R
PRECIS R package
If you use R then you are very familiar with the SUMMARY function.
If you use R then you are very familiar with the name Hadley Wickham. He has produced some really cool packages for R.
He has produced a new R package and function that complements the commonly used SUMMARY R function.
The following outlines how you can install this new R package from GitHub (Hadley’s GitHub is https://github.com/hadley/).
Install the R devtools package. This will allow you to download the package code from GitHub.
install.packages("devtools")
Install the package from Hadley’s GitHub repository.
devtools::install_github("hadley/precis")
Load the library.
library(precis)
The following displays information produced by the SUMMARY and the PRECIS function.
> summary(mtcars)
mpg cyl disp hp drat wt
Min. :10.40 Min. :4.000 Min. : 71.1 Min. : 52.0 Min. :2.760 Min. :1.513
1st Qu.:15.43 1st Qu.:4.000 1st Qu.:120.8 1st Qu.: 96.5 1st Qu.:3.080 1st Qu.:2.581
Median :19.20 Median :6.000 Median :196.3 Median :123.0 Median :3.695 Median :3.325
Mean :20.09 Mean :6.188 Mean :230.7 Mean :146.7 Mean :3.597 Mean :3.217
3rd Qu.:22.80 3rd Qu.:8.000 3rd Qu.:326.0 3rd Qu.:180.0 3rd Qu.:3.920 3rd Qu.:3.610
Max. :33.90 Max. :8.000 Max. :472.0 Max. :335.0 Max. :4.930 Max. :5.424
qsec vs am gear carb
Min. :14.50 Min. :0.0000 Min. :0.0000 Min. :3.000 Min. :1.000
1st Qu.:16.89 1st Qu.:0.0000 1st Qu.:0.0000 1st Qu.:3.000 1st Qu.:2.000
Median :17.71 Median :0.0000 Median :0.0000 Median :4.000 Median :2.000
Mean :17.85 Mean :0.4375 Mean :0.4062 Mean :3.688 Mean :2.812
3rd Qu.:18.90 3rd Qu.:1.0000 3rd Qu.:1.0000 3rd Qu.:4.000 3rd Qu.:4.000
Max. :22.90 Max. :1.0000 Max. :1.0000 Max. :5.000 Max. :8.000
> precis(mtcars)
# data.frame [32 x 11]
name type precis
1 mpg dbl 10.4 [ 15.4 ( 19.2) 22.8] 33.9
2 cyl dbl 4 (11) 6 (7) 8 (14)
3 disp dbl 71.1 [121.0 (196.0) 334.0] 472.0
4 hp dbl 52 [ 96 ( 123) 180] 335
5 drat dbl 2.76 [ 3.08 ( 3.70) 3.92] 4.93
6 wt dbl 1.51 [ 2.54 ( 3.32) 3.65] 5.42
7 qsec dbl 14.5 [ 16.9 ( 17.7) 18.9] 22.9
8 vs dbl 0 (18) 1 (14)
9 am dbl 0 (19) 1 (13)
10 gear dbl 3 (15) 4 (12) 5 (5)
11 carb dbl 1 [ 2 ( 2) 4] 8
> precis(mtcars, histogram=TRUE)
# data.frame [32 x 11]
name type precis
1 mpg dbl 10.4 ▂▁▇▃▅▅▂▂▁▁▂▂ 33.9
2 cyl dbl 4 ▅▁▁▁▁▁▁▁▁▃▁▁▁▁▁▁▁▁▁▇ 8
3 disp dbl 71.1 ▅▁▁▃▇▂▁▁▁▁▃▁▃▁▅▁▁▁▁▁▁ 472.0
4 hp dbl 52 ▁▅▅▇▂▂▇▁▂▁▂▁▁▁▁ 335
5 drat dbl 2.76 ▂▂▇▂▁▅▇▃▂▁▁▁ 4.93
6 wt dbl 1.51 ▁▁▂▂▁▁▂▁▂▁▇▂▂▁▁▁▁▁▁▂▁ 5.42
7 qsec dbl 14.5 ▂▂▁▁▃▇▅▁▇▂▂▂▁▁▁▁▁ 22.9
8 vs dbl 0 ▇▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▅ 1
9 am dbl 0 ▇▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▅ 1
10 gear dbl 3 ▇▁▁▁▁▁▁▁▁▅▁▁▁▁▁▁▁▁▁▂ 5
11 carb dbl 1 ▅▇▁▂▁▇▁▁▁▁▁▁▁▁ 8
Managing memory allocation for Oracle R Enterprise Embedded Execution
When working with Oracle R Enterprise and particularly when you are using the ORE functions that can spawn multiple R processes, on the DB Server, you need to be very aware of the amount of memory that will be consumed for each call of the ORE function.
ORE has two sets of parallel functions for running your user defined R scripts stored in the database, as part of the Embedded R Execution feature of ORE. The R functions are called ore.groupApply, ore.rowApply and ore.indexApply. When using SQL there are “rqGroupApply” and rqRowApply. (There is no SQL function equivalent of the R function ore.indexApply)
For each parallel R process that is spawned on the DB server a certain amount of memory (RAM) will be allocated to this R process. The default size of memory to be allocated can be found by using the following query.
select name, value from sys.rq_config; NAME VALUE ----------------------------------- ----------------------------------- VERSION 1.5 MIN_VSIZE 32M MAX_VSIZE 4G MIN_NSIZE 2M MAX_NSIZE 20M
The memory allocation is broken out into the amount of memory allocated for Cells and NCells for each R process.
If your parallel ORE function create a large number of parallel R processes then you can see that the amount of overall memory consumed can be significant. I’ve seen a few customers who very quickly run out of memory on their DB servers. Now that is something you do not want to happen.
How can you prevent this from happening ?
There are a few things you need to keep in mind when using the parallel enabled ORE functions. The first one is, how many R processes will be spawned. For most cases this can be estimated or calculated to a high degree of accuracy. Secondly, how much memory will be used to process each of the R processes. Thirdly, how memory do you have available on the DB server. Fourthly, how many other people will be running parallel R processes at the same time?
Examining and answering each of these may look to be a relatively trivial task, but the complexity behind these can increase dramatically depending on the answer to the fourth point/question above.
To calculate the amount of memory used during the ORE user defined R script, you can use the R garbage function to calculate the memory usage at the start and at the end of the R script, and then return the calculated amount. Yes you need to add this extra code to your R script and then remove it when you have calculated the memory usage.
gc.start <- gc(reset=TRUE) ... gc.end <- gc() gc.used <- gc.end[,7] - gc.start[,7] # amount consumed by the processing
Using this information and the answers to the points/questions I listed above you can now look at calculating how much memory you need to allocated to the R processes. You can set this to be static for all R processes or you can use some code to allocate the amount of memory that is needed for each R process. But this starts to become messy. The following gives some examples (using R) of changing the R memory allocations in the Oracle Database. Similar commands can be issued using SQL.
> sys.rqconfigset('MIN_VSIZE', '10M') -- min heap 10MB, default 32MB
> sys.rqconfigset('MAX_VSIZE', '100M') -- max heap 100MB, default 4GB
> sys.rqconfigset('MIN_NSIZE', '500K') -- min number cons cells 500x1024, default 1M
> sys.rqconfigset('MAX_NSIZE', '2M') -- max number cons cells 2M, default 20M
Some guidelines – as with all guidelines you have to consider all the other requirements for the Database, and in reality you will have to try to find a balance between what is listed here and what is actually possible.
- Set parallel_degree_policy to MANUAL.
- Set parallel_min_servers to the number of parallel slave processes to be started when the database instances start, this avoids start up time for the R processes. This is not a problem for long running processes. But can save time with processes running for 10s seconds
- To avoid overloading the CPUs if the parallel_max_servers limit is reached, set the hidden parameter _parallel_statement_queuing to TRUE. Avoids overloading and lets processes wait.
- Set application tables and their indexes to DOP 1 to reinforce the ability of ORE to determine when to use parallelism.
Understanding the memory requirements for your ORE processes can be tricky business and can take some time to work out the right balance between what is needed by the spawned parallel R processes and everything else that is going on in the Database. There will be a lot of trial and error in working this out and it is always good to reach out for some help. If you have a similar scenario and need some help or guidance let me know.
OUG Ireland 2017 Presentation
Here are the slides from my presentation at OUG Ireland 2017. All about running R using SQL.
Formatting results from ORE script in a SELECT statement
This blog post looks at how to format the output or the returned returns from an Oracle R Enterprise (ORE), user defined R function, that is run using a SELECT statement in SQL.
Sometimes this can be a bit of a challenge to work out, but it can be relatively easy once you have figured out how to do it. The following examples works through some scenarios of different results sets from a user defined R function that is stored in the Oracle Database.
To run that user defined R function using a SELECT statement I can use one of the following ORE SQL functions.
- rqEval
- rqTableEval
- “rqGroupEval“
- rqRowEval
For simplicity we will just use the first of these ORE SQL functions to illustrate the problem and how to go about solving it. The rqEval ORE SQL function is a generate purpose function to call a user defined R script stored in the database. The function does not require any input data set and but it will return some data. You could use this to generate some dummy/test data or to find some information in the database. Here is noddy example that returns my name.
BEGIN
--sys.rqScriptDrop('GET_NAME');
sys.rqScriptCreate('GET_NAME',
'function() {
res<-data.frame("Brendan")
res
} ');
END;
To call this user defined R function I can use the following SQL.
select *
from table(rqEval(null,
'select cast(''a'' as varchar2(50)) from dual',
'GET_NAME') );
For text strings returned you need to cast the returned value giving a size.
If we have a numeric value being returned we can don’t have to use the cast and instead use ‘1’ as shown in the following example. This second example extends our user defined R function to return my name and a number.
BEGIN
sys.rqScriptDrop('GET_NAME');
sys.rqScriptCreate('GET_NAME',
'function() {
res<-data.frame(NAME="Brendan", YEAR=2017)
res
} ');
END;
To call the updated GET_NAME function we now have to process two returned columns. The first is the character string and the second is a numeric.
select *
from table(rqEval(null,
'select cast(''a'' as varchar2(50)) as "NAME", 1 AS YEAR from dual',
'GET_NAME') );
These example illustrate how you can process character strings and numerics being returned by the user defined R script.
The key to setting up the format of the returned values is knowing the structure of the data frame being returned by the user defined R script. Once you know that the rest is (in theory) easy.
Creating and Reading SPSS and SAS data sets in R
Have you ever been faced with having to generate a data set in the format that is needed by another analytics tool? or having to generate a data set in a particular format but you don’t have the software that generates that format? For example, if you are submitting data to the FDA and other bodies, you may need to submit the data in a SAS formatted file. There are a few ways you can go about this.
One option is that you can use the Haven R package to generate your dataset in SAS and SPSS formats. But you can also read in SAS and SPSS formatted files. I have to deal with these formatted data files all the time, and it can be a challenge, but I’ve recently come across the Haven R package that has just made my life just a little bit/lots easier. Now I can easily generate SAS and SPSS formatted data sets for my data in my Oracle Database, using R and ORE. ORE we can now use the embedded feature to build the generation of these data sets into some of our end-user applications.
Let us have a look at Haven and what it can do.
Firstly there is very little if any documentation online for it. That is ok so we will have to rely on the documentation that comes with the R packages. Again there isn’t much to help and that is because the R package mainly consists of functions to Read in these data sets, functions to Write these data sets and some additional functions for preparing data.
For reading in data sets we have the following functions:
# SAS
read_sas("mtcars.sas7bdat")
# Stata
read_dta("mtcars.dta")
# SPSS
read_sav("mtcars.sav")
For writing data sets we have the following functions:
# SAS write_sas(mtcars, "mtcars.sas7bdat") # Stata write_dta(mtcars, "mtcars.dta") # SPSS write_sav(mtcars, "mtcars.sav")
Let us now work through an example of creating a SAS data set. We can use some of the sample data sets that come with the Oracle Database in the SH schema. I’m going to use the data in the CUSTOMER table to create a SAS data set. In the following code I’m using ORE to connect to the database but you can use your preferred method.
> library(ORE)
> # Create your connection to the schema in the DB
> ore.connect(user="sh", password="sh", host="localhost", service_name="PDB12C",
port=1521, all=TRUE)
> dim(CUSTOMERS)
[1] 55500 23
> names(CUSTOMERS)
[1] "CUST_ID" "CUST_FIRST_NAME" "CUST_LAST_NAME"
[4] "CUST_GENDER" "CUST_YEAR_OF_BIRTH" "CUST_MARITAL_STATUS"
[7] "CUST_STREET_ADDRESS" "CUST_POSTAL_CODE" "CUST_CITY"
[10] "CUST_CITY_ID" "CUST_STATE_PROVINCE" "CUST_STATE_PROVINCE_ID"
[13] "COUNTRY_ID" "CUST_MAIN_PHONE_NUMBER" "CUST_INCOME_LEVEL"
[16] "CUST_CREDIT_LIMIT" "CUST_EMAIL" "CUST_TOTAL"
[19] "CUST_TOTAL_ID" "CUST_SRC_ID" "CUST_EFF_FROM"
[22] "CUST_EFF_TO" "CUST_VALID"
Next we can prepare the data, take a subset of the data, reformat the data, etc. For me I just want to use the data as it is. All I need to do now is to pull the data from the database to my local R environment.
dat <- ore.pull(CUSTOMERS)
Then I need to load the Haven library and then create the SAS formatted file.
library(haven) write_sas(dat, "c:/app/my_customers.sas7bdat")
That’s it. Nice and simple.
But has it worked? Has it created the file correctly? Will it load into my SAS tool?
There is only one way to test this and that is to only it in SAS. I have an account on SAS OnDemand with access to several SAS products. I’m going to use SAS Studio.
Well it works! The following image shows SAS Studio after I had loaded the data set with the variables and data shown.
WARNING: When you load the data set into SAS you may get a warning message saying that it isn’t a SAS data set. What this means is that it is not a data set generated by SAS. But as you can see in the image above all the data got loaded OK and you can work away with it as normal in your SAS tools.
The next step is to test the loading of a SAS data set into R. I’m going to use one of the standard SAS data sets called PVA97NK.SAS7BDAT. If you have worked with SAS products then you will have come across this data set.
When you use Haven to load in your SAS data set, it will create the data in tribble format. This is a slight varient of a data.frame. So if you want the typical format of a data.frmae then you will need to convert the loaded data, as shown in the following code.
> data_read dim(data_read) [1] 9686 28 > d class(data_read) [1] "tbl_df" "tbl" "data.frame" > class(d) [1] "data.frame" > head(d) TARGET_B ID TARGET_D GiftCnt36 GiftCntAll GiftCntCard36 GiftCntCardAll 1 0 00014974 NA 2 4 1 3 2 0 00006294 NA 1 8 0 3 3 1 00046110 4 6 41 3 20 ...
I think this package to going to make my life a little bit easier, and if you work with SPSS and SAS data sets then hopefully some of your tasks have become a little bit easier too.
Machine Learning notebooks (and Oracle)
Over the past 12 months there has been an increase in the number of Machine Learning notebooks becoming available.
What is a Machine Learning notebook?
As the name implies it can be used to perform machine learning using one or more languages and allows you to organise your code, scripts and other details in one application.
The ML notebooks provide an interactive environment (sometimes browser based) that allows you to write, run, view results, share/collaborate code and results, visualise data, etc.
Some of these ML notebooks come with one language and others come with two or more languages, and have the ability to add other ML related languages. The most common languages are Spark, Phython and R.
Based on these languages ML notebooks are typically used in the big data world and on Hadoop.
Examples of Machine Learning notebooks include: (Starting with the more common ones)
- Apache Zeppelin
- Jupyter Notebook (formally known as IPython Notebook)
- Azure ML R Notebook
- Beaker Notebook
- SageMath
At Oracle Open World (2016), Oracle announced that they are currently working creating their own ML notebook and it is based on Apache Zeppelin. They seemed to indicate that a beta version might be available in 2017. Here are some photos from that presentation, but with all things that Oracle talk about you have to remember and take into account their Safe Habor.
I’m looking forward to getting my hands on this new product when it is available.
Oracle Text, Oracle R Enterprise and Oracle Data Mining – Part 1
A project that I’ve been working on for a while now involves the use of Oracle Text, Oracle R Enterprise and Oracle Data Mining. Oracle Text comes with your Oracle Database licence. Oracle R Enterprise and Oracle Data Mining are part of the Oracle Advanced Analytics (extra cost) option.
What I will be doing over the course of 4 or maybe 5 blog posts is how these products can work together to help you gain a grater insight into your data, and part of your data being large text items like free format text, documents (in various forms e.g. html, xml, pdf, ms word), etc.
Unfortunately I cannot show you examples from the actual project I’ve been working on (and still am, from time to time). But what I can do is to show you how products and components can work together.
In this blog post I will just do some data setup. As with all project scenarios there can be many ways of performing the same tasks. Some might be better than others. But what I will be showing you is for demonstration purposes.
The scenario: The scenario for this blog post is that I want to extract text from some webpages and store them in a table in my schema. I then want to use Oracle Text to search the text from these webpages.
Schema setup: We need to create a table that will store the text from the webpages. We also want to create an Oracle Text index so that this text is searchable.
drop sequence my_doc_seq; create sequence my_doc_seq; drop table my_documents; create table my_documents ( doc_pk number(10) primary key, doc_title varchar2(100), doc_extracted date, data_source varchar2(200), doc_text clob); create index my_documents_ot_idx on my_documents(doc_text) indextype is CTXSYS.CONTEXT;
In the table we have a number of descriptive attributes and then a club for storing the website text. We will only be storing the website text and not the html document (More on that later). In order to make the website text searchable in the DOC_TEXT attribute we need to create an Oracle Text index of type CONTEXT.
There are a few challenges with using this type of index. For example when you insert a new record or update the DOC_TEXT attribute, the new values/text will not be reflected instantly, just like we are use to with traditional indexes. Instead you have to decide when you want to index to be updated. For example, if you would like the index to be updated after each commit then you can create the index using the following.
create index my_documents_ot_idx on my_documents(doc_text)
indextype is CTXSYS.CONTEXT
parameters ('sync (on commit)');
Depending on the number of documents you have being committed to the DB, this might not be for you. You need to find the balance. Alternatively you could schedule the index to be updated by passing an interval to the ‘sync’ in the above command. Alternatively you might want to use DBMS_JOB to schedule the update.
To manually sync (or via DBMS_JOB) the index, assuming we used the first ‘create index’ statement, we would need to run the following.
EXEC CTX_DDL.SYNC_INDEX('my_documents_ot_idx');
This function just adds the new documents to the index. This can, over time, lead to some fragmentation of the index, and will require it to the re-organised on a semi-regular basis. Perhaps you can schedule this to happen every night, or once a week, or whatever makes sense to you.
BEGIN
CTX_DDL.OPTIMIZE_INDEX('my_documents_ot_idx','FULL');
END;
(I could talk a lot more about setting up some basics of Oracle Text, the indexes, etc. But I’ll leave that for another day or you can read some of the many blog posts that already exist on the topic.)
Extracting text from a webpage using R: Some time ago I wrote a blog post on using some of the text mining features and packages in R to produce a word cloud based on some of the Oracle Advanced Analytics webpages.
I’m going to use the same webpages and some of the same code/functions/packages here.
The first task you need to do is to get your hands on the ‘htmlToText function. You can download the htmlToText function on github. This function requires the ‘Curl’ and ‘XML’ R packages. So you may need to install these.
I also use the str_replace_all function (“stringer’ R package) to remove some of the html that remains, to remove some special quotes and to replace and occurrences of ‘&’ with ‘and’.
# Load the function and required R packages
source(“c:/app/htmltotext.R”)
library(stringr)
data1 <- str_replace_all(htmlToText("http://www.oracle.com/technetwork/database/options/advanced-analytics/overview/index.html"), "[\r\n\t\"\'\u201C\u201D]" , "")
data1 <- str_replace_all(data1, "&", "and")
data2 <- str_replace_all(str_replace_all(htmlToText("http://www.oracle.com/technetwork/database/options/advanced-analytics/odm/index.html"), "[\r\n\t\"\'\u201C\u201D]" , ""), "&", "and")
data2 <- str_replace_all(data2, "&", "and")
data3 <- str_replace_all(str_replace_all(htmlToText("http://www.oracle.com/technetwork/database/database-technologies/r/r-technologies/overview/index.html"), "[\r\n\t\"\'\u201C\u201D]" , ""), "&", "and")
data3 <- str_replace_all(data3, "&", "and")
data4 <- str_replace_all(str_replace_all(htmlToText("http://www.oracle.com/technetwork/database/database-technologies/r/r-enterprise/overview/index.html"), "[\r\n\t\"\'\u201C\u201D]" , ""), "&", "and")
data4 <- str_replace_all(data4, "&", "and")
We now have the text extracted and cleaned up.
Create a data frame to contain all our data: Now that we have the text extracted, we can prepare the other data items we need to insert the data into our table (‘my_documents’). The first stept is to construct a data frame to contain all the data.
data_source = c("http://www.oracle.com/technetwork/database/options/advanced-analytics/overview/index.html",
"http://www.oracle.com/technetwork/database/options/advanced-analytics/odm/index.html",
"http://www.oracle.com/technetwork/database/database-technologies/r/r-technologies/overview/index.html",
"http://www.oracle.com/technetwork/database/database-technologies/r/r-enterprise/overview/index.html")
doc_title = c("OAA_OVERVIEW", "OAA_ODM", "R_TECHNOLOGIES", "OAA_ORE")
doc_extracted = Sys.Date()
data_text <- c(data1, data2, data3, data4)
my_docs <- data.frame(doc_title, doc_extracted, data_source, data_text)
Insert the data into our database table: With the data in our data fram (my_docs) we can now use this data to insert into our database table. There are a number of ways of doing this in R. What I’m going to show you here is how to do it using Oracle R Enterprise (ORE). The thing with ORE is that there is no explicit functionality for inserting and updating records in a database table. What you need to do is to construct, in my case, the insert statement and then use ore.exec to execute this statement in the database.
