Update reproducible analysis outputs

notebooks/logit_review_boots.ipynb

@@ -22,7 +22,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
+   "id": "7aea473c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "063c7f0a",
    "metadata": {},
    "outputs": [],
@@ -55,6 +56,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "c3028cad",
    "metadata": {},
    "source": [
     "## Data"
@@ -62,7 +64,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
+   "id": "ec16d25e",
    "metadata": {},
    "outputs": [
     {
@@ -90,7 +93,7 @@
          "type": "integer"
         }
        ],
-       "ref": "60c072e3-2d98-40c6-80d2-643b56a43a26",
+       "ref": "0af80a19-b7c6-4b14-adf0-ba42b59dcf4d",
        "rows": [
         [
          "0",
@@ -837,7 +840,7 @@
        "57          58  1.439417  0"
       ]
      },
-     "execution_count": 2,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -875,7 +878,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
+   "id": "f9715e44",
    "metadata": {},
    "outputs": [
     {
@@ -921,6 +925,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "4ddf0526",
    "metadata": {},
    "source": [
     "## Fit and asymptotic uncertainty"
@@ -928,14 +933,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
+   "id": "a8dcfb7b",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'pars': array([-11.68387205,   5.68696545]), 'cost': np.float64(7.394195051363892), 'success': True, 'message': 'CONVERGENCE: NORM OF PROJECTED GRADIENT <= PGTOL', 'nit': 4}\n",
+      "{'theta': array([-11.68387205,   5.68696544]), 'cost': np.float64(7.3941950513638925), 'success': True, 'message': 'CONVERGENCE: RELATIVE REDUCTION OF F <= FACTR*EPSMCH', 'nit': 4}\n",
       "covariance matrix:\n",
       " [[12.32303702 -6.71291913]\n",
       " [-6.71291913  3.81878393]]\n"
@@ -966,19 +972,19 @@
          "type": "float"
         }
        ],
-       "ref": "9a26be77-8ece-495e-b19d-aa26391bdd50",
+       "ref": "5748fc65-6a20-485c-9df3-90afa8d4ed4c",
        "rows": [
         [
          "b0",
-         "-11.683872048612786",
-         "-18.564165593323825",
-         "-4.803578503901749"
+         "-11.68387204779878",
+         "-18.564165591914772",
+         "-4.803578503682786"
         ],
         [
          "b1",
-         "5.686965445003518",
-         "1.8568608508060875",
-         "9.517070039200949"
+         "5.6869654445521",
+         "1.8568608506533293",
+         "9.51707003845087"
         ]
        ],
        "shape": {
@@ -1033,7 +1039,7 @@
        "b1   5.686965   1.856861  9.517070"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1060,7 +1066,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
+   "id": "1d28f481",
    "metadata": {},
    "outputs": [
     {
@@ -1093,16 +1100,21 @@
          "type": "float"
         },
         {
-         "name": "chi2",
+         "name": "deviance",
          "rawType": "float64",
          "type": "float"
         },
         {
-         "name": "p-value(chi2)",
+         "name": "p-value(deviance_bootstrap)",
          "rawType": "float64",
          "type": "float"
         },
         {
+         "name": "deviance_bootstrap_samples",
+         "rawType": "int64",
+         "type": "integer"
+        },
+        {
          "name": "n",
          "rawType": "int64",
          "type": "integer"
@@ -1118,23 +1130,24 @@
          "type": "integer"
         }
        ],
-       "ref": "6a60656c-a27d-4a81-a68a-d1725d9c323e",
+       "ref": "b9f3e3b1-8f4d-4c13-9e7d-cafdfb95e867",
        "rows": [
         [
          "0",
-         "-7.394195051363892",
-         "18.78839010272778",
-         "22.90927612382062",
+         "-7.3941950513638925",
+         "18.788390102727785",
+         "22.909276123820625",
          "0.9655172413793104",
-         "23.103221367618744",
-         "0.9999706242978951",
+         "14.788390102727785",
+         "0.3946053946053946",
+         "1000",
          "58",
          "2",
          "56"
         ]
        ],
        "shape": {
-        "columns": 9,
+        "columns": 10,
         "rows": 1
        }
       },
@@ -1161,8 +1174,9 @@
        "      <th>AIC</th>\n",
        "      <th>BIC</th>\n",
        "      <th>A</th>\n",
-       "      <th>chi2</th>\n",
-       "      <th>p-value(chi2)</th>\n",
+       "      <th>deviance</th>\n",
+       "      <th>p-value(deviance_bootstrap)</th>\n",
+       "      <th>deviance_bootstrap_samples</th>\n",
        "      <th>n</th>\n",
        "      <th>k</th>\n",
        "      <th>dof</th>\n",
@@ -1175,8 +1189,9 @@
        "      <td>18.78839</td>\n",
        "      <td>22.909276</td>\n",
        "      <td>0.965517</td>\n",
-       "      <td>23.103221</td>\n",
-       "      <td>0.999971</td>\n",
+       "      <td>14.78839</td>\n",
+       "      <td>0.394605</td>\n",
+       "      <td>1000</td>\n",
        "      <td>58</td>\n",
        "      <td>2</td>\n",
        "      <td>56</td>\n",
@@ -1186,14 +1201,14 @@
        "</div>"
       ],
       "text/plain": [
-       "        LLF       AIC        BIC         A       chi2  p-value(chi2)   n  k  \\\n",
-       "0 -7.394195  18.78839  22.909276  0.965517  23.103221       0.999971  58  2   \n",
+       "        LLF       AIC        BIC         A  deviance  \\\n",
+       "0 -7.394195  18.78839  22.909276  0.965517  14.78839   \n",
        "\n",
-       "   dof  \n",
-       "0   56  "
+       "   p-value(deviance_bootstrap)  deviance_bootstrap_samples   n  k  dof  \n",
+       "0                     0.394605                        1000  58  2   56  "
       ]
      },
-     "execution_count": 5,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1206,7 +1221,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
+   "id": "ed8167bb",
    "metadata": {},
    "outputs": [
     {
@@ -1253,6 +1269,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "ea737bf6",
    "metadata": {},
    "source": [
     "## Bootstrap parameter samples"
@@ -1260,7 +1277,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
+   "id": "ee951c08",
    "metadata": {},
    "outputs": [
     {
@@ -1290,7 +1308,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
+   "id": "cf651adb",
    "metadata": {},
    "outputs": [
     {
@@ -1335,7 +1354,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
+   "id": "2008c950",
    "metadata": {},
    "outputs": [
     {
@@ -1483,6 +1503,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "35aecc30",
    "metadata": {},
    "source": [
     "## Comparison of confidence bands\n",
@@ -1492,7 +1513,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
+   "id": "1ca796d8",
    "metadata": {},
    "outputs": [
     {

results/logit_mono-cubic4paper/beta_CI_long.txt

@@ -0,0 +1,70 @@
+\begin{tabular}{llllrrr}
+\toprule
+scale & dataset & method & coefficient & estimate & LCL & UCL \\
+\midrule
+log & FULL & normal & $\beta_0$ & -40.709397 & -80.514824 & 0.576810 \\
+log & FULL & normal & $\beta_1$ & 152.898365 & 34.454749 & 345.981009 \\
+log & FULL & normal & $\beta_2$ & -186.375741 & -434.565154 & -38.043109 \\
+log & FULL & normal & $\beta_3$ & 75.727683 & 13.775938 & 183.597710 \\
+log & FULL & nonparam_boots & $\beta_0$ & -40.709397 & -362.341899 & -14.457646 \\
+log & FULL & nonparam_boots & $\beta_1$ & 152.898365 & 0.008195 & 1941.547918 \\
+log & FULL & nonparam_boots & $\beta_2$ & -186.375741 & -3466.701526 & 2.548176 \\
+log & FULL & nonparam_boots & $\beta_3$ & 75.727683 & 2.070028 & 2059.363688 \\
+log & FULL & nonparam_stratified_boots & $\beta_0$ & -40.709397 & -369.351128 & -14.205809 \\
+log & FULL & nonparam_stratified_boots & $\beta_1$ & 152.898365 & 0.014464 & 1980.246721 \\
+log & FULL & nonparam_stratified_boots & $\beta_2$ & -186.375741 & -3528.049144 & 2.305803 \\
+log & FULL & nonparam_stratified_boots & $\beta_3$ & 75.727683 & 1.751783 & 2094.675746 \\
+log & FULL & parametric_boots & $\beta_0$ & -40.709397 & -310.971797 & -8.945695 \\
+log & FULL & parametric_boots & $\beta_1$ & 152.898365 & 0.134978 & 1223.357752 \\
+log & FULL & parametric_boots & $\beta_2$ & -186.375741 & -1600.454296 & 6.086761 \\
+log & FULL & parametric_boots & $\beta_3$ & 75.727683 & 0.984105 & 1828.297047 \\
+log & TRIM & normal & $\beta_0$ & -318.624647 & -776.659317 & 157.809374 \\
+log & TRIM & normal & $\beta_1$ & 1693.446514 & 113.742593 & 4971.801432 \\
+log & TRIM & normal & $\beta_2$ & -3000.867759 & -8798.941523 & -199.771987 \\
+log & TRIM & normal & $\beta_3$ & 1772.560127 & 124.155987 & 5163.107174 \\
+log & TRIM & nonparam_boots & $\beta_0$ & -318.624647 & -400.128827 & -17.348309 \\
+log & TRIM & nonparam_boots & $\beta_1$ & 1693.446514 & 0.001076 & 2136.483263 \\
+log & TRIM & nonparam_boots & $\beta_2$ & -3000.867759 & -3801.243116 & 2.791405 \\
+log & TRIM & nonparam_boots & $\beta_3$ & 1772.560127 & 64.697359 & 2251.261055 \\
+log & TRIM & nonparam_stratified_boots & $\beta_0$ & -318.624647 & -399.079252 & -17.585934 \\
+log & TRIM & nonparam_stratified_boots & $\beta_1$ & 1693.446514 & 0.001151 & 2130.156884 \\
+log & TRIM & nonparam_stratified_boots & $\beta_2$ & -3000.867759 & -3786.236311 & 2.695133 \\
+log & TRIM & nonparam_stratified_boots & $\beta_3$ & 1772.560127 & 67.815305 & 2242.960062 \\
+log & TRIM & parametric_boots & $\beta_0$ & -318.624647 & -388.501147 & -23.345353 \\
+log & TRIM & parametric_boots & $\beta_1$ & 1693.446514 & 1.521692 & 2462.926783 \\
+log & TRIM & parametric_boots & $\beta_2$ & -3000.867759 & -5226.607876 & -42.998302 \\
+log & TRIM & parametric_boots & $\beta_3$ & 1772.560127 & 133.499510 & 3697.150084 \\
+plain & FULL & normal & $\beta_0$ & -123.992084 & -233.949431 & -9.562457 \\
+plain & FULL & normal & $\beta_1$ & 163.793487 & 45.151309 & 347.318752 \\
+plain & FULL & normal & $\beta_2$ & -71.447936 & -153.877505 & -18.651542 \\
+plain & FULL & normal & $\beta_3$ & 10.388707 & 2.602959 & 22.798786 \\
+plain & FULL & nonparam_boots & $\beta_0$ & -123.992084 & -662.077285 & -20.931699 \\
+plain & FULL & nonparam_boots & $\beta_1$ & 163.793487 & 7.451974 & 1082.620980 \\
+plain & FULL & nonparam_boots & $\beta_2$ & -71.447936 & -586.956425 & -3.339263 \\
+plain & FULL & nonparam_boots & $\beta_3$ & 10.388707 & 0.769656 & 108.791615 \\
+plain & FULL & nonparam_stratified_boots & $\beta_0$ & -123.992084 & -647.740990 & -21.412504 \\
+plain & FULL & nonparam_stratified_boots & $\beta_1$ & 163.793487 & 7.756705 & 1057.043993 \\
+plain & FULL & nonparam_stratified_boots & $\beta_2$ & -71.447936 & -576.953166 & -13.715894 \\
+plain & FULL & nonparam_stratified_boots & $\beta_3$ & 10.388707 & 6.602426 & 106.656112 \\
+plain & FULL & parametric_boots & $\beta_0$ & -123.992084 & -519.918596 & -14.267928 \\
+plain & FULL & parametric_boots & $\beta_1$ & 163.793487 & 0.269142 & 858.638061 \\
+plain & FULL & parametric_boots & $\beta_2$ & -71.447936 & -504.895600 & -1.304426 \\
+plain & FULL & parametric_boots & $\beta_3$ & 10.388707 & 2.109768 & 101.827455 \\
+plain & TRIM & normal & $\beta_0$ & -450.087847 & -995.828448 & 117.691886 \\
+plain & TRIM & normal & $\beta_1$ & 727.847722 & 93.232075 & 1984.937554 \\
+plain & TRIM & normal & $\beta_2$ & -395.533373 & -1126.854471 & -33.273309 \\
+plain & TRIM & normal & $\beta_3$ & 72.298288 & 4.774418 & 215.847819 \\
+plain & TRIM & nonparam_boots & $\beta_0$ & -450.087847 & -737.807108 & -20.618997 \\
+plain & TRIM & nonparam_boots & $\beta_1$ & 727.847722 & 7.141145 & 1228.613108 \\
+plain & TRIM & nonparam_boots & $\beta_2$ & -395.533373 & -683.232490 & -13.178434 \\
+plain & TRIM & nonparam_boots & $\beta_3$ & 72.298288 & 7.726781 & 126.703570 \\
+plain & TRIM & nonparam_stratified_boots & $\beta_0$ & -450.087847 & -715.579363 & -21.029663 \\
+plain & TRIM & nonparam_stratified_boots & $\beta_1$ & 727.847722 & 7.447028 & 1190.138080 \\
+plain & TRIM & nonparam_stratified_boots & $\beta_2$ & -395.533373 & -659.482995 & -13.645705 \\
+plain & TRIM & nonparam_stratified_boots & $\beta_3$ & 72.298288 & 8.284455 & 121.892100 \\
+plain & TRIM & parametric_boots & $\beta_0$ & -450.087847 & -543.464811 & -30.306043 \\
+plain & TRIM & parametric_boots & $\beta_1$ & 727.847722 & 13.581994 & 948.315529 \\
+plain & TRIM & parametric_boots & $\beta_2$ & -395.533373 & -571.500600 & -21.861143 \\
+plain & TRIM & parametric_boots & $\beta_3$ & 72.298288 & 11.728998 & 112.101168 \\
+\bottomrule
+\end{tabular}

results/logit_mono-cubic4paper/theta_CI_long.txt

@@ -0,0 +1,22 @@
+\begin{tabular}{lllllllllllllllll}
+\toprule
+ & scale & dataset & idx & beta & theta & SE & LCL[Wald] & UCL[Wald] & LCL[normal] & UCL[normal] & LCL[nonparam_boots] & UCL[nonparam_boots] & LCL[nonparam_stratified_boots] & UCL[nonparam_stratified_boots] & LCL[parametric_boots] & UCL[parametric_boots] \\
+\midrule
+0 & log & FULL & 0 & -40.709397 & -40.709397 & 20.369622 & -80.633122 & -0.785672 & -80.514824 & 0.576810 & -362.341899 & -14.457646 & -369.351128 & -14.205809 & -310.971797 & -8.945695 \\
+1 & log & FULL & 1 & 152.898365 & 0.000000 & 0.000000 & -0.000000 & 0.000001 & -0.000000 & 0.000000 & -0.000013 & 0.000014 & -0.000011 & 0.000012 & -0.000220 & 0.000241 \\
+2 & log & FULL & 2 & -186.375741 & 15.072593 & 4.286259 & 6.671680 & 23.473505 & 6.428671 & 23.468982 & -35.741173 & 78.600834 & -35.750994 & 79.271857 & -74.060051 & 48.619996 \\
+3 & log & FULL & 3 & 75.727683 & -12.365208 & 3.203398 & -18.643753 & -6.086662 & -18.600565 & -5.869817 & -44.062999 & 2.279963 & -44.499963 & 2.280283 & -34.976531 & 17.689025 \\
+4 & log & TRIM & 0 & -318.624647 & -318.624647 & 234.978512 & -779.174069 & 141.924774 & -776.659317 & 157.809374 & -400.128827 & -17.348309 & -399.079252 & -17.585934 & -388.501147 & -23.345353 \\
+5 & log & TRIM & 1 & 1693.446514 & 0.000000 & 0.000000 & -0.000000 & 0.000000 & -0.000000 & 0.000001 & -0.000252 & 0.000234 & -0.000231 & 0.000239 & -0.000502 & 0.000010 \\
+6 & log & TRIM & 2 & -3000.867759 & 72.922427 & 26.483574 & 21.015576 & 124.829279 & -124.456103 & -19.188869 & -82.181404 & 36.533438 & -82.029752 & 36.475705 & -105.315954 & 35.116438 \\
+7 & log & TRIM & 3 & 1772.560127 & -41.151507 & 15.096946 & -70.740977 & -11.562037 & 10.507731 & 70.511002 & -1.526074 & 46.222108 & -1.518301 & 46.153623 & -3.260625 & 49.627883 \\
+8 & plain & FULL & 0 & -123.992084 & -123.992084 & 56.445124 & -234.622494 & -13.361674 & -233.949431 & -9.562457 & -662.077285 & -20.931699 & -647.740990 & -21.412504 & -519.918596 & -14.267928 \\
+9 & plain & FULL & 1 & 163.793487 & 0.000000 & 0.000000 & -0.000000 & 0.000000 & -0.000096 & 0.000008 & -2.420179 & 0.000387 & -2.530518 & 0.210722 & -2.558559 & 0.017588 \\
+10 & plain & FULL & 2 & -71.447936 & 5.582663 & 1.376914 & 2.883961 & 8.281364 & 2.794437 & 8.270209 & -11.027820 & 17.817660 & -11.034868 & 17.537221 & -17.294438 & 14.727337 \\
+11 & plain & FULL & 3 & 10.388707 & -12.798183 & 2.984920 & -18.648518 & -6.947848 & -18.636490 & -6.719472 & -32.838801 & 5.789172 & -32.436639 & 5.801690 & -28.083489 & 26.411133 \\
+12 & plain & TRIM & 0 & -450.087847 & -450.087847 & 279.831967 & -998.548424 & 98.372730 & -995.828448 & 117.691886 & -737.807108 & -20.618997 & -715.579363 & -21.029663 & -543.464811 & -30.306043 \\
+13 & plain & TRIM & 1 & 727.847722 & -2.558506 & 1.770662 & -6.028940 & 0.911929 & -6.031993 & 0.925499 & -2.675272 & 0.000010 & -2.710152 & 0.000013 & -3.922263 & 0.000003 \\
+14 & plain & TRIM & 2 & -395.533373 & -14.727351 & 5.467168 & -25.442804 & -4.011898 & 3.766396 & 25.446875 & -11.143352 & 19.496428 & -11.122698 & 19.122665 & -10.773395 & 18.058431 \\
+15 & plain & TRIM & 3 & 72.298288 & 26.857062 & 9.038609 & 9.141713 & 44.572410 & -44.501614 & -8.598248 & -35.051578 & 5.858238 & -34.496500 & 5.851761 & -30.760968 & 5.677179 \\
+\bottomrule
+\end{tabular}