Difference between revisions of "RPR-Data-Import"
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Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
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| − | < | + | <li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li> |
| − | + | <li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li> | |
| − | < | + | <li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li> |
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| + | === Evaluation === | ||
| + | <b>Evaluation: NA</b><br /> | ||
| + | <div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div> | ||
== Contents == | == Contents == | ||
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== Further reading, links and resources == | == Further reading, links and resources == | ||
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<div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> | <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> | ||
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| + | == Notes == | ||
| + | <references /> | ||
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Latest revision as of 01:41, 23 September 2020
Importing data in R
(Data import from unstructured text, structured text, spreadsheets, online repositories, and Web pages)
Abstract:
Practical for data import from text files, spreadsheets and Web pages.
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Objectives: |
Outcomes: |
Deliverables:
Prerequisites:
This page is not currently being maintained since it is not part of active learning sections.
Contents
Evaluation
Evaluation: NA
This unit is not evaluated for course marks.
Contents
- Line endings
- Unstructured text files, headers, skip, omit, and rownames
- Caution with stringsAsFactors
- Caution with coerced data
- Text files with keywords
- Text-files: changing state
- Text-files: csv and tsv (and Excel sheets)
- Text-files: slurping, chunking and streaming
- curl
- httr GET and POST
- XML - libraries and cpath
- Binary Data
- text objects: readLines() and writeLines()
- R objects: save() and load(); saveRDS() and readRDS().
Regex for screenscraping example:
Screenscraping
Write a PHP program that screenscrapes resolution data for a protein structure file from the PDB.
Here is a link to a PDB record to illustrate the URL format.
Fetch the contents of the URL into a string. Use a regex that captures the data you want to retrieve as part of some unique pattern in the HTML source. Print.
;The regex::
/\s*(\d+\.\d+)/
**\s*... probably followed by whitespace, ... *(\d+\.\d+)... the "payload" of the match: one or more digits, a literal dot and and one or more digits.
;The code: <source lang="PHP"> <?php $URLpath = "http://www.pdb.org/pdb/explore/explore.do?structureId="; $PDBid = "2imm"; $source = file_get_contents($URLpath . $PDBid);preg_match('/\s*?(\d+\.\d+)/', $source, $resolution);
print($resolution[1]); ?>
Self-evaluation
Further reading, links and resources
Notes
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-09-17
Modified:
- 2018-01-31
Version:
- 1.0
Version history:
- 1.0 first live version
- 0.2 Contents outline
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
This page is not currently being maintained since it is not part of active learning sections.
