differences for PR #91

4-minimal-reproducible-code.md

@@ -127,6 +127,14 @@ 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?
+# --> 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
+# --> what about that cut-off year? What was that about and should that be accounted for here?
+
+###  **EDIT-end** ###
+
 counts_per_day %>%
   ggplot(aes(x = plot_type, y = count_per_day, fill = species_id, group = interaction(plot_type, species_id)))+
   geom_boxplot(outlier.size = 0.5)+
@@ -136,7 +144,48 @@ counts_per_day %>%
        y = "Individuals per day",
        fill = "Species")
 
+### ***EDIT-start *** ###
+
+# If I were to try and attempt to plot "krats per day, per plot this is what I would do:
+counts_per_day %>%
+  ggplot(aes(x=plot_type, y=count_per_day, fill=species_id)) +
+  geom_boxplot() 
+
+# 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?
+
+###  **EDIT-end** ###
+
 # B. For Spectabilis-specific exclosure, we expect a lower proportion of spectabilis there than in the other plots.
+
+### ***EDIT-start *** ###
+#
+# Here is a plot that shows the proportions... but it doesn't use counts_per_day
+krats %>%
+  ggplot(aes(x= species_id, fill=plot_type)) +
+  geom_bar(position='fill') # easy error, forget the '' around fill
+# or
+krats %>%
+  ggstatsplot::grouped_ggbarstats(x=plot_type, y=year,
+                          palette = 'Set2',
+                          grouping.var = species_id)
+#
+# But I now see you did it over time.
+# First you calculated the proportion of captured DS among plots each year, which means
+
+prop_DS <- krats %>%
+  group_by(year, species_id, plot_type) %>%
+  summarise(total_n = n()) %>%
+  mutate(prop = total_n/sum(total_n)) %>%
+  filter(species_id == 'DS')
+
+# then you want to plot it
+ggplot(prop_DS, aes(x=year, y=prop, colour=plot_type)) +
+  geom_line() 
+# DIFFERENCE: I included all the plots in calculating the proportions.
+###  **EDIT-end** ###
+
 control_spectab <- krats %>%
   filter(plot_type %in% c("Control", "Spectab exclosure"))
 
@@ -146,6 +195,12 @@ 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...
+
+### *EDIT-end ###
+
 prop_spectab %>%
   ggplot(aes(x = year, y = prop, col = plot_type))+
   geom_point()+

config.yaml

@@ -0,0 +1,81 @@
+
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor training for instance)
+# incubator: The Carpentries Incubator
+carpentry: 'incubator'
+
+# Overall title for pages.
+title: 'RRRRR, I’m stuck!'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created: 2024-05-14
+
+# Comma-separated list of keywords for the lesson
+keywords: 'R, reprex, help, The Carpentries, error, debug, reproducible example'
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'pre-alpha'
+
+# License of the lesson
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/carpentries-incubator/R-help-reprexes'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: '[email protected]'
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes:
+- 1-intro-reproducible-examples.md
+- 2-identify-the-problem.Rmd
+- 3-minimal-reproducible-data.Rmd
+- 4-minimal-reproducible-code.Rmd
+- 5-asking-your-question.md
+
+# Information for Learners
+learners:
+
+# Information for Instructors
+instructors:
+
+# Learner Profiles
+profiles:
+
+# Customisation ---------------------------------------------
+#
+# This space below is where custom yaml items (e.g. pinning
+# sandpaper and varnish versions) should live

md5sum.txt

@@ -8,7 +8,7 @@
 "episodes/1-intro-reproducible-examples.md" "d35aba14cf01b6e083d983e1f4c60fb6" "site/built/1-intro-reproducible-examples.md" "2024-12-12"
 "episodes/2-identify-the-problem.Rmd" "1cff6d8c0094033c70066efe4b7830e2" "site/built/2-identify-the-problem.md" "2024-12-12"
 "episodes/3-minimal-reproducible-data.Rmd" "b3853a92d2af1955e860871e5e9f1f79" "site/built/3-minimal-reproducible-data.md" "2024-12-12"
-"episodes/4-minimal-reproducible-code.Rmd" "0525a28e51a80c68aae1455891db4c2b" "site/built/4-minimal-reproducible-code.md" "2024-12-12"
+"episodes/4-minimal-reproducible-code.Rmd" "504b4ba412ce7bdef4d09d3251d289c1" "site/built/4-minimal-reproducible-code.md" "2024-12-12"
 "episodes/5-asking-your-question.md" "416be4365580e63c6f05974f34608907" "site/built/5-asking-your-question.md" "2024-12-12"
 "instructors/instructor-notes.md" "984429120cb60a82d505b6110d255794" "site/built/instructor-notes.md" "2024-12-12"
 "learners/reference.md" "1c7cc4e229304d9806a13f69ca1b8ba4" "site/built/reference.md" "2024-12-12"