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Which notebook to edit? #2

Closed infotroph closed 2 years ago

infotroph commented 4 years ago

I see two (apparently identical) copies of the notebook for the M1.1 benchmark -- one in the project root and one in the M1.1 directory. Which one is canonical? Should the other be deleted?

I ask because I'm working on the M1 benchmarks in OpenSimRoot and have fixed a typo[1] in my copy of the M1.1 notebook. I'm happy to submit a pull request with my fix, but am not sure which file it should edit.

[1] The typo is that variable model gets set for both dicot and monocot MDS, then permanova throws an error when it tries to use the monocot model in the dicot adonis call. To fix, give different names to the two variables:

     "abline(a=0, b=1, col=\"red\", lwd=2)\n",
     "\n",
     "#Plot MDS for dicot\n",
-    "model<-datadicot[datadicot$Time==11, \"model\"]\n",
-    "datamds<-data.frame(mds.dicot$points, model=model)\n",
+    "model_dicot<-datadicot[datadicot$Time==11, \"model\"]\n",
+    "datamds<-data.frame(mds.dicot$points, model=model_dicot)\n",
     "colnames(datamds)<-c(paste(rep(\"MDS\", k), c(1:k), sep=\"\"), \"model\")\n",
     "\n",
     "ggplot(datamds)+\n",
-    "geom_point(aes(MDS1, MDS2, colour=model))+\n",
+    "geom_point(aes(MDS1, MDS2, colour=model_dicot))+\n",
     "geom_hline(yintercept=0)+\n",
     "geom_vline(xintercept=0)+\n",
     "ggtitle(\"Metric multidimensional scaling\")+\n",
@@ -1049,13 +1049,13 @@
     "plot(realdist, confdist, xlab=\"Real distances\", ylab=\"Distances in configuration\", pch=16, main=\"Shepard plot\", las=1)\n",
     "abline(a=0, b=1, col=\"red\", lwd=2)\n",
     "\n",
-    "#Plot MDS for dicot\n",
-    "model<-datamonocot[datamonocot$Time==8, \"model\"]\n",
-    "datamds<-data.frame(mds.monocot$points, model=model)\n",
+    "#Plot MDS for monocot\n",
+    "model_monocot<-datamonocot[datamonocot$Time==8, \"model\"]\n",
+    "datamds<-data.frame(mds.monocot$points, model=model_monocot)\n",
     "colnames(datamds)<-c(paste(rep(\"MDS\", k), c(1:k), sep=\"\"), \"model\")\n",
     "\n",
     "ggplot(datamds)+\n",
-    "geom_point(aes(MDS1, MDS2, colour=model))+\n",
+    "geom_point(aes(MDS1, MDS2, colour=model_monocot))+\n",
     "geom_hline(yintercept=0)+\n",
     "geom_vline(xintercept=0)+\n",
JPFZJ commented 4 years ago

Please check with the upstream repo at github. If it als contains two, check with andrea schnepf

On Sat, Feb 22, 2020 at 5:08 PM Chris Black notifications@github.com<mailto:notifications@github.com> wrote:

I see two (apparently identical) copies of the notebook for the M1.1 benchmark -- one in the project root and one in the M1.1 directory. Which one is canonical? Should the other be deleted?

I ask because I'm working on the M1 benchmarks in OpenSimRoot and have fixed a typo[1] in my copy of the M1.1 notebook. I'm happy to submit a pull request with my fix, but am not sure which file it should edit.

[1] The typo is that variable model gets set for both dicot and monocot MDS, then permanova throws an error when it tries to use the monocot model in the dicot adonis call. To fix, give different names to the two variables:

 "abline(a=0, b=1, col=\"red\", lwd=2)\n",
 "\n",
 "#Plot MDS for dicot\n",

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infotroph commented 4 years ago

@JPFZJ This is the upstream repo ;)

JPFZJ commented 4 years ago

https://github.com/RSA-benchmarks/collaborative-comparison

On Wed, Feb 26, 2020 at 10:50 AM Chris Black notifications@github.com<mailto:notifications@github.com> wrote:

@JPFZJhttps://github.com/JPFZJ This is the upstream repo ;)

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-- Dr. Ir. Johannes A. Postma Forschungszentrum Jülich IBG-2: Plant Sciences rm 015 Wilhelm-Johnen-Straße 52428 Jülich Germany +49 2461 61 4333

[osr_dpi900_2.png]https://rootmodels.gitlab.io/

Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt

infotroph commented 4 years ago

@JPFZJ This whole thread already lives at the address you posted. Are you confusing notifications from GitHub (upstream) with those from GitLab (OSR sandbox repository?)

JPFZJ commented 4 years ago

yes, seems so. My apologies.

On Wed, Feb 26, 2020 at 12:11 PM Chris Black notifications@github.com<mailto:notifications@github.com> wrote:

@JPFZJhttps://github.com/JPFZJ This whole thread already lives at the address you posted. Are you confusing notifications from GitHub (upstream) with those from GitLab (OSR sandbox repository?)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/RSA-benchmarks/collaborative-comparison/issues/2?email_source=notifications&email_token=AD27QZSHJKSQO3SL4XC7OYLREZE7LA5CNFSM4KZSTJX2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM72DCQ#issuecomment-591372682, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD27QZVTX2L3YNWLD72S6R3REZE7LANCNFSM4KZSTJXQ.

-- Dr. Ir. Johannes A. Postma Forschungszentrum Jülich IBG-2: Plant Sciences rm 015 Wilhelm-Johnen-Straße 52428 Jülich Germany +49 2461 61 4333

[osr_dpi900_2.png]https://rootmodels.gitlab.io/

Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt

schnepfa commented 2 years ago

The M1 Jupyter Notebooks are still in this repository for completeness, but Benjamin Delory is currently working on the data analysis and comparisons, including also your results. I am not sure if there is a public repository for his pipeline currently available, but you will here from him soon and further steps will be discussed!