CamilleAny
commented
5 years ago Thank you for the feed back !
The black bar does represent 9,5 nm. Sorry it was poorly formulated.
Best, Camille
Open AlexanderBackis opened 5 years ago
CamilleAny
commented
5 years ago Thank you for the feed back !
The black bar does represent 9,5 nm. Sorry it was poorly formulated.
Best, Camille
———————————————————————————————————————————————————————————————————————————————————————— Review of ‘ANOVA (Analysis of Variance) on the result of a TOXCAT experiment’ by Camille Garcia ———————————————————————————————————————————————————————————————————————————————————————— Reviewer: Alexander Backis Date : 7/1-2019 ————————————————————————————————————————————————————————————————————————————————————————
———————————————————————————————————————————————————————————————————————————————————————— Q: Includes rich documentation using Markdown (equations, tables, links, images or videos) A: Yes, the notebook uses the Markdown feature extensively. It includes figures, links, equations, tables and descriptive texts. It also provides interpretations of the results. Furthermore, it goes into great effort to explain the analytical tools used to perform the analysis, which facilitates the reading.
Q: Includes instructions on how to run the notebook A: Partially. It includes information on how install and activate the environment, but it does not include information on how to start the notebook (this might not be obvious when using a notebook for the first time).
Q: Includes the required packages in an ‘environment.yml’ file A: Yes, everything runs smoothly within the environment.
Q: Is reproducible, i.e., someone else should be able to redo the steps A: Yes, the code is written in a clear and concise way, which makes it easy to follow. The notebook narrates in a clear way, making the goal and procedure obvious. However, since it is not my field of research, so it is difficult for me to follow some of the details about the membranes and statistical procedures.
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Q: Uses pandas to read large data sets or numpy to load data from text files A: Yes.
Q: Uses pandas to save to disk the processed or generated data A: No.
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Q: Performs numerical operations (numpy, scipy, pandas) or manipulates, groups, and aggregates a data set (pandas) A: Yes. For example, it uses pandas to aggregate several data frames of data.
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Q: Includes at least one composite plot (inset or multiple panels) A: Yes.
Q: The figures are 89 mm wide (single column) or 183 mm wide (double column) A: Yes.
Q: The axes are labeled A: Yes.
Q: The font sizes are sufficiently large A: Yes.
Q: The figures are saved as rasterized images (300 dpi) or vector art A: Yes
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Q: Is archived in a repository with a digital object identifier (DOI) A: Yes.
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The notebook is well written with an excellent use of references, figures and links to read up on statistical methods. All the files are stored in a neat folder structure and everything works nicely. Since I am not the target audience of this notebook, it is difficult for me to follow the chemistry/biology. However, the code is easy to follow and it uses a lot of comments, which makes it easier to get an overview. At some parts I would line break to make it easier to see (for example line 3), but for the most part it looks great!
In Fig. 1A), does the black bar in the lower right corner represent 9.5 nm? Maybe the scale could be shown in the figure as well!
Finally, I would like to thank you for a well prepared notebook with excellent figures and clean code!
Cheers, Alexander