry.org/R-ecology-lesson/05-r-and-databases.html).
First, below are the packages I have loaded:
[1] "forcats" "stringr" "purrr" "readr" "tidyr" "tibble"
"ggplot2" "tidyverse" "dbplyr" "RMySQL" "DBI"
[12] "dplyr" "RSQLite" "stats" "graphics" "grDevices" "utils"
"datasets" "methods" "base"
>
Second,
Second, is the text of the last section of the last chapter titled “Creating a
New SQLite Database”.
Second, below is the text from the tutorial. The black type is from the
tutorial. The green and blue is the suggested R code. My comments are in red.
Creating a new SQLite database
So far, we have used a previously prepared SQLite database. But we can also use
R to create a new database, e.g. from existing csv files. Let’s recreate the
mammals database that we’ve been working with, in R. First let’s download and
read in the csv files. We’ll import tidyverse to gain access to the read_csv()
function.
download.file("https://ndownloader.figshare.com/files/3299483";,
"data_raw/species.csv")
download.file("https://ndownloader.figshare.com/files/10717177";,
"data_raw/surveys.csv")
download.file("https://ndownloader.figshare.com/files/3299474";,
"data_raw/plots.csv")
library(tidyverse)
species <- read_csv("data_raw/species.csv")No problem here. I’m pulling three
databases from the Web and saving them to a folder on my hard drive.
(...data_raw/species.csv) etc.surveys <- read_csv("data_raw/surveys.csv") plots
<- read_csv("data_raw/plots.csv")Again no problem. I’m just creating an R data
files. But here is where I loose it. I’m creating something named my_db_file
from another file named portal-database-output with an sqlite extension and
then creating my_db from the My_db_file. Not sure where the sqlite extension
file came from. Creating a new SQLite database with dplyr is easy. You can
re-use the same command we used above to open an existing .sqlite file. The
create = TRUE argument instructs R to create a new, empty database instead.
Caution: When create = TRUE is added, any existing database at the same
location is overwritten without warning.
my_db_file <- "data/portal-database-output.sqlite"
my_db <- src_sqlite(my_db_file, create = TRUE)Currently, our new database is
empty, it doesn’t contain any tables:
my_db#> src: sqlite 3.29.0 [data/portal-database-output.sqlite]
#> tbls:To add tables, we copy the existing data.frames into the database one
by one:
copy_to(my_db, surveys)
copy_to(my_db, plots)
my_dbI can follow the directions to fill in my_db but I have no idea how to
access the tables. The text from the tutorial below says to check the location
of our database. Huh! Can someone give me some direction. Thanks.
If you check the location of our database you’ll see that data is automatically
being written to disk. R and dplyr not only provide easy ways to query existing
databases, they also allows you to easily create your own databases from flat
files!
Here is where I loose it.
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