XOR feedback for Kaija - went through the analyses #91
Conversation
Added what I would have done and some questions. Overall I didn't come up with any big issues, although the whole thing doesn't feel right? Are we going about this the right way? I did find a discrepancy with the proportions
Thank you!Thank you for your pull request 😃 🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}. If you have files that automatically render output (e.g. R Markdown), then you should check for the following:
Rendered Changes🔍 Inspect the changes: https://github.com/carpentries-incubator/R-help-reprexes/compare/md-outputs..md-outputs-PR-91 The following changes were observed in the rendered markdown documents: What does this mean?If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation. ⏱️ Updated at 2024-12-12 21:21:13 +0000 |
kaijagahm
added
the
episode:reproducible code
| @@ -128,6 +128,14 @@ counts_per_day <- krats %>% | |||
| group_by(year, plot_id, plot_type, month, day, species_id) %>% | |||
| summarize(count_per_day = n()) | |||
|
|
|||
| ### ***EDIT-start *** ### | |||
|
|
|||
| # --> Why doesn't this use "date" like we had set up earlier? | |||
There was a problem hiding this comment.
Good point--I don't remember when we set up date, and I should definitely go back and use that. Will keep in mind this continuity point for future.
| ### ***EDIT-start *** ### | ||
|
|
||
| # --> Why doesn't this use "date" like we had set up earlier? | ||
| # --> Is per day even the best way to do it? This isn't even average per day, just total per day.... Doesn't seem right |
There was a problem hiding this comment.
Can you expand on what you mean by "doesn't seem right"? My goal here was to calculate the total number of individuals caught per day, so that then I could use boxplots to see the general range of how many individuals tended to be caught on a given day in each plot.
| ggplot(aes(x=plot_type, y=count_per_day, fill=species_id)) + | ||
| geom_boxplot() | ||
|
|
||
| # what is the group=interaction() adding? |
There was a problem hiding this comment.
you're right that this is not necessary. Anyway in the new episode I've simplified this part of the analysis considerably, so it becomes moot!
|
|
||
| # what is the group=interaction() adding? | ||
|
|
||
| # I feel like we need to figure out what these exclosures are doing and if it's an over-time kinda thing then that needs to be accounted for. This just doesn't look right to me? |
There was a problem hiding this comment.
Absolutely. I was trying to keep the questions reeeeeealllly simple here because we just don't have the space to dive into investigating the biological dynamics in a lot of detail. We can discuss changing the research question to a more temporal one if you think that would be more easily understandable to illustrate the problems!
There was a problem hiding this comment.
I was just thinking we should double-check what the exclosures were doing within the time frame we are looking at, because if they originally weren't exclosures then of course they weren't working, which could be a nugget that we add later too. I just want to make sure we get the biological interpretation of the data right, if that makes sense? And to make sure there is continuity across the episodes. I don't remember what didn't look right right now, I'll look at it again in the rendered version
| @@ -147,6 +196,12 @@ prop_spectab <- control_spectab %>% | |||
| mutate(prop = total_count/sum(total_count)) %>% | |||
| filter(species_id == "DS") # keep only spectabilis | |||
|
|
|||
| ### **EDIT-start ### | |||
|
|
|||
| # these proportions don't look right to me... not in the way that I was thinking about them at least... | |||
There was a problem hiding this comment.
Can you explain what you mean by not right? How were you thinking about them?
There was a problem hiding this comment.
HA! That's hilarious, a thoroughly unhelpful comment on my part, I think I was thinking "let's discuss at our next meeting." I don't really remember right now without looking at it... Let me see if it makes sense when I look at the rendered website and if not remind me to get back to it! I think it was a question of how the proportions were being calculated compared to what I had done... I need to look at the outputs again
xortizross
changed the title
Added what I would have done and some questions. Overall I didn't come up with any big issues, although the whole thing doesn't feel right? Are we going about this the right way? I did find a discrepancy with the proportions.
@kaijagahm You don't need to approve the pull, but this gives you a chance to review it?