diff --git a/dockerHDDM_Workflow.ipynb b/dockerHDDM_Workflow.ipynb index ca8135b..fbf8efd 100644 --- a/dockerHDDM_Workflow.ipynb +++ b/dockerHDDM_Workflow.ipynb @@ -11,14 +11,15 @@ "\n", "- Wanke Pan (panwanke2023@gmail.com) @Nanjing Normal University\n", "- Hu Chuan-Peng (corresponding author, hcp4715@hotmail.com) @Nanjing Normal University\n", + "- Ru-Yuan Zhang (corresponding author, ruyuanzhang@sjtu.edu.cn) @Shanghai Jiao Tong University\n", "\n", "This is a supplementary notebook for the introductary paper *A Hitchhiker’s Guide to Bayesian Hierarchical Drift-Diffusion Modeling with dockerHDDM*. \n", "\n", - "This notebook was tested in docker image [`hcp4715/hddm:0.9.8-amd64`](https://hub.docker.com/r/hcp4715/hddm/tags), where the packages `hddm` and `kabuki` were rectfied to RC version as below code box.\n", + "This notebook was tested in docker image [`hcp4715/hddm:0.9.8-amd64`](https://hub.docker.com/r/hcp4715/hddm/tags), where the packages `kabuki` were rectfied to RC version as below code box.\n", "\n", "Preprint of this manuscript: https://psyarxiv.com/6uzga/\n", "\n", - "![workflow](./figs/fig4/workflow.png)" + "Github repository at: https://github.com/hcp4715/dockerHDDM" ] }, { @@ -31,7 +32,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 4, "id": "d5205ced", "metadata": { "scrolled": true @@ -44,7 +45,7 @@ "The current HDDM version is: 0.9.8RC\n", "The current kabuki version is: 0.6.5RC3\n", "The current PyMC version is: 2.3.8\n", - "The current ArviZ version is: 0.14.0\n" + "The current ArviZ version is: 0.15.1\n" ] } ], @@ -75,54 +76,6 @@ "print(\"The current ArviZ version is: \", az.__version__)" ] }, - { - "cell_type": "code", - "execution_count": 2, - "id": "9f8c78f3-73f1-4965-a3e1-56a36d59877e", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CPU times: user 2min 1s, sys: 9.51 s, total: 2min 10s\n", - "Wall time: 2min 10s\n" - ] - } - ], - "source": [ - "%%time\n", - "m0_infdata = az.from_netcdf(\"model_fitted/m0.nc\")\n", - "m1_infdata = az.from_netcdf(\"model_fitted/m1.nc\")\n", - "m2_infdata = az.from_netcdf(\"model_fitted/m2.nc\")\n", - "m3_infdata = az.from_netcdf(\"model_fitted/m3.nc\")\n", - "m4_infdata = az.from_netcdf(\"model_fitted/m4.nc\")" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "id": "98679226-30c0-427e-b870-bb28c08013f6", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CPU times: user 8.13 s, sys: 194 ms, total: 8.33 s\n", - "Wall time: 8.55 s\n" - ] - } - ], - "source": [ - "%%time\n", - "m0 = hddm.load(\"model_fitted/m0.hddm\")\n", - "m1 = hddm.load(\"model_fitted/m1.hddm\")\n", - "m2 = hddm.load(\"model_fitted/m2.hddm\")\n", - "m3 = hddm.load(\"model_fitted/m3.hddm\")\n", - "m4 = hddm.load(\"model_fitted/m4.hddm\")" - ] - }, { "cell_type": "markdown", "id": "03047e29", @@ -164407,7 +164360,7 @@ "metadata": {}, "outputs": [], "source": [ - "axes.ravel()[0].figure.savefig(\"figs/fig6a.pdf\")" + "axes.ravel()[0].figure.savefig(\"fig6a.pdf\")" ] }, { @@ -165832,7 +165785,7 @@ { "cell_type": "code", "execution_count": 48, - "id": "154e5507", + "id": "d49561a2", "metadata": {}, "outputs": [], "source": [ @@ -165849,7 +165802,7 @@ }, { "cell_type": "markdown", - "id": "656765cc", + "id": "1a38226c", "metadata": {}, "source": [ "First, let's spend some time generating posterior predictions. Note that we set `n_ppc` is 500 means we generate 500 samples for each draws in each parameters. " @@ -165906,7 +165859,7 @@ { "cell_type": "code", "execution_count": null, - "id": "e2b39874-7d80-452e-af72-2d64dea76a1e", + "id": "04473921", "metadata": {}, "outputs": [ { @@ -165947,7 +165900,7 @@ "metadata": {}, "outputs": [], "source": [ - "axes.ravel()[0].figure.savefig(\"figs/fig7a1.pdf\")" + "axes.ravel()[0].figure.savefig(\"fig7a1.pdf\")" ] }, { @@ -165994,7 +165947,7 @@ "metadata": {}, "outputs": [], "source": [ - "axes.ravel()[0].figure.savefig(\"figs/fig7a2.pdf\")" + "axes.ravel()[0].figure.savefig(\"fig7a2.pdf\")" ] }, { @@ -166052,12 +166005,13 @@ "metadata": {}, "outputs": [], "source": [ - "axes.ravel()[0].figure.savefig(\"figs/fig7b1.pdf\")" + "axes.ravel()[0].figure.savefig(\"fig7b1.pdf\")" ] }, { "cell_type": "code", "execution_count": null, + "id": "96c97eab", "metadata": {}, "outputs": [ { @@ -166099,7 +166053,7 @@ "metadata": {}, "outputs": [], "source": [ - "axes.ravel()[0].figure.savefig(\"figs/fig7b2.pdf\")" + "axes.ravel()[0].figure.savefig(\"fig7b2.pdf\")" ] }, { @@ -166126,7 +166080,7 @@ { "cell_type": "code", "execution_count": null, - "id": "aa606c40", + "id": "b5762ceb", "metadata": {}, "outputs": [ { @@ -166171,7 +166125,7 @@ "metadata": {}, "outputs": [], "source": [ - "axes.figure.savefig(\"figs/fig8a.pdf\")" + "axes.figure.savefig(\"fig8a.pdf\")" ] }, { @@ -166241,7 +166195,7 @@ { "cell_type": "code", "execution_count": null, - "id": "c3945a07", + "id": "91498072", "metadata": {}, "outputs": [ { @@ -166281,7 +166235,7 @@ { "cell_type": "code", "execution_count": null, - "id": "84965ad3", + "id": "ae13df5b", "metadata": {}, "outputs": [ { @@ -166315,7 +166269,7 @@ "metadata": {}, "outputs": [], "source": [ - "axes.ravel()[0].figure.savefig(\"figs/fig8b.pdf\")" + "axes.ravel()[0].figure.savefig(\"fig8b.pdf\")" ] }, {