docs(logbook): update day 4 and create day 5

pythonhealthdatascience · Sep 27, 2024 · 26aacb1 · 26aacb1
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diff --git a/logbook/posts/2024_09_26/figure6.png b/logbook/posts/2024_09_26/figure6.png
diff --git a/logbook/posts/2024_09_26/index.qmd b/logbook/posts/2024_09_26/index.qmd
@@ -38,6 +38,8 @@ As before, this function gave a great starting point to get matching figure, alt
 * Article appears to plot ascending throughput, and perhaps a subsample
 * When add fill colour by pre-screen, realise that it's including multiple rows in the same plot. This doesn't appear to be the case in the original. They also don't have any consecutive graphs with the same throughput. Hence, it appears I'd maybe need to remove duplicates with same throughput? I tried this and it looked like it maybe is heading in the right direction
 
+![Figure 6 from 10 pop 1 gen](figure6.png)
+
 ## 14.30-14.47: Running on remote machine
 
 Cloned and built environment on remote machine (more computational power than my local machine, but not HPC). Had to install conda -

diff --git a/logbook/posts/2024_09_27/figure5_100pop_1gen.png b/logbook/posts/2024_09_27/figure5_100pop_1gen.png
diff --git a/logbook/posts/2024_09_27/figure5_10pop_1gen.png b/logbook/posts/2024_09_27/figure5_10pop_1gen.png
diff --git a/logbook/posts/2024_09_27/figure6_100pop_1gen.png b/logbook/posts/2024_09_27/figure6_100pop_1gen.png
diff --git a/logbook/posts/2024_09_27/figure6_10pop_1gen.png b/logbook/posts/2024_09_27/figure6_10pop_1gen.png
diff --git a/logbook/posts/2024_09_27/index.qmd b/logbook/posts/2024_09_27/index.qmd
@@ -0,0 +1,69 @@
+---
+title: "Day 5"
+author: "Amy Heather"
+date: "2024-09-27"
+categories: [reproduce]
+bibliography: ../../../quarto_site/references.bib
+---
+
+::: {.callout-note}
+
+X. Total time used: Xh Xm (X%)
+
+:::
+
+## 09.51-09.57, 10.52-10.55: Resuming attempt to run on remote machine
+
+As left off yesterday, getting error:
+
+```
+...
+13, in <module>
+    import ExperimentRunner
+  File "ExperimentRunner.py", line 15, in <module>
+    import SimulatorRunner
+  File "SimulatorRunner.py", line 11, in <module>
+    import PODSimulation
+  File "PODSimulation.py", line 13, in <module>
+    import SimPy.SimPlot as simplot
+  File "/home/amyremote/miniconda3/envs/hernandez2015/lib/python2.7/site-packages/SimPy/SimPlot.py", line 68, in <module>
+    class SimPlot(object):
+  File "/home/amyremote/miniconda3/envs/hernandez2015/lib/python2.7/site-packages/SimPy/SimPlot.py", line 69, in SimPlot
+    def __init__(self, root = Tk()):
+  File "/home/amyremote/miniconda3/envs/hernandez2015/lib/python2.7/lib-tk/Tkinter.py", line 1815, in __init__
+    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
+_tkinter.TclError: no display name and no $DISPLAY environment variable
+```
+
+This is related to import of `simpy.simplot`, but as simplot isn't used anywhere, I tried commenting out this import in `PODSimulation.py`. This resolved the error!
+
+The original was population 100 and 50 generations. I anticipate this will be very long, so working up to it...
+
+10 population, 1 generation: just a few minutes
+
+![fig5 10 pop 1 gen](figure5_10pop_1gen.png)
+![fig6 10 pop 1 gen](figure6_10pop_1gen.png)
+
+100 population, 1 generation: 37 minutes
+
+![fig5 100 pop 1 gen](figure5_100pop_1gen.png)
+![fig6 100 pop 1 gen](figure6_100pop_1gen.png)
+
+But seems will be important to try and run with the full version - particularly as Figure 9 is an experiment of that impact of that.
+
+## Timings
+
+```{python}
+import sys
+sys.path.append('../')
+from timings import calculate_times
+
+# Minutes used prior to today
+used_to_date = 386
+
+# Times from today
+times = [
+    ('09.51', '09.57')]
+
+calculate_times(used_to_date, times)
+```
diff --git a/reproduction/r_outputs/figure5.png b/reproduction/r_outputs/figure5.png
diff --git a/reproduction/r_outputs/figure6.png b/reproduction/r_outputs/figure6.png