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Merged
merged 3 commits into from
Oct 22, 2025
+26,102 −7
Merged

Notebooks #22

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064e453
release 1st notebook
rbarillot Oct 8, 2025
4b772f2
Add second notebook
rbarillot Oct 9, 2025
faa383b
fix bugs #22
rbarillot Oct 21, 2025
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1,174 changes: 1,174 additions & 0 deletions example/Notebooks/01_simple_run_vegetative_stages.ipynb
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538 changes: 538 additions & 0 deletions example/Notebooks/02_multiple_scenarios.ipynb
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Empty file added example/Notebooks/graphs/simple_run_vegetative_stages/.gitignore
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12 changes: 12 additions & 0 deletions example/Notebooks/inputs/Ljutovac2002.csv
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metamer,leaf_Lmax,lamina_Lmax,sheath_Lmax,internode_Lmax,lamina_Wmax,lamina_area,facteurForme_lamina,RER,RER_confint
1,11.066,8.213,2.853,,0.3,1.883,0.75,,
2,12.104,9.231,2.873,,0.33,2.152,0.71,,
3,12.277,9.412,2.865,,0.4,2.78,0.73,,
4,13.314,9.987,3.327,,0.45,3.318,0.74,,
5,15.476,11.398,4.077,,0.56,4.664,0.73,2.79E-06,3.35E-07
6,19.971,13.646,6.326,0.101,0.75,7.713,0.75,1.76E-06,2.07E-07
7,25.504,16.434,9.071,1.913,1.01,12.287,0.74,1.62E-06,8.33E-08
8,31.816,19.665,12.151,6.091,1.21,17.758,0.75,1.44E-06,7.73E-08
9,39.164,25.108,14.056,9.715,1.28,24.215,0.75,1.44E-06,5.56E-08
10,45.994,28.683,17.311,14.497,1.43,30.762,0.75,1.44E-06,5.40E-08
11,42.709,23.947,18.762,17.013,1.8,32.556,0.75,1.42E-06,4.61E-08
Binary file added example/Notebooks/inputs/adel0000.pckl
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6 changes: 6 additions & 0 deletions example/Notebooks/inputs/axes_initial_state.csv
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plant,axis,status,nb_leaves,GA,SAM_height,SAM_temperature,delta_teq,delta_teq_roots,teq_since_primordium,sum_TT,cohort,mstruct,senesced_mstruct,minerals_plant
1,MS,vegetative,10,False,0,20,3600,3600,0,0,1,0.05468138,0,0.002734069
1,T1,vegetative,7,False,0,20,3600,3600,0,0,4,NA,0,NA
1,T2,vegetative,6,False,0,20,3600,3600,0,0,5,NA,0,NA
1,T3,vegetative,5,False,0,20,3600,3600,0,0,6,NA,0,NA
1,T4,vegetative,4,False,0,20,3600,3600,0,0,7,NA,0,NA
7 changes: 7 additions & 0 deletions example/Notebooks/inputs/elements_initial_state.csv
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plant,axis,metamer,organ,element,age,length,Wmax,is_growing,mstruct,senesced_mstruct,Nstruct,amino_acids,proteins,fructan,sucrose,green_area,cytokinins,max_proteins,starch,nitrates,senesced_length_element,Nresidual,max_mstruct,is_over,Ag,Tr,Ts,triosesP
1,MS,1,blade,LeafElement1,240,0.082,0.003,False,0.004106768,0,2.05E-05,1.69E+00,16.93543686,0,24.15745785,0.00019556,0.349075266,4.40E+03,0,0,0,0,0.004106768,False,0,0,20,0
1,MS,1,sheath,StemElement,240,0.0285,,False,0.00171,0,0.00000855,0.202319701,2.023197008,0,10.05882353,0.000269,0.04104,1.13E+03,0,0,0,0,0.00171,False,0,0,20,0
1,MS,2,blade,LeafElement1,160,0.092,0.0033,False,0.004837643,0,2.42E-05,2.36E+00,23.63639357,0,28.4567234,0.000230364,0.488601941,4.40E+03,0,0,0,0,0.004837643,False,0,0,20,0
1,MS,2,sheath,HiddenElement,160,0.0285,,False,0.00228,0,0.0000114,0.382633557,3.826335573,6.705882353,13.41176471,0.000248,0.0798,1.60E+03,0,0,0,0,0.00228,False,0,0,20,0
1,MS,2,sheath,StemElement,160,0.0005,,False,0.00004,0,0.0000002,0.006712869,0.067128694,0,0.235294118,0.000005,0.0014,1.60E+03,0,0,0,0,0.00004,False,0,0,20,0
1,MS,3,blade,LeafElement1,80,0.060421565,0.004,True,0.00417081,0,2.09E-05,2.24E+00,22.44062573,0,24.53417647,0.00019861,0.46295991,0,0,0,0,0,0.00417081,False,0,0,20,0
31 changes: 31 additions & 0 deletions example/Notebooks/inputs/hiddenzones_initial_state.csv
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plant,axis,metamer,hiddenzone_age,leaf_pseudo_age,internode_pseudo_age,leaf_is_growing,internode_is_growing,leaf_is_remobilizing,internode_is_remobilizing,leaf_pseudostem_length,internode_distance_to_emerge,leaf_L,internode_L,delta_leaf_pseudo_age,delta_internode_pseudo_age,delta_internode_distance_to_emerge,delta_internode_L,delta_leaf_L,delta_leaf_pseudostem_length,leaf_Lmax,leaf_Lmax_em,lamina_Lmax,sheath_Lmax,leaf_Wmax_int,leaf_Wmax,SSLW,LSSW,leaf_is_emerged,internode_Lmax,internode_Lmax_lig,LSIW,internode_is_visible,sucrose,amino_acids,fructan,proteins,leaf_enclosed_mstruct,internode_enclosed_mstruct,mstruct,leaf_enclosed_Nstruct,internode_enclosed_Nstruct,Nstruct,mean_conc_sucrose,is_over,ratio_DZ
1,MS,3,3835440,1570000,864000,True,True,False,False,0.02895,0.0289,0.0925,0.00005,3600,3600,0,0,0,0,0.1228,0.1228,0.093426659,0.029373341,NA,0.004,22,0.09,True,NA,NA,1,False,1.21E+01,1.01E+00,6.03E+00,1.01E+01,2.05E-03,1.32E-06,2.05E-03,1.02E-05,6.62E-09,1.02E-05,1800,False,1.00E+00
1,MS,4,3287520,757000,0,True,True,False,False,0.02894,0.02893,0.0265,0.00001,3600,0,0,0,0,0,0.1331,0.1331,0.099106478,0.033993522,NA,NA,NA,NA,False,NA,NA,NA,False,2.92E+00,4.79E-01,3.50E+00,4.79E+00,4.96E-04,1.69E-07,4.96E-04,2.48E-06,8.44E-10,2.48E-06,1800,False,1.00E+00
1,MS,5,2739600,0,0,True,False,False,False,0.02894,0.02894,0.002,0,0,0,0,0,0,0,NA,NA,NA,NA,0.004780451,NA,NA,NA,False,NA,NA,NA,False,6.58E-02,2.11E-02,0.00E+00,2.11E-01,1.12E-05,0.00E+00,1.12E-05,5.59E-08,0.00E+00,5.59E-08,1800,False,1.00E+00
1,MS,6,2191680,0,0,True,False,False,False,0.02894,0.02894,0.00072,0,0,0,0,0,0,0,NA,NA,NA,NA,6.42E-06,NA,NA,NA,False,NA,NA,NA,False,1.79E-02,5.76E-03,0.00E+00,5.76E-02,3.05E-06,0.00E+00,3.05E-06,1.52E-08,0.00E+00,1.52E-08,NA,False,1.00E+00
1,MS,7,1643760,0,0,True,False,False,False,0.02894,0.02894,0.00031,0,0,0,0,0,0,0,NA,NA,NA,NA,2.33E-06,NA,NA,NA,False,NA,NA,NA,False,6.19E-03,1.99E-03,0.00E+00,1.99E-02,1.05E-06,0.00E+00,1.05E-06,5.27E-09,0.00E+00,5.27E-09,NA,False,1.00E+00
1,MS,8,1095840,0,0,True,False,False,False,0.02894,0.02894,0.00016,0,0,0,0,0,0,0,NA,NA,NA,NA,9.17E-07,NA,NA,NA,False,NA,NA,NA,False,2.75E-03,8.82E-04,0.00E+00,8.82E-03,4.67E-07,0.00E+00,4.67E-07,2.33E-09,0.00E+00,2.33E-09,NA,False,1.00E+00
1,MS,9,547920,0,0,True,False,False,False,0.02894,0.02894,0.00007,0,0,0,0,0,0,0,NA,NA,NA,NA,3.87E-07,NA,NA,NA,False,NA,NA,NA,False,1.05E-03,3.39E-04,0.00E+00,3.39E-03,1.79E-07,0.00E+00,1.79E-07,8.97E-10,0.00E+00,8.97E-10,NA,False,1.00E+00
1,MS,10,0,0,0,True,False,False,False,0.02894,0.02894,0.00005,0,0,0,0,0,0,0,NA,NA,NA,NA,0.0000002,NA,NA,NA,False,NA,NA,NA,False,7.40E-04,2.38E-04,0.00E+00,2.38E-03,1.26E-07,0.00E+00,1.26E-07,6.29E-10,0.00E+00,6.29E-10,NA,False,1.00E+00
1,T1,1,3287520,757000,0,True,True,False,False,0.02894,0.02893,0.0265,0.00001,3600,0,0,0,0,0,0.1331,0.1331,0.099106478,0.033993522,NA,NA,NA,NA,False,NA,NA,NA,False,2.918527682,0.479263866,3.502233218,4.792638657,4.96E-04,1.69E-07,4.96E-04,2.48E-06,8.44E-10,2.48E-06,1800,False,1.00E+00
1,T1,2,2739600,0,0,True,False,False,False,0.02894,0.02894,0.002,0,0,0,0,0,0,0,NA,NA,NA,NA,0.004780451,NA,NA,NA,False,NA,NA,NA,False,0.065815234,0.021145753,0,2.11E-01,1.12E-05,0.00E+00,1.12E-05,5.59E-08,0.00E+00,5.59E-08,1800,False,1.00E+00
1,T1,3,2191680,0,0,True,False,False,False,0.02894,0.02894,0.00072,0,0,0,0,0,0,0,NA,NA,NA,NA,6.42E-06,NA,NA,NA,False,NA,NA,NA,False,0.017912645,0.005755147,0,5.76E-02,3.05E-06,0.00E+00,3.05E-06,1.52E-08,0.00E+00,1.52E-08,NA,False,1.00E+00
1,T1,4,1643760,0,0,True,False,False,False,0.02894,0.02894,0.00031,0,0,0,0,0,0,0,NA,NA,NA,NA,2.33E-06,NA,NA,NA,False,NA,NA,NA,False,0.006194272,0.001990156,0,1.99E-02,1.05E-06,0.00E+00,1.05E-06,5.27E-09,0.00E+00,5.27E-09,NA,False,1.00E+00
1,T1,5,1095840,0,0,True,False,False,False,0.02894,0.02894,0.00016,0,0,0,0,0,0,0,NA,NA,NA,NA,9.17E-07,NA,NA,NA,False,NA,NA,NA,False,0.002745596,0.000882132,0,8.82E-03,4.67E-07,0.00E+00,4.67E-07,2.33E-09,0.00E+00,2.33E-09,NA,False,1.00E+00
1,T1,6,547920,0,0,True,False,False,False,0.02894,0.02894,0.00007,0,0,0,0,0,0,0,NA,NA,NA,NA,3.87E-07,NA,NA,NA,False,NA,NA,NA,False,0.001054766,0.000338886,0,3.39E-03,1.79E-07,0.00E+00,1.79E-07,8.97E-10,0.00E+00,8.97E-10,NA,False,1.00E+00
1,T1,7,0,0,0,True,False,False,False,0.02894,0.02894,0.00005,0,0,0,0,0,0,0,NA,NA,NA,NA,0.0000002,NA,NA,NA,False,NA,NA,NA,False,0.000740215,0.000237823,0,2.38E-03,1.26E-07,0.00E+00,1.26E-07,6.29E-10,0.00E+00,6.29E-10,NA,False,1.00E+00
1,T2,1,2739600,0,0,True,False,False,False,0.02894,0.02894,0.002,0,0,0,0,0,0,0,NA,NA,NA,NA,0.004780451,NA,NA,NA,False,NA,NA,NA,False,0.065815234,0.021145753,0,2.11E-01,1.12E-05,0.00E+00,1.12E-05,5.59E-08,0.00E+00,5.59E-08,1800,False,1.00E+00
1,T2,2,2191680,0,0,True,False,False,False,0.02894,0.02894,0.00072,0,0,0,0,0,0,0,NA,NA,NA,NA,6.42E-06,NA,NA,NA,False,NA,NA,NA,False,0.017912645,0.005755147,0,5.76E-02,3.05E-06,0.00E+00,3.05E-06,1.52E-08,0.00E+00,1.52E-08,1800,False,1.00E+00
1,T2,3,1643760,0,0,True,False,False,False,0.02894,0.02894,0.00031,0,0,0,0,0,0,0,NA,NA,NA,NA,2.33E-06,NA,NA,NA,False,NA,NA,NA,False,0.006194272,0.001990156,0,1.99E-02,1.05E-06,0.00E+00,1.05E-06,5.27E-09,0.00E+00,5.27E-09,NA,False,1.00E+00
1,T2,4,1095840,0,0,True,False,False,False,0.02894,0.02894,0.00016,0,0,0,0,0,0,0,NA,NA,NA,NA,9.17E-07,NA,NA,NA,False,NA,NA,NA,False,0.002745596,0.000882132,0,8.82E-03,4.67E-07,0.00E+00,4.67E-07,2.33E-09,0.00E+00,2.33E-09,NA,False,1.00E+00
1,T2,5,547920,0,0,True,False,False,False,0.02894,0.02894,0.00007,0,0,0,0,0,0,0,NA,NA,NA,NA,3.87E-07,NA,NA,NA,False,NA,NA,NA,False,0.001054766,0.000338886,0,3.39E-03,1.79E-07,0.00E+00,1.79E-07,8.97E-10,0.00E+00,8.97E-10,NA,False,1.00E+00
1,T2,6,0,0,0,True,False,False,False,0.02894,0.02894,0.00005,0,0,0,0,0,0,0,NA,NA,NA,NA,0.0000002,NA,NA,NA,False,NA,NA,NA,False,0.000740215,0.000237823,0,2.38E-03,1.26E-07,0.00E+00,1.26E-07,6.29E-10,0.00E+00,6.29E-10,NA,False,1.00E+00
1,T3,1,2191680,0,0,True,False,False,False,0.02894,0.02894,0.00072,0,0,0,0,0,0,0,NA,NA,NA,NA,6.42E-06,NA,NA,NA,False,NA,NA,NA,False,0.017912645,0.005755147,0,5.76E-02,3.05E-06,0.00E+00,3.05E-06,1.52E-08,0.00E+00,1.52E-08,NA,False,1.00E+00
1,T3,2,1643760,0,0,True,False,False,False,0.02894,0.02894,0.00031,0,0,0,0,0,0,0,NA,NA,NA,NA,2.33E-06,NA,NA,NA,False,NA,NA,NA,False,0.006194272,0.001990156,0,1.99E-02,1.05E-06,0.00E+00,1.05E-06,5.27E-09,0.00E+00,5.27E-09,1800,False,1.00E+00
1,T3,3,1095840,0,0,True,False,False,False,0.02894,0.02894,0.00016,0,0,0,0,0,0,0,NA,NA,NA,NA,9.17E-07,NA,NA,NA,False,NA,NA,NA,False,0.002745596,0.000882132,0,8.82E-03,4.67E-07,0.00E+00,4.67E-07,2.33E-09,0.00E+00,2.33E-09,1800,False,1.00E+00
1,T3,4,547920,0,0,True,False,False,False,0.02894,0.02894,0.00007,0,0,0,0,0,0,0,NA,NA,NA,NA,3.87E-07,NA,NA,NA,False,NA,NA,NA,False,0.001054766,0.000338886,0,3.39E-03,1.79E-07,0.00E+00,1.79E-07,8.97E-10,0.00E+00,8.97E-10,NA,False,1.00E+00
1,T3,5,0,0,0,True,False,False,False,0.02894,0.02894,0.00005,0,0,0,0,0,0,0,NA,NA,NA,NA,0.0000002,NA,NA,NA,False,NA,NA,NA,False,0.000740215,0.000237823,0,2.38E-03,1.26E-07,0.00E+00,1.26E-07,6.29E-10,0.00E+00,6.29E-10,NA,False,1.00E+00
1,T4,1,1643760,0,0,True,False,False,False,0.02894,0.02894,0.00031,0,0,0,0,0,0,0,NA,NA,NA,NA,2.33E-06,NA,NA,NA,False,NA,NA,NA,False,0.006194272,0.001990156,0,1.99E-02,1.05E-06,0.00E+00,1.05E-06,5.27E-09,0.00E+00,5.27E-09,NA,False,1.00E+00
1,T4,2,1095840,0,0,True,False,False,False,0.02894,0.02894,0.00016,0,0,0,0,0,0,0,NA,NA,NA,NA,9.17E-07,NA,NA,NA,False,NA,NA,NA,False,0.002745596,0.000882132,0,8.82E-03,4.67E-07,0.00E+00,4.67E-07,2.33E-09,0.00E+00,2.33E-09,NA,False,1.00E+00
1,T4,3,547920,0,0,True,False,False,False,0.02894,0.02894,0.00007,0,0,0,0,0,0,0,NA,NA,NA,NA,3.87E-07,NA,NA,NA,False,NA,NA,NA,False,0.001054766,0.000338886,0,3.39E-03,1.79E-07,0.00E+00,1.79E-07,8.97E-10,0.00E+00,8.97E-10,NA,False,1.00E+00
1,T4,4,0,0,0,True,False,False,False,0.02894,0.02894,0.00005,0,0,0,0,0,0,0,NA,NA,NA,NA,0.0000002,NA,NA,NA,False,NA,NA,NA,False,0.000740215,0.000237823,0,2.38E-03,1.26E-07,0.00E+00,1.26E-07,6.29E-10,0.00E+00,6.29E-10,1800,False,1.00E+00
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