funcompbio / assignment-6

Assignment 6 for the FCB subject at UPF

Assignment 6 - FCB 2022

Deadline: 11/11/2022 - 23:59

Submission procedure

This assignment has to be submitted using GitHub Classroom. This means that you should have cloned the GitHub repo of this assignment from the organization account for FCB in the academic year 2022-23 at https://github.com/funcompbio2022 using the submission link provided at the FCB Moodle site.

Once you have cloned the GitHub repo which has assignment-6 and your GitHub username as repo name, then you can work on it in your local disk and push your changes whenever you like, but make sure that you have pushed the last version of your assignment before the deadline. There is no submit button or any other specific submission procedure or action than just pushing your changes to you GitHub assignment repo. When correcting the assignment, the version available at the deadline will be retrieved. If the first version available is posterior to the deadline, then the mark of the assignment will have a penalty.

To complete your submission (see rubric below) please agree to the following academic integrity statement by editing this README file and placing the letter X between the squared brackets preceding the statement:

• [] The work here submitted has been entirely developed by myself and is the result of my own work.

Description

The goal of this assignment is to create an R script that produces a CSV file called COVID19CATlast6months.csv with COVID19 data for Catalonia derived from the general population, starting on June 1st, 2021, with older data at the beginning of the file and more recent data at the end of the file. To achieve this goal you should follow these 2 steps:

1. Create an R script called analysis.R with the R commands that read the CSV file catalunya_setmanal.csv provided in the repo of the assignment and make the necesssary transformations and calculations to obtain a data.frame object with the columns DATA_INI, R0_CONFIRMAT_M, IA14 and PERC_PCRTAR_POSITIVES, whose first lines look like this:

    DATA_INI R0_CONFIRMAT_M     IA14 PERC_PCRTAR_POSITIVES
1 2021-06-01       0.937658 102.9883                3.5296
2 2021-06-02       0.952521  99.3055                3.5322
3 2021-06-03       0.965133  96.5175                3.5561
4 2021-06-04       0.973635  94.3649                3.6365
5 2021-06-05       0.972995  92.0826                3.5797
6 2021-06-06       0.965863  91.2267                3.5496

2. Let the data.frame object of the resulting data be called dtf, the last line of your script should write to disk that object into a CSV file called COVID19CATlast6months.csv with the following R command:

write.csv(dtf, "COVID19CATlast6months.csv", row.names=FALSE)

Your assignment repo should have the following files:

1. This README.md file.
2. The COVID19 data CSV file catalunya_setmanal.csv.
3. The R script file analysis.R.
4. The resulting CSV file COVID19CATlast6months.csv.

The file COVID19CATlast6months.csv should have the following characteristics:

1. It should be a CSV file using the comma (,) as column separator and non-numeric values should be quoted with double quotes (").
2. It should have the following line as first (column header) line:

   "DATA_INI","R0_CONFIRMAT_M","IA14","PERC_PCRTAR_POSITIVES"
   

3. The second and following lines should contain the values corresponding to the columns specified above, ordered by date with the oldest date in the first row and the most recent in the last one. The data should be derived from the general population, that is, excluding the data from geriatric residences. For instance, the first line should look like this one:

   "2021-06-01",0.937658,102.9883,3.5296
   

This assignment incorporates an autograding feature using a so-called GitHub Actions Worflow, which will help you to automatically test whether your R script is correctly working after every push. More concretely, a few minutes after you pushed your changes to your remote GitHub repo, the badge labeled FCB-Python-autograding on top of this README file will be red and display the message failing if the autograding has not been successful, and green with the message passing otherwise. You may click on badge to look at output of the autograding tests to understand why it has failed, if that was the case. This feature provides you with formative assessment and to work with it you need to edit your R script in a file called analysis.R at the root of your GitHub repo and leave intact the file catalunya_setmanal.csv.

Evaluation rubric

The rubric to evaluate this assignment consists of the following items:

• Did you agree to the academic integrity statement?
• Does the assignment contain the required files?
• Does the file COVID19CATlast6months.csv contain the four required columns?
• Is the file COVID19CATlast6months.csv ordered chronologically starting on June 1st, 2021 and does it contain the COVID19 data derived from the general population for the four required columns?
• Does the R code run without errors?
• Does the R code produce the expected result?