reorganized tutorials

jakobrunge · Dec 10, 2022 · 4411ef6 · 4411ef6
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diff --git a/README.md b/README.md
@@ -24,8 +24,6 @@ Further, Tigramite provides several causal discovery methods that can be used un
 | PCMCIplus | Causal stationarity, no hidden variables    | Directed lagged links, directed and undirected contemp. links (Time series CPDAG) |
 | LPCMCI | Causal stationarity    | Time series PAG |
 
-(Also consider the bootstrap-versions of above methods called by *get_bootsrap_of(...)*.)
-
 
 | Conditional independence test | Assumptions                                  |
 |--------|---------------------------------------------------------------------------|

diff --git a/tigramite/independence_tests/regressionCI.py b/tigramite/independence_tests/regressionCI.py
@@ -10,7 +10,7 @@
 from sklearn.linear_model import LinearRegression, LogisticRegression
 from sklearn import metrics
 
-from independence_tests_base import CondIndTest
+from .independence_tests_base import CondIndTest
 # from numba import jit   # could make it even faster, also acticate @jit(forceobj=True)
 
 

diff --git a/...te_tutorial_explaining_correlations.ipynb → ...te_tutorial_explaining_correlations.ipynb b/...te_tutorial_explaining_correlations.ipynb → ...te_tutorial_explaining_correlations.ipynb
@@ -20,16 +20,7 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/jakobrunge/work/code/python_code/tigramite/tigramite_v4/tigramite/tigramite/independence_tests/gpdc_torch.py:33: UserWarning: ('Version mismatch. Installed version of torch', '1.10.2', 'Please install torch>=', '1.11.0')\n",
-      "  warnings.warn(str(e))\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Imports\n",
     "import numpy as np\n",
@@ -271,7 +262,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/jakobrunge/work/code/python_code/tigramite/tigramite_v4/tigramite/tigramite/models.py:1659: UserWarning: test_indices - maxlag(predictors) [or tau_max] overlaps with train_indices: Choose test_indices such that there is a gap of max_lag to train_indices!\n",
+      "/home/jakobrunge/work/code/python_code/tigramite/tigramite_v4/tigramite/tigramite/models.py:1643: UserWarning: test_indices - maxlag(predictors) [or tau_max] overlaps with train_indices: Choose test_indices such that there is a gap of max_lag to train_indices!\n",
       "  warnings.warn(\"test_indices - maxlag(predictors) [or tau_max] \"\n"
      ]
     }

diff --git a/tutorials/figures/causal_stationarity_2.jpg → ...scovery/figures/causal_stationarity_2.jpg b/tutorials/figures/causal_stationarity_2.jpg → ...scovery/figures/causal_stationarity_2.jpg
diff --git a/tutorials/figures/ts_DAG.png → ...rials/causal_discovery/figures/ts_DAG.png b/tutorials/figures/ts_DAG.png → ...rials/causal_discovery/figures/ts_DAG.png
diff --git a/tutorials/figures/ts_DMAG.png → ...ials/causal_discovery/figures/ts_DMAG.png b/tutorials/figures/ts_DMAG.png → ...ials/causal_discovery/figures/ts_DMAG.png
diff --git a/tutorials/figures/ts_DMAG_2.png → ...ls/causal_discovery/figures/ts_DMAG_2.png b/tutorials/figures/ts_DMAG_2.png → ...ls/causal_discovery/figures/ts_DMAG_2.png
diff --git a/tutorials/figures/ts_DMAG_a.png → ...ls/causal_discovery/figures/ts_DMAG_a.png b/tutorials/figures/ts_DMAG_a.png → ...ls/causal_discovery/figures/ts_DMAG_a.png
diff --git a/tutorials/figures/ts_DPAG.png → ...ials/causal_discovery/figures/ts_DPAG.png b/tutorials/figures/ts_DPAG.png → ...ials/causal_discovery/figures/ts_DPAG.png
diff --git a/tutorials/figures/tsg_graph.png → ...ls/causal_discovery/figures/tsg_graph.png b/tutorials/figures/tsg_graph.png → ...ls/causal_discovery/figures/tsg_graph.png
diff --git a/tutorials/figures/xyz_graph.png → ...ls/causal_discovery/figures/xyz_graph.png b/tutorials/figures/xyz_graph.png → ...ls/causal_discovery/figures/xyz_graph.png
diff --git a/tutorials/figures/xyzl_graph.png → ...s/causal_discovery/figures/xyzl_graph.png b/tutorials/figures/xyzl_graph.png → ...s/causal_discovery/figures/xyzl_graph.png
diff --git a/tutorials/figures/xyzl_graph_bi.png → ...ausal_discovery/figures/xyzl_graph_bi.png b/tutorials/figures/xyzl_graph_bi.png → ...ausal_discovery/figures/xyzl_graph_bi.png
diff --git a/...ials/tigramite_tutorial_assumptions.ipynb → ...very/tigramite_tutorial_assumptions.ipynb b/...ials/tigramite_tutorial_assumptions.ipynb → ...very/tigramite_tutorial_assumptions.ipynb
diff --git a/tutorials/tigramite_tutorial_basics.ipynb → ...discovery/tigramite_tutorial_basics.ipynb b/tutorials/tigramite_tutorial_basics.ipynb → ...discovery/tigramite_tutorial_basics.ipynb
diff --git a/tutorials/causal_discovery/tigramite_tutorial_causal_discovery_overview.ipynb b/tutorials/causal_discovery/tigramite_tutorial_causal_discovery_overview.ipynb
diff --git a/tutorials/causal_discovery/tigramite_tutorial_conditional_independence_tests.ipynb b/tutorials/causal_discovery/tigramite_tutorial_conditional_independence_tests.ipynb
diff --git a/...tutorial_heteroskedastic_ParCorrWLS.ipynb → ...tutorial_heteroskedastic_ParCorrWLS.ipynb b/...tutorial_heteroskedastic_ParCorrWLS.ipynb → ...tutorial_heteroskedastic_ParCorrWLS.ipynb
diff --git a/...als/tigramite_tutorial_latent-pcmci.ipynb → ...ery/tigramite_tutorial_latent-pcmci.ipynb b/...als/tigramite_tutorial_latent-pcmci.ipynb → ...ery/tigramite_tutorial_latent-pcmci.ipynb
@@ -37,16 +37,7 @@
    "execution_count": 1,
    "id": "c998706d",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/jakobrunge/work/code/python_code/tigramite/tigramite_v4/tigramite/tigramite/independence_tests/gpdc_torch.py:33: UserWarning: ('Version mismatch. Installed version of torch', '1.10.2', 'Please install torch>=', '1.11.0')\n",
-      "  warnings.warn(str(e))\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import numpy as np\n",
     "\n",
@@ -1012,9 +1003,9 @@
       "with rule list:  [['APR'], ['ER-08'], ['ER-02'], ['ER-01'], ['ER-00-d'], ['ER-00-c'], ['ER-03'], ['R-04'], ['ER-09'], ['ER-10'], ['ER-00-b'], ['ER-00-a']]\n",
       "\n",
       "APR:\n",
+      "Marked:    (2,-1) -!> (2, 0) ==> (2,-1) --> (2, 0) \n",
       "Marked:    (1,-1) -!> (1, 0) ==> (1,-1) --> (1, 0) \n",
       "Marked:    (1,-2) -!> (2, 0) ==> (1,-2) --> (2, 0) \n",
-      "Marked:    (2,-1) -!> (2, 0) ==> (2,-1) --> (2, 0) \n",
       "Writing:   (1,-1) -!> (1, 0) ==> (1,-1) --> (1, 0) \n",
       "Writing:   (1,-2) -!> (2, 0) ==> (1,-2) --> (2, 0) \n",
       "Writing:   (2,-1) -!> (2, 0) ==> (2,-1) --> (2, 0) \n",
@@ -1063,13 +1054,7 @@
       "R-04:\n",
       "Found nothing\n",
       "\n",
-      "ER-09:\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "ER-09:\n",
       "Found nothing\n",
       "\n",
       "ER-10:\n",
@@ -1284,10 +1269,10 @@
       "with rule list:  [['APR'], ['ER-08'], ['ER-02'], ['ER-01'], ['ER-00-d'], ['ER-00-c'], ['ER-03'], ['R-04'], ['ER-09'], ['ER-10'], ['ER-00-b'], ['ER-00-a']]\n",
       "\n",
       "APR:\n",
+      "Marked:    (2,-1) -!> (2, 0) ==> (2,-1) --> (2, 0) \n",
       "Marked:    (1,-1) -!> (1, 0) ==> (1,-1) --> (1, 0) \n",
       "Marked:    (1,-2) -!> (2, 0) ==> (1,-2) --> (2, 0) \n",
       "Marked:    (0,-1) -!> (0, 0) ==> (0,-1) --> (0, 0) \n",
-      "Marked:    (2,-1) -!> (2, 0) ==> (2,-1) --> (2, 0) \n",
       "Writing:   (0,-1) -!> (0, 0) ==> (0,-1) --> (0, 0) \n",
       "Writing:   (1,-1) -!> (1, 0) ==> (1,-1) --> (1, 0) \n",
       "Writing:   (1,-2) -!> (2, 0) ==> (1,-2) --> (2, 0) \n",
@@ -1403,13 +1388,7 @@
       "ER-00-c:\n",
       "Found nothing\n",
       "\n",
-      "ER-03:\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "ER-03:\n",
       "Found nothing\n",
       "\n",
       "R-04:\n",

diff --git a/...als/tigramite_tutorial_pcmci_fullci.ipynb → ...ery/tigramite_tutorial_pcmci_fullci.ipynb b/...als/tigramite_tutorial_pcmci_fullci.ipynb → ...ery/tigramite_tutorial_pcmci_fullci.ipynb
diff --git a/tutorials/tigramite_tutorial_pcmciplus.ipynb → ...covery/tigramite_tutorial_pcmciplus.ipynb b/tutorials/tigramite_tutorial_pcmciplus.ipynb → ...covery/tigramite_tutorial_pcmciplus.ipynb
diff --git a/...te_tutorial_sliding_window_analysis.ipynb → ...te_tutorial_sliding_window_analysis.ipynb b/...te_tutorial_sliding_window_analysis.ipynb → ...te_tutorial_sliding_window_analysis.ipynb
@@ -15,16 +15,7 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/jakobrunge/work/code/python_code/tigramite/tigramite_v4/tigramite/tigramite/independence_tests/gpdc_torch.py:33: UserWarning: ('Version mismatch. Installed version of torch', '1.10.2', 'Please install torch>=', '1.11.0')\n",
-      "  warnings.warn(str(e))\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Imports\n",
     "import numpy as np\n",

diff --git a/tutorials/causal_effect_estimation/figures/causal_stationarity_2.jpg b/tutorials/causal_effect_estimation/figures/causal_stationarity_2.jpg
diff --git a/tutorials/causal_effect_estimation/figures/ts_DAG.png b/tutorials/causal_effect_estimation/figures/ts_DAG.png
diff --git a/tutorials/causal_effect_estimation/figures/ts_DMAG.png b/tutorials/causal_effect_estimation/figures/ts_DMAG.png
diff --git a/tutorials/causal_effect_estimation/figures/ts_DMAG_2.png b/tutorials/causal_effect_estimation/figures/ts_DMAG_2.png
diff --git a/tutorials/causal_effect_estimation/figures/ts_DMAG_a.png b/tutorials/causal_effect_estimation/figures/ts_DMAG_a.png
diff --git a/tutorials/causal_effect_estimation/figures/ts_DPAG.png b/tutorials/causal_effect_estimation/figures/ts_DPAG.png
diff --git a/tutorials/causal_effect_estimation/figures/tsg_graph.png b/tutorials/causal_effect_estimation/figures/tsg_graph.png
diff --git a/tutorials/causal_effect_estimation/figures/xyz_graph.png b/tutorials/causal_effect_estimation/figures/xyz_graph.png
diff --git a/tutorials/causal_effect_estimation/figures/xyzl_graph.png b/tutorials/causal_effect_estimation/figures/xyzl_graph.png
diff --git a/tutorials/causal_effect_estimation/figures/xyzl_graph_bi.png b/tutorials/causal_effect_estimation/figures/xyzl_graph_bi.png
diff --git a/...rial_general_causal_effect_analysis.ipynb → ...rial_general_causal_effect_analysis.ipynb b/...rial_general_causal_effect_analysis.ipynb → ...rial_general_causal_effect_analysis.ipynb
diff --git a/tutorials/causal_effect_estimation/tigramite_tutorial_linear_causal_effects_mediation.ipynb b/tutorials/causal_effect_estimation/tigramite_tutorial_linear_causal_effects_mediation.ipynb
diff --git a/...rials/tigramite_tutorial_prediction.ipynb → ...ction/tigramite_tutorial_prediction.ipynb b/...rials/tigramite_tutorial_prediction.ipynb → ...ction/tigramite_tutorial_prediction.ipynb
diff --git a/tutorials/dataset_challenges/figures/causal_stationarity_2.jpg b/tutorials/dataset_challenges/figures/causal_stationarity_2.jpg
diff --git a/tutorials/dataset_challenges/figures/ts_DAG.png b/tutorials/dataset_challenges/figures/ts_DAG.png
diff --git a/tutorials/dataset_challenges/figures/ts_DMAG.png b/tutorials/dataset_challenges/figures/ts_DMAG.png
diff --git a/tutorials/dataset_challenges/figures/ts_DMAG_2.png b/tutorials/dataset_challenges/figures/ts_DMAG_2.png
diff --git a/tutorials/dataset_challenges/figures/ts_DMAG_a.png b/tutorials/dataset_challenges/figures/ts_DMAG_a.png
diff --git a/tutorials/dataset_challenges/figures/ts_DPAG.png b/tutorials/dataset_challenges/figures/ts_DPAG.png
diff --git a/tutorials/dataset_challenges/figures/tsg_graph.png b/tutorials/dataset_challenges/figures/tsg_graph.png
diff --git a/tutorials/dataset_challenges/figures/xyz_graph.png b/tutorials/dataset_challenges/figures/xyz_graph.png
diff --git a/tutorials/dataset_challenges/figures/xyzl_graph.png b/tutorials/dataset_challenges/figures/xyzl_graph.png
diff --git a/tutorials/dataset_challenges/figures/xyzl_graph_bi.png b/tutorials/dataset_challenges/figures/xyzl_graph_bi.png
diff --git a/.../tigramite_tutorial_missing_masking.ipynb → .../tigramite_tutorial_missing_masking.ipynb b/.../tigramite_tutorial_missing_masking.ipynb → .../tigramite_tutorial_missing_masking.ipynb
@@ -26,16 +26,7 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/jakobrunge/work/code/python_code/tigramite/tigramite_v4/tigramite/tigramite/independence_tests/gpdc_torch.py:33: UserWarning: ('Version mismatch. Installed version of torch', '1.10.2', 'Please install torch>=', '1.11.0')\n",
-      "  warnings.warn(str(e))\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Imports\n",
     "import numpy as np\n",
@@ -495,13 +486,7 @@
       "            Y = [(1, 0)]\n",
       "            Z = [(1, -1), (0, -1)]\n",
       "            extraZ = []\n",
-      "            with missing values = 999.0 removed\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "            with missing values = 999.0 removed\n",
       "        val = -0.013 | pval = 0.90014 \n",
       "    Subset 0: ($X^1$ -1) ($X^0$ -1)  gives pval = 0.90014 / val = -0.013\n",
       "    Non-significance detected.\n",
@@ -920,13 +905,7 @@
       "            Y = [(1, 0)]\n",
       "            Z = [(1, -1), (0, -1), (0, -3)]\n",
       "            extraZ = []\n",
-      "            with missing values = 999.0 removed\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "            with missing values = 999.0 removed\n",
       "        val =  0.098 | pval = 0.34941 \n",
       "\n",
       "        link ($X^1$ -1) --> $X^1$ (4/8):\n",

diff --git a/...igramite_tutorial_multiple_datasets.ipynb → ...igramite_tutorial_multiple_datasets.ipynb b/...igramite_tutorial_multiple_datasets.ipynb → ...igramite_tutorial_multiple_datasets.ipynb
@@ -128,16 +128,7 @@
    "metadata": {
     "scrolled": true
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/jakobrunge/work/code/python_code/tigramite/tigramite_v4/tigramite/tigramite/independence_tests/gpdc_torch.py:33: UserWarning: ('Version mismatch. Installed version of torch', '1.10.2', 'Please install torch>=', '1.11.0')\n",
-      "  warnings.warn(str(e))\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import numpy as np\n",
     "np.random.seed(42)\n",

diff --git a/tutorials/tigramite_tutorial_linear_causal_effects_mediation.ipynb b/tutorials/tigramite_tutorial_linear_causal_effects_mediation.ipynb