-We provide here only instructions for debian-based distributions. Feel +We provide here only instructions for Debian-based distributions. Feel free to contribute to this document to provide up-to-date information for other distributions (e.g.n redhat, fedora).
@@ -132,9 +133,9 @@ which is now deprecated.
Note: macOS comes with a prehistoric command-line-only version of Emacs located at /usr/bin/emacs. It's best to forget about it.
/Applications.
Install the .exe file from Vincent Goulet:
https://vigou3.github.io/emacs-modified-windows/. It ships with recent
@@ -202,21 +203,13 @@ versions:
-To have code pretty printing when exporting to html, it appears like
-you should install the htmlize package, which is done by opening emacs
-and typing the following command:
-
-M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key then the "x" key -
-In all the following instructions, it is common to refer to your home
+In the following instructions, we refer to your home
directory through the (UNIX) ~/ notation. On Windows, your home
directory should be something like C:\Users\yourname. Therefore,
whenever we mention the ~/org/ (resp. the ~/.emacs.d/) directory this
@@ -225,17 +218,16 @@ means we are referring to C:\Users\yourname\org (resp.
-When running a command, windows will look for the command in the
+When running a command, Windows will look for the command in the
directories indicated in the PATH environment variable. If none of
these directories contains the command, Windows will stop and indicate
-the command does not exist. To make sure R (, which may be in
-something like C:/Program Files/R/R-3.5.1/bin/x64/) and Python (,
-which may be in something like C:/Program Files/Python/Python37/) can
-easily be run from emacs, you should thus configure the PATH variable
+the command does not exist. To make sure R (which may be in
+something like C:/Program Files/R/R-3.5.1/bin/x64/) and Python (which may be in something like C:/Program Files/Python/Python37/) can
+easily be run from Emacs, you should thus configure the PATH variable
accordingly.
Open an DOS console and type the following command:
@@ -282,11 +274,25 @@ starting withbackend, which amounts to use the default Agg
+To have code pretty printing when exporting to HTML, you should
+install the htmlize package, which is done by opening emacs and
+typing the following command:
+
+M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key then the "x" key ++
This section is illustrated in a video tutorial ("Mise en place Emacs/Orgmode" in French). Watching it before following the @@ -305,14 +311,14 @@ adding a few org-mode specific configurations.
-The procedure we propose will wipe your already existing custom emacs
-configuration if you already have one. You should thus beforehand make
-a backup of ~/.emacs and of ~/.emacs.d/init.el (if these file
-exists).
+The procedure we propose will wipe your already existing custom Emacs
+configuration if you have one. You should thus beforehand make
+a backup of ~/.emacs and of ~/.emacs.d/init.el (if these files
+exist).
@@ -328,9 +334,9 @@ rr_org/journal.org
Create an org/ directory in the top of your home:
org/ directory in the top of your home:
Then copy rr_org/journal.org file in your ~/org/ directory. This
file will be your laboratory notebook and all the notes you will
capture with C-c c will go automatically go in this file. The first
-entry of this notebook is populated with many emacs shortcuts that you
+entry of this notebook is populated with many Emacs shortcuts that you
should give a try.
Copy rr_org/init.el in your ~/.emacs.d/ directory.
emacs -q -l rr_org/init.el
There are two situations in which it might be necessary to modify
init.el:
@@ -392,9 +398,9 @@ beginning of the file for instructions.
Open a new instance of Emacs and open a
In step 1, you were told to create an journal in
This section is illustrated in a video tutorial ("Écrire un article
réplicable avec Emacs/Orgmode" in French). Watching it before
@@ -473,7 +479,7 @@ tar zxf replicable_article.tgz; cd repli
If the
-Learning emacs and org-mode can be difficult as there is an inordinate
+Learning Emacs and Org-Mode can be difficult as there is an inordinate
amount of shortcuts. Many people have thus come up with
cheat-sheats. Here is a selection in case it helps:
For those of you who prefer video explanations, here is a Youtube
channel with many step by step emacs tutorials.
Company-mode is a text completion framework for Emacs. It allows to
have smart completion in emacs for the most common languages. If you
@@ -563,18 +569,18 @@ official Web page: http://company-mode.
-Magit is an emacs interface for Git. Its usage is briefly illustrated
+Magit is an Emacs interface for Git. Its usage is briefly illustrated
in the context of this MOOC in a video tutorial ("Utilisation
Emacs/git" in French).
It is very powerful and we use it on a daily basis but you should
-definitely understand what git does behind the scene beforehand. If
+definitely understand what git does behind the scenes beforehand. If
you feel this would be useful for you, you should follow this visual
walk-through or this really short "crash course". If you installed the
previous "reproducible research" emacs configuration, you can easily
@@ -583,9 +589,9 @@ invoke magit by using
-This document is particularly important if you follow the Rstudio or
-the Org-Mode course. If you follow the Jupyter course, it can be
-ignored in a first step as we have closely integrated Jupyter and
+This document is particularly important if you follow the RStudio or
+the Org-Mode path. If you follow the Jupyter path, it can be
+ignored at first as we have closely integrated Jupyter and
GitLab in the context of this MOOC.
-We provide here only instructions for debian-based distributions. Feel
+We provide here only instructions for Debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
-for other distributions (e.g., redhat, fedora).
+for other distributions (e.g., RedHat, Fedora).
@@ -83,13 +83,13 @@ Run (as root):
@@ -105,15 +105,15 @@ Rstudio):
Set a Git username and email:
You may be behind a proxy, in which case you may have trouble cloning
or fetching from a remote repository or you may get an error like
@@ -164,11 +164,14 @@ will be prompted for it every time it is needed.
-Warning (Jupyter users) : changing your default Gitlab password will prevent you from committing in Jupyter. You will have to do the extra step of changing your Jupyter
-If you wish to modify your password, you shoul go to
If you clone your repository by simply pasting the GitLab URL, you will be
prompted for your login and your password every time you want to
@@ -278,9 +281,9 @@ Use it at your own risk.
There are two ways of authenticating and synchronizing your local
repository with GitLab: through HTTPS or through SSH. The first one is
@@ -293,17 +296,17 @@ your SSH public key on GitLab. This section provides with information
on how to do this.
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
-for other distributions (e.g., redhat, fedora).
+for other distributions (e.g., RedHat, Fedora).
@@ -315,15 +318,15 @@ Run (as root):
You do not have anything to do as it is installed by default.
You should install the Putty client. Once it is installed, look for
the section on generating an SSH key.
@@ -332,9 +335,9 @@ the section on generati
Here are all the official explanations on how to set up your SSH key
on GitLab. Alternatively, you may also want to have a look at this
@@ -345,15 +348,15 @@ video:
This section describes a generic (through the command line) way to
synchronize your local files with Gitlab. You will not need this if
-you follow the Jupyter course. If you follow the Rstudio course, all
-these operations can be done through Rstudio and you may want to read
-the corresponding instructions. If you follow the Org-Mode course, all
+you follow the Jupyter path. If you follow the RStudio path, all
+these operations can be done through RStudio and you may want to read
+the corresponding instructions. If you follow the Org-Mode path, all
these operations can be done through Magit and you may want to read
the corresponding instructions.
The following webpage lists several Jupyter tricks (in particular, it
-illustrates many
-For any reason, you may be unsatisfied with the use of R or of
-Python. Many other languages are available:
+Jupyter is not limited to Pytyhon and R. Many other languages are available:
https://github.com/jupyter/jupyter/wiki/Jupyter-kernels, including
-non-free languages like SAS, Mathematica, Matlab…
+non-free languages like SAS, Mathematica, Matlab… Note that the maturity of these kernels differs widely.
None of these other languages have been deployed in the context of our
-MOOC but you may want to read the next sections to know more about how
-to set up your own Jupyter notebooks on your computer and benefit from these
-extensions.
+MOOC but you may want to read the next sections to learn how
+to set up your own Jupyter on your computer and benefit from these extensions.
+
+Since the question was asked several times, if you really need to stay
+with SAS, you should know that SAS can be used within Jupyter using
+either the Python SASKernel or the Python SASPy package (step by step
+explanations about this are given here).
+
+Since proprietary software such as SAS cannot easily be inspected, we discourage its use as it hinders reproducibility by
+essence. But perfection does not exist anyway and using Jupyter
+literate programming approach allied with systematic control version
+and environment control will certainly help anyway.
-In this Section, we provide information on how to set up on your own
-computer a Jupyter environment similar to the one deployed for this
-MOOC.
+In this section, we explain how to set up a Jupyter environment on
+your own computer similar to the one deployed for this MOOC.
@@ -117,15 +127,13 @@ Note that Jupyter notebooks are only a small part of the picture and
that Jupyter is now part of a bigger project: JupyterLab, which allows
you to mix various components (including notebooks) in your
browser. In the context of this MOOC, our time frame was too short to
-benefit from JupyterLab which was still under active development but
-this is probably the best option now if you want to benefit from
-cutting-edge Jupyter notebooks.
+benefit from JupyterLab which was still under active development. You may, however, prefer JupyterLab when doing an installation on your own computer.
Follow these instructions if you wish to have a Jupyter environment on
your own computer similar to the one we set up for this MOOC.
@@ -158,18 +166,18 @@ jupyter notebook
-The previous environment should ship with R but if you proceeded
-otherwise and only have python available in Jupyter, you may want to
-read the following section.
+The environment described in the last section should include R, but if
+you proceeded otherwise and only have Python available in Jupyter, you
+may want to read the following section.
Do the following in R console:
On Linux, the rpy2 package is available in standard distributions
-An other (not really recommended if the first one is available)
-alternative consists in going through the python package manager with
+An alternative (not really recommended if the first one is available)
+consists in going through the python package manager with
-Download
@@ -250,15 +258,15 @@ Install also
-Here is what we had to install on our recent debian computer to make sure
+Here is what we had to install on a recent Debian computer to make sure
the notebook export via LaTeX works:
-Download and install MiKTeX from the MiKTeX webpage
-by choosing the right operating system. You will be prompted to install some specific
+Download and install MiKTeX from the MiKTeX webpage by choosing the
+right operating system. You will be prompted to install some specific
packages when exporting to pdf.
Here are a few extensions that can ease your life:
-To ease your experience, we added some pull/push buttons that allow
+To ease your experience, we added pull/push buttons that allow
you to commit and sync with GitLab. This development was specific to
the MOOC but inspired from a previous proof of concept. We have
recently discovered that someone else developed about at the same time
@@ -358,38 +363,7 @@ is a long an interesting discussion about various options on
-Last but not least, remember that Jupyter notebooks are only a small
-part of the picture and that Jupyter is now part of a bigger project:
-JupyterLab, which allows you to mix various components (including
-notebooks) in your browser. A specific JupyterLab git plugin has been
-developed to offer a nice version control experience.
-
-For any reason, you may be unsatisfied with the use of R or of
-Python. Many other languages are available:
-https://github.com/jupyter/jupyter/wiki/Jupyter-kernels, including
-non-free languages like SAS, Mathematica, Matlab…
-
-Since the question was asked several times, if you really need to stay
-with SAS, you should know that SAS can be used within Jupyter using
-either the Python SASKernel or the Python SASPy package (step by step
-explanations about this are given here).
-
-Since such software cannot easily be opened for inspection not widely
-used, we discourage this approach as it hinders reproducibility by
-essence. But perfection does not exist anyway and using Jupyter
-literate programming approach allied with systematic control version
-and environment control will certainly help anyway.
+For those who use JupyterLab rather than the plain Jupyter, a specific JupyterLab git plugin has been developed to offer a nice version control experience.
-This document provides information on how to install Rstudio.
-
-If you have never used git with Rstudio, we strongly advise that you
-follow our tutorial on using git from Rstudio ("Rstudio et Gitlab" in French). Before
-proceeding, make sure you also have followed the "git/GitLab
-configuration" tutorial (in French).
-
-Alternatively, you may want to watch this video (in English). If you
-do not like videos, you should have a look at the step-by-step
-explanations from Software Carpentry. It comes with many screenshots
-and is quite progressive.
-
-Last, you should know that the Rstudio team has created a lot of very
-good material and tutorials. You should definitively look at the Cheat
-sheets webpage. In particular you may want to have look at the
-following ones:
-
-In case it helps, here are some (sometimes outdated) French versions
-of these documents:
-
-We provide here only instructions for debian-based distributions. Feel
+We provide here only instructions for Debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
-for other distributions (e.g., redhat, fedora).
+for other distributions (e.g., RedHat, Fedora).
Today, the stable versions of the most common distributions provide
-recent enough versions of emacs and org-mode:
+recent enough versions of R:
-Beforehand, you need to install the R language and convenient packages
+First, you need to install the R language and convenient packages
by running (as root):
-Rstudio is unfortunately not packaged within debian so the easiest is
-to download the corresponding debian package on the Rstudio webpage
-and then to install it manually (depending on when you do this, you
-can obviously change the version number). Here is how to install it:
+RStudio is unfortunately not packaged within Debian so the easiest is
+to download the corresponding Debian package on the RStudio webpage
+and then to install it manually (you may have to adjust the version number in the following example). Here is how to install it:
Some instructions on installing R and knitr must be missing. This
@@ -160,9 +119,9 @@ should be tested and improved.
+The RStudio team has created a lot of very good material and
+tutorials. You should definitively look at the Cheat sheets
+webpage. In particular you may want to have look at the following
+ones:
+
+In case it helps, here are some (sometimes outdated) French versions
+of these documents:
+
+If you have never used git with RStudio, we strongly advise that you
+follow our tutorial on using git from RStudio ("RStudio et Gitlab"
+in French). Before proceeding, make sure you also have followed the
+"git/GitLab configuration" tutorial (in French).
+
+Alternatively, you may want to watch this video (in English). If you
+do not like videos, you should have a look at the step-by-step
+explanations from Software Carpentry. It comes with many screenshots
+and is quite progressive.
+
Open RStudio and do the following steps:
-Get the url from your gitlab repository:
+Get the URL from your GitLab repository:
As we explained, the programming language used in an analysis has a
clear influence on the reproducibility of your analysis. It is not a
@@ -56,12 +56,12 @@ committee (even though some compilers may not respect this norm).
On the other end of the spectrum, Python had a much more organic
-development based on a readability philosophy and has evolved with
-time. Furthermore, python is commonly used as a wrapping language
-(e.g., to easily use C or FORTRAN libraries) and has its own packaging
-system to make everyone's life easier. All these design choices tend
-to make reproducibility often a bit painful with python, even though
-the community is slowly taking this into account.
+development based on a readability philosophy and valuing continuous
+improvement over backwards-compatibility. Furthermore, Python is
+commonly used as a wrapping language (e.g., to easily use C or FORTRAN
+libraries) and has its own packaging system. All these design choices
+tend to make reproducibility often a bit painful with Python, even
+though the community is slowly taking this into account. The transition from Python 2 to the not fully backwards compatible Python 3 has been a particularly painful process, not least because the two languages are so similar that is it not always easy to figure out if a given script or module is written in Python 2 or Python 3. It isn't even rare to see Python scripts that work under both Python 2 and Python 3, but produce different results due to the change in the behavior of integer division.
@@ -72,32 +72,32 @@ solid/stable. R is obviously not immune to evolutions that break old
versions and hinder reproducibility/backward compatibility. Here is a
relatively recent true story about this and some colleagues who worked
on the statistics introductory course with R on FUN reported us
-several issues with functions from a few functions (
This being said, the R development community is generally quite
-careful about stability. We (the authors of this MOOC) think open
-source (, which allows to inspect how computation is done and to
-identify both mistakes and sources of non reproducibility) is more
-important than the rock solid stability of SAS, which is a proprietary
+careful about stability. We (the authors of this MOOC) believe that open
+source (which allows to inspect how computation is done and to
+identify both mistakes and sources of non-reproducibility) is more
+important than the rock solid stability of SAS, which is proprietary
software. Yet, if you really need to stay with SAS (similar solutions
probably exist for other languages as well), you should know that SAS
can be used within Jupyter using either the Python SASKernel or the
Python SASPy package (step by step explanations about this are given
here). Using such literate programming approach allied with systematic
-control version and environment control will help anyway.
+version and environment control will always help.
As we mentioned in the video sequences, there are several solutions to
control your environment:
@@ -108,8 +108,8 @@ control your environment:
clean environment and install only what's strictly necessary (and document it):
Ensuring software is properly archived, i.e, is safely stored so that
it can be accessed in a perennial way, can be quite tricky. If you
@@ -145,15 +145,15 @@ project, this is a must see. htt
For regular data, we highly recommend using https://www.zenodo.org/
-whenever data is not sensitive.
+whenever the data is not sensitive.
-In the video sequences, we mentioned workflows (original domain in parenthesis):
+In the video sequences, we mentioned workflow managers (original application domain in parenthesis):
-These topics could only be mentioned in our MOOC but could by no way
-be properly covered. We only suggest here a few interesting talks
+We have mentioned these topics in our MOOC but we could by no way
+cover them properly. We only suggest here a few interesting talks
about this.
You may want to have a look at the following two webinars:
-Experimentation was not covered in this MOOC whereas it is an
+Experimentation was not covered in this MOOC, although it is an
essential part of science. The main reason is that practices and
-constraints can vary so wildly from a domain to an other that it could
+constraints can vary so wildly from one domain to another that it could
not be properly covered in a first edition. We would be happy to
gather references you consider as interesting in your domain so do not
hesitate to provide us with such references by using the forum and we
@@ -230,13 +230,13 @@ Science.
When taking notes, it may be difficult to remember which version of
the code or of a file was used. This is what version control is useful
@@ -295,7 +295,7 @@ new directories it did not previously know about.
-Then, I often include commands at the end of my notebook indicating
+Then, we often include commands at the end of our notebook indicating
how to commit the results (adding the new files, committing with a
clear message and pushing). E.g.,
This topic is discussed on StackOverflow. When using
-Here for example how I get these information on my machine:
+Here is for example how I get this information on my machine:
Without resorting to pip (that will list all available packages), you
may want to know which modules are loaded in a Python session as well
-as their version. Inspiring from StackOverflow, here is a simple
+as their version. Inspired by StackOverflow, here is a simple
function that lists loaded package (that have a
The easiest way to go is as follows:
The Jupyter environment we deployed on our servers for the MOOC is
based on the version 4.5.4 of Miniconda and Python 3.6. In this
@@ -592,13 +594,13 @@ It is even possible to install a specific (possibly much older) version, e.g.,:
The best way seems to be to rely on the
Some actually advocate that writing a reproducible research compendium
-can be done by writing an R package. Those of you willing to have a
+is best done by writing an R package. Those of you willing to have a
clean R dependency management should thus have a look at Packrat.
Finally, it is good to know that there is a built-in R command
(
This section is mostly a cut and paste from the recent post by Ian
-Pylvainen on this topic. It comprises a very clear explanation on how
+Pylvainen on this topic. It comprises a very clear explanation of how
to proceed.
If you're on a Debian or a Ubuntu system, it may be difficult to
access a specific version without breaking your system. So unless you
@@ -959,8 +961,8 @@ install.packages(packageurl, repos=Using devtools
The simplest method to install the version you need is to use the
-If you devtools fails or if you do not want to depend on it, you can
-install it from source via foo.org file. Copy the
following lines in this file:
@@ -425,22 +431,22 @@ is demonstrated in the
-Step 5: Open and play with your journal:
-Step 5: Open and play with your journal:
+~org/journal.org. First you probably want to make sure this file is
-backed up in a revision control system like git. We leave it up to you
+stored in a version control system like git. We leave it up to you
to set this up but if you have any trouble, feel free to ask on the
FUN forums.
A stub of replicable article
-A stub of a replicable article
+
make command fails (especially on Mac), it may be because
-emacs or something else is not correctly installed. In that case,
+Emacs or something else is not correctly installed. In that case,
open the article directly with the following command:
Emacs Tips and tricks
-Emacs tips and tricks
+Cheat-sheets
-Cheat-sheets
+Emacs
-Emacs
+
-
Org-mode
-Org-mode
+
Video tutorials
-Video tutorials
+Additional useful emacs packages
-Additional useful emacs packages
+Company-mode
-Company-mode
+Magit
-Magit
+C-x g.
Other resources
-Other resources
+
Table of Contents
-
-
Installing Git
-Installing Git
+Linux (debian, ubuntu)
-Linux (Debian, Ubuntu)
+Mac OSX and Windows
-Mac OSX and Windows
+
Configuring Git
-Configuring Git
+Telling Git who you are: Name and Email
-Telling Git who you are: Name and Email
+
-
Dealing with proxies
-Dealing with proxies
+Getting your default password on GitLab (and possibly changing it)
-Getting your default password on GitLab (and possibly changing it)
+~/.git-credentials
+Warning (Jupyter users) : changing your default Gitlab password will
+prevent you from committing in Jupyter. You will have to do the extra
+step of changing your ~/.git-credentials in the Jupyter environment
+(possibly several times).
@@ -224,13 +227,13 @@ button).
Account > Settings > Password
+If you wish to modify your password, you should go to Account > Settings > Password
and define your password using the default
password you just retrieved. Again, if you use the Jupyter
notebooks we have deployed for the MOOC, remember that changing
your default Gitlab password will prevent you from committing in
Jupyter. You will have to do the extra step of changing your
-Jupyter ~/.git-credentials through a jupyter console (see next
+Jupyter ~/.git-credentials through a Jupyter console (see next
section).
Remembering your password locally
-Remembering your password locally
+Optional: authenticating through SSH
-Optional: authenticating through SSH
+Installing SSH
-Installing SSH
+
-
-
+
-
+
-
+Setting up SSH on GitLab
-Setting up SSH on GitLab
+Using Git through the command line to synchronize your local files with Gitlab
-Using Git through the command line to synchronize your local files with Gitlab
+Table of Contents
-
-
@@ -34,20 +32,20 @@
-
1. Jupyter Tips and tricks
-1. Jupyter tips and tricks
+Ipython magic commands) that should improve your
+illustrates many IPython magic commands) that should improve your
efficiency (note that this blog post is about two years old so some of
the tricks may have been integrated in the default behavior of Jupyter
now).
Running R and Python in the same notebook
-Running R and Python in the same notebook
+rpy2 package allows to use both languages in the same notebook by:
Other languages
-Other languages
+2. Installing and configuring Jupyter on your computer
-2. Installing and configuring Jupyter on your computer
+2.1 Installing Jupyter
-2.1 Installing Jupyter
+2.2 Making sure Jupyter allows you to use R
-2.2 Making sure Jupyter allows you to use R
+• Installing IRKernel (R package)
-• Installing IRKernel (R package)
+• Installing rpy2 (Python package)
-• Installing rpy2 (Python package)
+pip3 install rpy2
@@ -229,7 +237,7 @@ alternative consists in going through the python package manager with
rpy2 binary file by choosing the right operating system.
+Download the rpy2 binary file by choosing the right operating system.
tzlocal:
2.3 Additional tips
-2.3 Additional tips
+• Exporting a notebook
-• Exporting a notebook
+• Side note about Jupyter, JupyterLab, JupyterHub…
-• Improving notebook readability
-• Improving notebook readability
+• Interacting with GitLab and GitHub
-• Interacting with GitLab and GitHub
+• Using other languages (e.g., SAS, Matlab, Mathematica, etc.)
-Table of Contents
-
-
-
-Installing Rstudio
-Installing RStudio
+Linux (debian, ubuntu)
-Linux (debian, ubuntu)
+
Installing R
-Installing R
+r-cran-gplot2 or r-cran-knitr
fails, you may want to install them locally (through the R packaging
system) and manually by running the following commands in R (or
-Rstudio):
+RStudio):
install.packages("knitr")
@@ -129,14 +89,13 @@ to run (as root):
Installing rstudio
-Installing RStudio
+Mac OSX and Windows
-Mac OSX and Windows
+
knitr and ggplot2:knitr and ggplot2:install.packages("knitr", dep=TRUE)
@@ -172,13 +131,56 @@ install.packages("ggplot2", dep=
Using Git from Rstudio
-RStudio documentation
+
+
+Cloning a repository
-Using Git from RStudio
+Cloning a repository
+File / New Project / Version Contr
Modifying a file
-Modifying a file
+
Module2/exo1/toy_document.Rmd and perform a simple
modification.Table of Contents
-
-
-
@@ -38,13 +38,13 @@
-
-
Additional references
-Additional references
+"Thoughts" on language/software stability
-"Thoughts" on language/software stability
+plotmeans from
-gplots, survfit from survival, or hclust) whose default
-parameters had changed over the years. It is thus probably a good
-practice to explicitly indicate in your code default values (, which
-can be cumbersome) and to restrict your dependencies as much as
-possible.
+several issues with a few functions (plotmeans from gplots,
+survfit from survival, or hclust) whose default parameters had
+changed over the years. It is thus probably good practice to give
+explicit values for all parameters (which can be cumbersome) instead
+of relying on default values, and to restrict your dependencies as much
+as possible.
Controlling your software environment
-Controlling your software environment
+
@@ -133,9 +133,9 @@ Hinsen on Active Papers (http://www.a
Preservation/Archiving
-Preservation/Archiving
+Workflows
-Workflows
+Numerical and statistical issues
-Numerical and statistical issues
+
@@ -190,16 +190,16 @@ reproducibility and present recent research work on this topic.
Publication practices
-Publication practices
+
Experimentation
-Experimentation
+Tracking environment information
-Tracking environment information
+Getting information about your Git repository
-Getting information about your Git repository
+Getting information about Python(3) libraries
-Getting information about Python(3) libraries
+Getting the list of installed packages and their version
-Getting the list of installed packages and their version
+pip (the Python
package installer) within a shell command, it is easy to query the
@@ -343,7 +343,7 @@ versions of Python are available on your machine
pip3 freeze
@@ -441,13 +441,13 @@ Requires: patsy, pandas
How to list imported modules?
-How to list imported modules?
+__version__ attribute,
which is unfortunately not completely standard).
def print_imported_modules():
import sys
- for name,val in sorted(sys.modules.items()):
+ for name, val in sorted(sys.modules.items()):
if(hasattr(val, '__version__')):
print(val.__name__, val.__version__)
+ else
+ print(val.__name__, "(unknown version)")
print("**** Package list in the beginning ****");
print_imported_modules()
@@ -504,9 +506,9 @@ zlib 1.0
Setting up an environment with pip
-Saving and restoring an environment with pip
+Installing a new package or a specific version
-Installing a new package or a specific version
+Getting information about R libraries
-Getting information about R libraries
+Getting the list imported modules and their version
-Getting the list imported modules and their version
+devtools package (if this
package is not installed, you should install it first by running in R
@@ -661,14 +663,14 @@ Packages ----------------------------------------------------------------------
Getting the list of installed packages and their version
-Getting the list of installed packages and their version
+installed.packages) allowing to retrieve and list the details of all
@@ -923,19 +925,19 @@ packages installed.
Installing a new package or a specific version
-Installing a new package or a specific version
+
-
-
+
-
+install_version() function of the devtools package (obviously, you
@@ -975,11 +977,12 @@ install_version("ggplot2", version =
-
+install.packages() directed to the right
+Alternatively, you may want to install an older package from source If
+devtools fails or if you do not want to depend on it, you can install
+it from source via install.packages() directed using the right
URL. This URL can be obtained by browsing the CRAN Package Archive.
-
