From c75462acb55396ab0ce6d75776433f8cf10d1422 Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Sun, 4 Oct 2020 15:11:00 -0700 Subject: [PATCH 01/17] param plots --- Exp.ipynb | 4612 ++----------------------------------------- chain-file-10_1.jls | Bin 0 -> 46855 bytes src/plots.jl | 2 + 3 files changed, 112 insertions(+), 4502 deletions(-) create mode 100644 chain-file-10_1.jls diff --git a/Exp.ipynb b/Exp.ipynb index 82a1e50..377828e 100644 --- a/Exp.ipynb +++ b/Exp.ipynb @@ -2,54 +2,15 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, - "metadata": {}, + "execution_count": 2, + "metadata": { + "tags": [] + }, "outputs": [ { - "name": "stderr", - "output_type": "stream", - "text": [ - "\u001b[32m\u001b[1m Updating\u001b[22m\u001b[39m registry at `~/.julia/registries/General`\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001b[?25l " - ] - }, - { - "name": "stderr", "output_type": "stream", - "text": [ - "\u001b[32m\u001b[1m Updating\u001b[22m\u001b[39m git-repo `https://github.com/JuliaRegistries/General.git`\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001b[2K\u001b[?25h[1mFetching:\u001b[22m\u001b[39m [========================================>] 100.0 % ] 71.4 %\u001b[36m\u001b[1mFetching:\u001b[22m\u001b[39m [===================================> ] 85.7 %" - ] - }, - { "name": "stderr", - "output_type": "stream", - "text": [ - "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Project.toml`\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Manifest.toml`\n", - "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Project.toml`\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Manifest.toml`\n", - "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Project.toml`\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Manifest.toml`\n", - "┌ Info: Precompiling TAMode [294f26d0-a9c2-4f6a-959f-92a060cb6778]\n", - "└ @ Base loading.jl:1278\n", - "WARNING: using Gadfly.plot in module TAMode conflicts with an existing identifier.\n" - ] + "text": "\u001b[32m\u001b[1m Updating\u001b[22m\u001b[39m registry at `~/.julia/registries/General`\n\u001b[?25l\u001b[2K\u001b[32m\u001b[1m Updating\u001b[22m\u001b[39m git-repo `https://github.com/JuliaRegistries/General.git`\n\u001b[?25h\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Project.toml`\n\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Manifest.toml`\n\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Project.toml`\n\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Manifest.toml`\n\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Project.toml`\n\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/TAMode.jl/Manifest.toml`\n┌ Info: Precompiling TAMode [294f26d0-a9c2-4f6a-959f-92a060cb6778]\n└ @ Base loading.jl:1278\nWARNING: using Gadfly.plot in module TAMode conflicts with an existing identifier.\n" } ], "source": [ @@ -66,42 +27,27 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "metadata": {}, "outputs": [ { + "output_type": "execute_result", "data": { - "text/plain": [ - "Summary Statistics\n", - " parameters mean std naive_se mcse ess r_hat\n", - " ───────────── ─────── ────── ──────── ────── ─────── ──────\n", - " AXLexpr 24.4652 1.7037 0.1078 0.6163 7.8061 1.1169\n", - " Ig2rev 0.1308 0.1487 0.0094 0.0749 5.4740 1.1725\n", - " gasCur 0.2270 0.2220 0.0140 0.1124 5.3856 1.1841\n", - " internalize 0.0453 0.0114 0.0007 0.0048 7.2654 1.1545\n", - " kDeg 0.0235 0.0072 0.0005 0.0045 4.9615 1.2561\n", - " kRec 0.0900 0.0580 0.0037 0.0296 5.8971 1.1813\n", - " pYinternalize 1.0769 0.1129 0.0071 0.0348 15.5465 1.0517\n", - " scale 0.0302 0.0115 0.0007 0.0071 4.7714 1.2904\n", - " scaleSurf 0.0002 0.0002 0.0000 0.0001 5.3632 1.1732\n", - " sortF 0.2971 0.0234 0.0015 0.0117 3.8863 1.5341\n", - " xFwd 0.0011 0.0039 0.0002 0.0014 5.9949 1.0791\n" - ] + "text/plain": "Summary Statistics\n \u001b[0m\u001b[1m parameters \u001b[0m \u001b[0m\u001b[1m mean \u001b[0m \u001b[0m\u001b[1m std \u001b[0m \u001b[0m\u001b[1m naive_se \u001b[0m \u001b[0m\u001b[1m mcse \u001b[0m \u001b[0m\u001b[1m ess \u001b[0m \u001b[0m\u001b[1m rhat \u001b[0m \u001b[0m\n \u001b[0m\u001b[90m Symbol \u001b[0m \u001b[0m\u001b[90m Float64 \u001b[0m \u001b[0m\u001b[90m Float64 \u001b[0m \u001b[0m\u001b[90m Float64 \u001b[0m \u001b[0m\u001b[90m Float64 \u001b[0m \u001b[0m\u001b[90m Float64 \u001b[0m \u001b[0m\u001b[90m Float64 \u001b[0m \u001b[0m\n \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m \u001b[0m\n \u001b[0m AXLexpr \u001b[0m \u001b[0m 33.7065 \u001b[0m \u001b[0m 3.1431 \u001b[0m \u001b[0m 0.1988 \u001b[0m \u001b[0m 1.4321 \u001b[0m \u001b[0m 5.4480 \u001b[0m \u001b[0m 1.1274 \u001b[0m \u001b[0m\n \u001b[0m Ig2rev \u001b[0m \u001b[0m 0.0329 \u001b[0m \u001b[0m 0.0635 \u001b[0m \u001b[0m 0.0040 \u001b[0m \u001b[0m 0.0267 \u001b[0m \u001b[0m 5.0778 \u001b[0m \u001b[0m 1.1228 \u001b[0m \u001b[0m\n \u001b[0m gasCur \u001b[0m \u001b[0m 0.1279 \u001b[0m \u001b[0m 0.0902 \u001b[0m \u001b[0m 0.0057 \u001b[0m \u001b[0m 0.0332 \u001b[0m \u001b[0m 7.2285 \u001b[0m \u001b[0m 1.0841 \u001b[0m \u001b[0m\n \u001b[0m internalize \u001b[0m \u001b[0m 0.0473 \u001b[0m \u001b[0m 0.0105 \u001b[0m \u001b[0m 0.0007 \u001b[0m \u001b[0m 0.0031 \u001b[0m \u001b[0m 11.1634 \u001b[0m \u001b[0m 1.0478 \u001b[0m \u001b[0m\n \u001b[0m kDeg \u001b[0m \u001b[0m 0.0212 \u001b[0m \u001b[0m 0.0048 \u001b[0m \u001b[0m 0.0003 \u001b[0m \u001b[0m 0.0026 \u001b[0m \u001b[0m 4.6812 \u001b[0m \u001b[0m 1.1543 \u001b[0m \u001b[0m\n \u001b[0m kRec \u001b[0m \u001b[0m 0.1071 \u001b[0m \u001b[0m 0.0119 \u001b[0m \u001b[0m 0.0008 \u001b[0m \u001b[0m 0.0031 \u001b[0m \u001b[0m 18.7062 \u001b[0m \u001b[0m 0.9973 \u001b[0m \u001b[0m\n \u001b[0m pYinternalize \u001b[0m \u001b[0m 1.0975 \u001b[0m \u001b[0m 0.1366 \u001b[0m \u001b[0m 0.0086 \u001b[0m \u001b[0m 0.0163 \u001b[0m \u001b[0m 9.8463 \u001b[0m \u001b[0m 1.0011 \u001b[0m \u001b[0m\n \u001b[0m scale \u001b[0m \u001b[0m 0.0212 \u001b[0m \u001b[0m 0.0066 \u001b[0m \u001b[0m 0.0004 \u001b[0m \u001b[0m 0.0034 \u001b[0m \u001b[0m 5.1126 \u001b[0m \u001b[0m 1.1014 \u001b[0m \u001b[0m\n \u001b[0m scaleSurf \u001b[0m \u001b[0m 0.0002 \u001b[0m \u001b[0m 0.0002 \u001b[0m \u001b[0m 0.0000 \u001b[0m \u001b[0m 0.0001 \u001b[0m \u001b[0m 5.4211 \u001b[0m \u001b[0m 1.1160 \u001b[0m \u001b[0m\n \u001b[0m sortF \u001b[0m \u001b[0m 0.6591 \u001b[0m \u001b[0m 0.1741 \u001b[0m \u001b[0m 0.0110 \u001b[0m \u001b[0m 0.1128 \u001b[0m \u001b[0m 2.5145 \u001b[0m \u001b[0m 1.3458 \u001b[0m \u001b[0m\n \u001b[0m xFwd \u001b[0m \u001b[0m 0.0008 \u001b[0m \u001b[0m 0.0030 \u001b[0m \u001b[0m 0.0002 \u001b[0m \u001b[0m 0.0010 \u001b[0m \u001b[0m 8.8701 \u001b[0m \u001b[0m 1.0646 \u001b[0m \u001b[0m\n" }, - "execution_count": 2, "metadata": {}, - "output_type": "execute_result" + "execution_count": 3 } ], "source": [ "using MCMCChains\n", - "chn = read(\"chain-file-6_26.jls\", Chains)\n", + "chn = read(\"chain-file-10_1.jls\", Chains)\n", "summarize(chn)" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -115,7 +61,7 @@ }, { "cell_type": "code", - "execution_count": 119, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -130,7 +76,7 @@ }, { "cell_type": "code", - "execution_count": 120, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -151,17 +97,15 @@ }, { "cell_type": "code", - "execution_count": 121, - "metadata": {}, + "execution_count": 7, + "metadata": { + "tags": [] + }, "outputs": [ { - "name": "stdout", "output_type": "stream", - "text": [ - "8480.415187244163\n", - "1420.243256459686\n", - "745.1883113619709\n" - ] + "name": "stdout", + "text": "7300.4776927547355\n1311.2359940244746\n576.5415499340174\n" } ], "source": [ @@ -183,513 +127,16 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 8, "metadata": {}, "outputs": [ { + "output_type": "execute_result", "data": { - "image/svg+xml": [ - "\n", - "\n", - "\n", - " \n", - " \n", - " \n", - "\n", - "\n", - "\n", - " \n", - " \n", - " \n", - "\n", - "\n", - "\n", - " \n", - " \n", - " \n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", 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- " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " Count\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " M1\n", - " \n", - " \n", - " \n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "\n", - "\n", - "\n", - "\n" - ], - "text/plain": [ - "Plot(...)" - ] + "text/plain": "Plot(...)", + "text/html": "\n\n\n \n \n \n\n\n \n \n \n Treatment\n \n \n \n \n \n \n \n Phosphyrlated AXL\n \n \n \n \n Phosphyrlated Tyro3\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n ReceptorType\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tyro3 Knockdown\n \n \n \n \n \n \n AXL Knockdown\n \n \n \n \n \n \n Normal\n \n \n \n \n \n \n 1 hr\n \n \n \n \n 8 hr\n \n \n \n \n \n \n 1 hr\n \n \n \n \n 8 hr\n \n \n \n \n \n \n 1 hr\n \n \n \n \n 8 hr\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 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200\n \n \n \n \n 250\n \n \n \n \n 300\n \n \n \n \n 350\n \n \n \n \n 400\n \n \n \n \n 450\n \n \n \n \n 500\n \n \n \n \n 550\n \n \n \n \n 600\n \n \n \n \n 650\n \n \n \n \n 700\n \n \n \n \n 750\n \n \n \n \n 800\n \n \n \n \n 850\n \n \n \n \n 900\n \n \n \n \n 950\n \n \n \n \n 1000\n \n \n \n \n 1050\n \n \n \n \n 1100\n \n \n \n \n 1150\n \n \n \n \n 1200\n \n \n \n \n 1250\n \n \n \n \n 1300\n \n \n \n \n 1350\n \n \n \n \n 1400\n \n \n \n \n 1450\n \n \n \n \n 1500\n \n \n \n \n 1550\n \n \n \n \n 1600\n \n \n \n \n -1000\n \n \n \n \n 0\n \n \n \n \n 1000\n \n \n \n \n 2000\n \n \n \n \n -800\n \n \n \n \n -750\n \n \n \n \n -700\n \n \n \n \n -650\n \n \n \n \n -600\n \n \n \n \n -550\n \n \n \n \n -500\n \n \n \n \n -450\n \n \n \n \n -400\n \n \n \n \n -350\n \n \n \n \n -300\n \n \n \n \n -250\n \n \n \n \n -200\n \n \n \n \n -150\n \n \n \n \n -100\n \n \n \n \n -50\n \n \n \n \n 0\n \n \n \n \n 50\n \n \n \n \n 100\n \n \n \n \n 150\n \n \n \n \n 200\n \n \n \n \n 250\n \n \n \n \n 300\n \n \n \n \n 350\n \n \n \n \n 400\n \n \n \n \n 450\n \n \n \n \n 500\n \n \n \n \n 550\n \n \n \n \n 600\n \n \n \n \n 650\n \n \n \n \n 700\n \n \n \n \n 750\n \n \n \n \n 800\n \n \n \n \n 850\n \n \n \n \n 900\n \n \n \n \n 950\n \n \n \n \n 1000\n \n \n \n \n 1050\n \n \n \n \n 1100\n \n \n \n \n 1150\n \n \n \n \n 1200\n \n \n \n \n 1250\n \n \n \n \n 1300\n \n \n \n \n 1350\n \n \n \n \n 1400\n \n \n \n \n 1450\n \n \n \n \n 1500\n \n \n \n \n 1550\n \n \n \n \n 1600\n \n \n \n \n \n \n \n \n \n Count\n \n \n \n \n \n \n M1\n \n \n \n\n\n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n\n", + "image/svg+xml": "\n\n\n \n \n \n\n\n \n \n \n Treatment\n \n \n \n \n \n \n \n Phosphyrlated AXL\n \n \n \n \n Phosphyrlated Tyro3\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n ReceptorType\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tyro3 Knockdown\n \n \n \n \n \n \n AXL Knockdown\n \n \n \n \n \n \n Normal\n \n \n \n \n \n \n 1 hr\n \n \n \n \n 8 hr\n \n \n \n \n \n \n 1 hr\n \n \n \n \n 8 hr\n \n \n \n \n \n \n 1 hr\n \n \n \n \n 8 hr\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 0\n \n \n \n \n 200\n \n \n \n \n 400\n \n \n \n \n 600\n \n \n \n \n 800\n \n \n \n \n \n \n \n \n \n Count\n \n \n \n \n \n \n M1\n \n \n \n\n\n \n \n \n \n \n \n \n \n \n \n \n \n\n\n" }, - "execution_count": 4, "metadata": {}, - "output_type": "execute_result" + "execution_count": 9 } ], "source": [ + "Pkg.add(\"DataFrames\")\n", + "using DataFrames\n", "TAMode.plotpYExpression(chn, AXLexpr, MerTKexpr, Tyro3expr, \"M1\")" ] + }, + { + "source": [ + "index = 100\n", + "scatter(x.kRec[index:250], x.kDeg[index:250], \n", + " xlabel = \"kRec\",\n", + " ylabel = \"kDeg\",\n", + " legend = false) # kRec vs kDeg" + ], + "cell_type": "code", + "metadata": { + "tags": [] + }, + "execution_count": 56, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "image/svg+xml": "\n\n\n \n \n \n\n\n\n \n \n \n\n\n\n \n \n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" + }, + "metadata": {}, + "execution_count": 56 + } + ] + }, + { + "cell_type": "code", + "execution_count": 57, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "image/svg+xml": "\n\n\n \n \n \n\n\n\n \n \n \n\n\n\n \n \n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" + }, + "metadata": {}, + "execution_count": 57 + } + ], + "source": [ + "scatter(x.gasCur[index:250], x.AXLexpr[index:250],\n", + " xlabel = \"gasCur\",\n", + " ylabel = \"AXLexpr\",\n", + " legend = false)" + ] + }, + { + "cell_type": "code", + "execution_count": 59, + "metadata": {}, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "image/svg+xml": "\n\n\n \n \n \n\n\n\n \n \n \n\n\n\n \n \n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" + }, + "metadata": {}, + "execution_count": 59 + } + ], + "source": [ + "scatter(x.internalize[index:250], x.xFwd[index:250],\n", + " xlabel = \"internalize\",\n", + " ylabel = \"xFwd\",\n", + " legend = false)" + ] } ], "metadata": { "kernelspec": { - "display_name": "Julia 1.5.0", + "display_name": "Julia 1.5.2", "language": "julia", "name": "julia-1.5" }, @@ -4646,9 +254,9 @@ "file_extension": ".jl", "mimetype": "application/julia", "name": "julia", - "version": "1.5.0" + "version": "3.8.2-final" } }, "nbformat": 4, "nbformat_minor": 4 -} +} \ No newline at end of file diff --git a/chain-file-10_1.jls b/chain-file-10_1.jls new file mode 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zEHn8N`*;@x%jSRdlB0)$nG__E_$sN`2Hk?*{dXvs*`*F;&K5Feap7@B^bi?)ELY}} zUPHz%2gLMQ)sZpwb@GxMaPpEHaRh?wHyjTA%7Ej*(JazzP&GN}806(cL$Bey*T*q{ zhQ-$2-qFj?*2CV>+Q-(XKTi)ATMuhT4@V#8U>dIf6=&_} z*f;TNVCbs*ZOZ_Y3RO0!gFrqsQ)((yyzAk>jG_-DB zG`#M%LDqjMa)XDpub-orFAcMYr~4njTKld_XYufNcl2?ww{`owZe}mj|5^KbUo?e` z_yZXD`#908_x1GgJBBbw+}~s{`1v?GB3r!tPSel@9Sd}jmt;agVn*?jmt;Y|ZCMT1 z Date: Sun, 4 Oct 2020 15:11:26 -0700 Subject: [PATCH 02/17] chains tests --- test/runtests.jl | 1 + test/testChains.jl | 5 +++++ 2 files changed, 6 insertions(+) create mode 100644 test/testChains.jl diff --git a/test/runtests.jl b/test/runtests.jl index d03280d..b69d251 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -15,3 +15,4 @@ include("testreactCode.jl") include("testCompModel.jl") include("testLS.jl") include("testSample.jl") +include("testChains.jl") diff --git a/test/testChains.jl b/test/testChains.jl new file mode 100644 index 0000000..1c1118c --- /dev/null +++ b/test/testChains.jl @@ -0,0 +1,5 @@ +using MCMCChains + +@testset "Test Chains Package." begin + chn = read("../chain-file-10_1.jls", Chains) +end \ No newline at end of file From 3348745a4733f1b80d512c6f7e39b148526377c7 Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Sun, 4 Oct 2020 20:40:30 -0700 Subject: [PATCH 03/17] added DataFrames dependency --- Manifest.toml | 28 ++++++++++++++++++++++++++++ Project.toml | 1 + 2 files changed, 29 insertions(+) diff --git a/Manifest.toml b/Manifest.toml index d093590..4c42094 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -92,6 +92,12 @@ git-tree-sha1 = "03a44490020826950c68005cafb336e5ba08b7e8" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.6+4" +[[CategoricalArrays]] +deps = ["DataAPI", "Future", "JSON", "Missings", "Printf", "Statistics", "StructTypes", "Unicode"] +git-tree-sha1 = "2ac27f59196a68070e132b25713f9a5bbc5fa0d2" +uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" +version = "0.8.3" + [[ChainRules]] deps = ["ChainRulesCore", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"] git-tree-sha1 = "60b76639ff1dc573b0708a68924539d03ed6520b" @@ -173,6 +179,12 @@ git-tree-sha1 = "176e23402d80e7743fc26c19c681bfb11246af32" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.3.0" +[[DataFrames]] +deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "a7c1c9a6e47a92321bbc9d500dab9b04cc4a6a39" +uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +version = "0.21.7" + [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] git-tree-sha1 = "0347f23484a96d56e7096eb1f55c6975be34b11a" @@ -331,6 +343,10 @@ git-tree-sha1 = "e4813d187be8c7b993cb7f85cbf2b7bfbaadc694" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" version = "1.1.1" +[[Future]] +deps = ["Random"] +uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" + [[GR]] deps = ["Base64", "DelimitedFiles", "HTTP", "JSON", "LinearAlgebra", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] git-tree-sha1 = "cd0f34bd097d4d5eb6bbe01778cf8a7ed35f29d9" @@ -667,6 +683,12 @@ git-tree-sha1 = "a4546c4046fe2a16042305006694a079d34e8f0b" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" version = "1.6.6" +[[PooledArrays]] +deps = ["DataAPI"] +git-tree-sha1 = "b1333d4eced1826e15adbdf01a4ecaccca9d353c" +uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" +version = "0.5.3" + [[PrettyTables]] deps = ["Crayons", "Formatting", "Parameters", "Reexport", "Tables"] git-tree-sha1 = "8458dc04a493ae5c2fed3796c1d3117972c69694" @@ -857,6 +879,12 @@ git-tree-sha1 = "8099ed9fb90b6e754d6ba8c6ed8670f010eadca0" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" version = "0.4.4" +[[StructTypes]] +deps = ["Dates", "UUIDs"] +git-tree-sha1 = "1ed04f622a39d2e5a6747c3a70be040c00333933" +uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" +version = "1.1.0" + [[SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" diff --git a/Project.toml b/Project.toml index 4d12a12..75b9d18 100644 --- a/Project.toml +++ b/Project.toml @@ -4,6 +4,7 @@ authors = ["Aaron Meyer "] version = "0.1.0" [deps] +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" From b30ea7c7d84b8275b85cd64b02f8fc2977b71abf Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Mon, 5 Oct 2020 09:46:41 -0700 Subject: [PATCH 04/17] added Gadfly --- Manifest.toml | 232 ++++++++++++++++++++++++++++++++++++++------------ Project.toml | 1 + 2 files changed, 179 insertions(+), 54 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index d75578b..9fbd635 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -59,6 +59,12 @@ git-tree-sha1 = "a7110d4291700c0d9ddbeb5fa41c3b9c4659c2aa" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" version = "2.13.3" +[[AxisAlgorithms]] +deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] +git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9" +uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" +version = "1.0.0" + [[AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] git-tree-sha1 = "f31f50712cbdf40ee8287f0443b57503e34122ef" @@ -76,9 +82,9 @@ version = "0.5.0" [[Bijectors]] deps = ["ArgCheck", "Compat", "Distributions", "LinearAlgebra", "MappedArrays", "NNlib", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics", "StatsFuns"] -git-tree-sha1 = "eef13682b2a23ebe30d9460a3829fd52ce0713b4" +git-tree-sha1 = "592165906d17456cc5595b9dad2369de16471b46" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.8.5" +version = "0.8.6" [[BinaryProvider]] deps = ["Libdl", "Logging", "SHA"] @@ -92,6 +98,12 @@ git-tree-sha1 = "03a44490020826950c68005cafb336e5ba08b7e8" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.6+4" +[[Calculus]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" +uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" +version = "0.5.1" + [[CategoricalArrays]] deps = ["DataAPI", "Future", "JSON", "Missings", "Printf", "Statistics", "StructTypes", "Unicode"] git-tree-sha1 = "2ac27f59196a68070e132b25713f9a5bbc5fa0d2" @@ -100,15 +112,15 @@ version = "0.8.3" [[ChainRules]] deps = ["ChainRulesCore", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"] -git-tree-sha1 = "60b76639ff1dc573b0708a68924539d03ed6520b" +git-tree-sha1 = "7ff00994ca6a7cf24079925b28af42488aa07b48" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "0.7.20" +version = "0.7.22" [[ChainRulesCore]] deps = ["LinearAlgebra", "MuladdMacro"] -git-tree-sha1 = "ac64a416997ae87eb86550020d0607ff608253d1" +git-tree-sha1 = "9abb94a911c36efeca17b7255f63160787d8822e" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "0.9.10" +version = "0.9.11" [[CodeTracking]] deps = ["InteractiveUtils", "UUIDs"] @@ -118,9 +130,9 @@ version = "1.0.3" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"] -git-tree-sha1 = "950f477dfe152a0dd2221124986a5722db385199" +git-tree-sha1 = "5d472aa8908568bc198564db06983913a6c2c8e7" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.10.0" +version = "3.10.1" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -147,9 +159,9 @@ version = "0.3.0" [[Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "043647e66a6effa7473e98a5370faa4deb6dce90" +git-tree-sha1 = "8cd7b7d1c7f6fcbe7e8743a58adf57788ec7f787" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.17.0" +version = "3.18.0" [[CompilerSupportLibraries_jll]] deps = ["Libdl", "Pkg"] @@ -157,6 +169,12 @@ git-tree-sha1 = "7c4f882c41faa72118841185afc58a2eb00ef612" uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" version = "0.3.3+0" +[[Compose]] +deps = ["Base64", "Colors", "DataStructures", "Dates", "IterTools", "JSON", "LinearAlgebra", "Measures", "Printf", "Random", "Requires", "UUIDs"] +git-tree-sha1 = "034174e607d254b8ca0853a1a9029b265114bf6c" +uuid = "a81c6b42-2e10-5240-aca2-a61377ecd94b" +version = "0.8.2" + [[ConsoleProgressMonitor]] deps = ["Logging", "ProgressMeter"] git-tree-sha1 = "3ab7b2136722890b9af903859afcf457fa3059e8" @@ -169,6 +187,12 @@ git-tree-sha1 = "d05a3a25b762720d40246d5bedf518c9c2614ef5" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" version = "0.5.5" +[[CoupledFields]] +deps = ["LinearAlgebra", "Statistics", "StatsBase"] +git-tree-sha1 = "6c9671364c68c1158ac2524ac881536195b7e7bc" +uuid = "7ad07ef1-bdf2-5661-9d2b-286fd4296dac" +version = "0.2.0" + [[CpuId]] deps = ["Markdown", "Test"] git-tree-sha1 = "f0464e499ab9973b43c20f8216d088b61fda80c6" @@ -192,10 +216,10 @@ uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" version = "0.21.7" [[DataStructures]] -deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "0347f23484a96d56e7096eb1f55c6975be34b11a" +deps = ["InteractiveUtils", "OrderedCollections"] +git-tree-sha1 = "88d48e133e6d3dd68183309877eac74393daa7eb" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.6" +version = "0.17.20" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -211,10 +235,16 @@ deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" [[DiffEqBase]] -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributed", "DocStringExtensions", "FunctionWrappers", "IterativeSolvers", "IteratorInterfaceExtensions", "LabelledArrays", "LinearAlgebra", "Logging", "MuladdMacro", "Parameters", "Printf", "RecipesBase", "RecursiveArrayTools", "RecursiveFactorization", "Requires", "Roots", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "TableTraits", "Tables", "TreeViews", "ZygoteRules"] -git-tree-sha1 = "949596defa7b0e24a35037253c8e8e87bd7a6c2c" +deps = ["ArrayInterface", "ChainRulesCore", "ConsoleProgressMonitor", "DataStructures", "Distributed", "DocStringExtensions", "FunctionWrappers", "IterativeSolvers", "IteratorInterfaceExtensions", "LabelledArrays", "LinearAlgebra", "Logging", "LoggingExtras", "MuladdMacro", "Parameters", "Printf", "ProgressLogging", "RecipesBase", "RecursiveArrayTools", "RecursiveFactorization", "Requires", "Roots", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "TableTraits", "TerminalLoggers", "TreeViews", "ZygoteRules"] +git-tree-sha1 = "4dde9a142bc3780f0216e564673f477ec6f6a6df" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.47.1" +version = "6.44.3" + +[[DiffEqDiffTools]] +deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "a4ed8a740484627ea41b47f7e1a25dd909a28353" +uuid = "01453d9d-ee7c-5054-8395-0335cb756afa" +version = "1.7.0" [[DiffResults]] deps = ["StaticArrays"] @@ -230,19 +260,19 @@ version = "1.0.1" [[Distances]] deps = ["LinearAlgebra", "Statistics"] -git-tree-sha1 = "bed62cc5afcff16de797a9f38fb358b74071f785" +git-tree-sha1 = "ac95c9cb69a901e8cedcfe736f792eb06240771a" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.9.0" +version = "0.9.1" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "StaticArrays", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "501c11d708917ca09ce357bed163dbaf0f30229f" +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "9c41285c57c6e0d73a21ed4b65f6eec34805f937" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.23.12" +version = "0.23.8" [[DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "DiffRules", "Distributions", "FillArrays", "ForwardDiff", "LinearAlgebra", "NaNMath", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsBase", "StatsFuns", "ZygoteRules"] @@ -258,9 +288,9 @@ version = "0.8.3" [[DynamicPPL]] deps = ["AbstractMCMC", "Bijectors", "ChainRulesCore", "Distributions", "MacroTools", "NaturalSort", "Random"] -git-tree-sha1 = "0d48b8509b4d40a673b63d10ad3f8681acdb86da" +git-tree-sha1 = "f17e63be7da4c5d252d7078d8842cf920b895635" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.9.1" +version = "0.9.3" [[EarCut_jll]] deps = ["Libdl", "Pkg"] @@ -297,6 +327,18 @@ git-tree-sha1 = "13a934b9e74a8722bf1786c989de346a9602e695" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" version = "4.3.1+2" +[[FFTW]] +deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"] +git-tree-sha1 = "8b7c16b56936047ca41bf25effa137ae0b381ae8" +uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" +version = "1.2.4" + +[[FFTW_jll]] +deps = ["Libdl", "Pkg"] +git-tree-sha1 = "6c975cd606128d45d1df432fb812d6eb10fee00b" +uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" +version = "3.3.9+5" + [[FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" uuid = "9aa1b823-49e4-5ca5-8b0f-3971ec8bab6a" @@ -307,9 +349,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "b955c227b0d1413a1a97e2ca0635a5de019d7337" +git-tree-sha1 = "4863cbb7910079369e258dee4add9d06ead5063a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.9.6" +version = "0.8.14" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] @@ -362,6 +404,12 @@ git-tree-sha1 = "cd0f34bd097d4d5eb6bbe01778cf8a7ed35f29d9" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" version = "0.52.0" +[[Gadfly]] +deps = ["Base64", "CategoricalArrays", "Colors", "Compose", "Contour", "CoupledFields", "DataStructures", "Dates", "Distributions", "DocStringExtensions", "Hexagons", "IndirectArrays", "IterTools", "JSON", "Juno", "KernelDensity", "LinearAlgebra", "Loess", "Measures", "Printf", "REPL", "Random", "Requires", "Showoff", "Statistics"] +git-tree-sha1 = "3d6d5025e08ce535c90979303ec6ab103c8a09b9" +uuid = "c91e804a-d5a3-530f-b6f0-dfbca275c004" +version = "1.3.0" + [[GenericSVD]] deps = ["LinearAlgebra"] git-tree-sha1 = "62909c3eda8a25b5673a367d1ad2392ebb265211" @@ -370,9 +418,9 @@ version = "0.3.0" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "49d13ebd048bd71315ff98bdc2c560ec16eda2b4" +git-tree-sha1 = "501161f4ac62835b10a70535dd247b721fe47235" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.3.1" +version = "0.3.2" [[GeometryTypes]] deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "StaticArrays"] @@ -391,6 +439,17 @@ git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" version = "0.8.19" +[[Hexagons]] +deps = ["Test"] +git-tree-sha1 = "de4a6f9e7c4710ced6838ca906f81905f7385fd6" +uuid = "a1b4810d-1bce-5fbd-ac56-80944d57a21f" +version = "0.2.0" + +[[IndirectArrays]] +git-tree-sha1 = "c2a145a145dc03a7620af1444e0264ef907bd44f" +uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959" +version = "0.5.1" + [[Inflate]] git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" @@ -408,10 +467,22 @@ git-tree-sha1 = "50b41d59e7164ab6fda65e71049fee9d890731ff" uuid = "505f98c9-085e-5b2c-8e89-488be7bf1f34" version = "0.3.0" +[[IntelOpenMP_jll]] +deps = ["Libdl", "Pkg"] +git-tree-sha1 = "fb8e1c7a5594ba56f9011310790e03b5384998d6" +uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" +version = "2018.0.3+0" + [[InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +[[Interpolations]] +deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] +git-tree-sha1 = "2b7d4e9be8b74f03115e64cf36ed2f48ae83d946" +uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" +version = "0.12.10" + [[IntervalSets]] deps = ["Dates", "EllipsisNotation", "Statistics"] git-tree-sha1 = "3b1cef135bc532b3c3401b309e1b8a2a2ba26af5" @@ -452,6 +523,18 @@ git-tree-sha1 = "5b9b328eeea7bb85caca1576c15041e8faeb9041" uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a" version = "0.8.1" +[[Juno]] +deps = ["Base64", "Logging", "Media", "Profile"] +git-tree-sha1 = "07cb43290a840908a771552911a6274bc6c072c7" +uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d" +version = "0.8.4" + +[[KernelDensity]] +deps = ["Distributions", "FFTW", "Interpolations", "Optim", "StatsBase", "Test"] +git-tree-sha1 = "c1048817fe5711f699abc8fabd47b1ac6ba4db04" +uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" +version = "0.5.1" + [[LAME_jll]] deps = ["Libdl", "Pkg"] git-tree-sha1 = "a7999edc634307964d5651265ebf7c2e14b4ef91" @@ -491,9 +574,9 @@ version = "0.4.1" [[LightGraphs]] deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "a0d4bcea4b9c056da143a5ded3c2b7f7740c2d41" +git-tree-sha1 = "6f85a35d2377cb2db1bc448ed0d6340d2bb1ea64" uuid = "093fc24a-ae57-5d10-9952-331d41423f4d" -version = "1.3.0" +version = "1.3.3" [[LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -505,6 +588,12 @@ version = "7.1.0" deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +[[Loess]] +deps = ["Distances", "Random", "Statistics", "Test"] +git-tree-sha1 = "0ee46caf683a422b595be4dfaed6cda28f541e25" +uuid = "4345ca2d-374a-55d4-8d30-97f9976e7612" +version = "0.5.0" + [[LogDensityProblems]] deps = ["ArgCheck", "BenchmarkTools", "DiffResults", "DocStringExtensions", "Parameters", "Random", "Requires", "TransformVariables"] git-tree-sha1 = "77ac6c4bb1eae4072a5d0fcfba621020f7802cc2" @@ -528,15 +617,21 @@ version = "0.8.26" [[LoweredCodeUtils]] deps = ["JuliaInterpreter"] -git-tree-sha1 = "ab33e17d4f5f897a1f86da4e05138fff6c8dc85e" +git-tree-sha1 = "00c64cd799a9450e4d1efe8ad6549de72702f7fe" uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b" -version = "1.2.1" +version = "1.2.3" [[MCMCChains]] deps = ["AbstractFFTs", "AbstractMCMC", "AxisArrays", "Compat", "Distributions", "Formatting", "IteratorInterfaceExtensions", "LinearAlgebra", "MLJModelInterface", "NaturalSort", "PrettyTables", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase", "TableTraits", "Tables"] -git-tree-sha1 = "f02b83d0adb4318f66ba73f5e1f50ef139fee6c2" +git-tree-sha1 = "9238e22fa1d5d81b8a7af87aee27c02aba773788" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "4.2.1" +version = "4.2.2" + +[[MKL_jll]] +deps = ["IntelOpenMP_jll", "Libdl", "Pkg"] +git-tree-sha1 = "eb540ede3aabb8284cb482aa41d00d6ca850b1f8" +uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" +version = "2020.2.254+0" [[MLJModelInterface]] deps = ["Random", "ScientificTypes"] @@ -576,6 +671,12 @@ git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" version = "0.3.1" +[[Media]] +deps = ["MacroTools", "Test"] +git-tree-sha1 = "75a54abd10709c01f1b86b84ec225d26e840ed58" +uuid = "e89f7d12-3494-54d1-8411-f7d8b9ae1f27" +version = "0.5.0" + [[Missings]] deps = ["DataAPI"] git-tree-sha1 = "ed61674a0864832495ffe0a7e889c0da76b0f4c8" @@ -591,10 +692,10 @@ uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" version = "0.2.2" [[NLSolversBase]] -deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "db63edd0199a4813a1fa117e3c840a4528b59d72" +deps = ["Calculus", "DiffEqDiffTools", "DiffResults", "Distributed", "ForwardDiff"] +git-tree-sha1 = "f1b8ed89fa332f410cfc7c937682eb4d0b361521" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.7.0" +version = "7.5.0" [[NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -604,9 +705,9 @@ version = "4.4.1" [[NNlib]] deps = ["Libdl", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "8ec4693a5422f0b064ce324f59351f24aa474893" +git-tree-sha1 = "1ef04283efe283be08e2d0de842f5e5286dd0b7a" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.7.4" +version = "0.7.5" [[NaNMath]] git-tree-sha1 = "c84c576296d0e2fbb3fc134d3e09086b3ea617cd" @@ -625,9 +726,9 @@ uuid = "c020b1a1-e9b0-503a-9c33-f039bfc54a85" version = "1.0.0" [[OffsetArrays]] -git-tree-sha1 = "9011c7c98769c451f83869a4d66461e2f23bc80b" +git-tree-sha1 = "3fdfca8a532507d65f39ff0ad34fe81097a55337" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.2.1" +version = "1.3.0" [[Ogg_jll]] deps = ["Libdl", "Pkg"] @@ -647,6 +748,12 @@ git-tree-sha1 = "d51c416559217d974a1113522d5919235ae67a87" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.3+3" +[[Optim]] +deps = ["Compat", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "c05aa6b694d426df87ff493306c1c5b4b215e148" +uuid = "429524aa-4258-5aef-a3af-852621145aeb" +version = "0.22.0" + [[Opus_jll]] deps = ["Libdl", "Pkg"] git-tree-sha1 = "cc90a125aa70dbb069adbda2b913b02cf2c5f6fe" @@ -660,9 +767,9 @@ version = "1.3.1" [[OrdinaryDiffEq]] deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "GenericSVD", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "b9690f74a5c28aa698c025f72c43174a3a4e4d1f" +git-tree-sha1 = "e6806009a3a5e74c5a6d44365c15b967daa7f798" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "5.42.9" +version = "5.42.3" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"] @@ -700,9 +807,9 @@ version = "1.0.7" [[Plots]] deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "GeometryTypes", "JSON", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"] -git-tree-sha1 = "a4546c4046fe2a16042305006694a079d34e8f0b" +git-tree-sha1 = "c499e18bbeab024f6de0e0ae285554d153eeb5c5" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.6.6" +version = "1.6.8" [[PooledArrays]] deps = ["DataAPI"] @@ -710,6 +817,12 @@ git-tree-sha1 = "b1333d4eced1826e15adbdf01a4ecaccca9d353c" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" version = "0.5.3" +[[PositiveFactorizations]] +deps = ["LinearAlgebra", "Test"] +git-tree-sha1 = "127c47b91990c101ee3752291c4f45640eeb03d1" +uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" +version = "0.2.3" + [[PrettyTables]] deps = ["Crayons", "Formatting", "Parameters", "Reexport", "Tables"] git-tree-sha1 = "8458dc04a493ae5c2fed3796c1d3117972c69694" @@ -755,6 +868,11 @@ git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d" version = "0.3.2" +[[Ratios]] +git-tree-sha1 = "37d210f612d70f3f7d57d488cb3b6eff56ad4e41" +uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" +version = "0.4.0" + [[RecipesBase]] git-tree-sha1 = "6ee6c35fe69e79e17c455a386c1ccdc66d9f7da4" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" @@ -768,9 +886,9 @@ version = "0.1.13" [[RecursiveArrayTools]] deps = ["ArrayInterface", "LinearAlgebra", "RecipesBase", "Requires", "StaticArrays", "Statistics", "ZygoteRules"] -git-tree-sha1 = "47e117a002fc1dbbe905557b333a84126c93671c" +git-tree-sha1 = "800236466c6932b9ddc78c1970706188fd8e14b4" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.7.0" +version = "2.7.1" [[RecursiveFactorization]] deps = ["LinearAlgebra", "LoopVectorization", "VectorizationBase"] @@ -786,15 +904,15 @@ version = "0.2.0" [[Requires]] deps = ["UUIDs"] -git-tree-sha1 = "2fc2e1ab606a5dca7bbad9036a694553c3a57926" +git-tree-sha1 = "28faf1c963ca1dc3ec87f166d92982e3c4a1f66d" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.0.3" +version = "1.1.0" [[Revise]] deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "UUIDs", "Unicode"] -git-tree-sha1 = "3ac52e8b8c0140ba894c81ecac0f6a38987609ab" +git-tree-sha1 = "b520a7f1a34326c8b5dd23947a71f24f5bb3657b" uuid = "295af30f-e4ad-537b-8983-00126c2a3abe" -version = "3.1.2" +version = "3.1.3" [[Rmath]] deps = ["Random", "Rmath_jll"] @@ -924,9 +1042,9 @@ version = "1.0.0" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "b7f762e9820b7fab47544c36f26f54ac59cf8abf" +git-tree-sha1 = "24a584cf65e2cfabdadc21694fb69d2e74c82b44" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.0.5" +version = "1.1.0" [[TerminalLoggers]] deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] @@ -958,9 +1076,9 @@ version = "0.3.0" [[Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedVI", "Bijectors", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker", "ZygoteRules"] -git-tree-sha1 = "e373c540502e5c4ea568185c26602f6fc369cba9" +git-tree-sha1 = "d1e5a976e3a33269f42a55182f439886d2b426de" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.14.4" +version = "0.14.6" [[UUIDs]] deps = ["Random", "SHA"] @@ -986,6 +1104,12 @@ git-tree-sha1 = "b9b450c99a3ca1cc1c6836f560d8d887bcbe356e" uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f" version = "0.1.2" +[[WoodburyMatrices]] +deps = ["LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "28ffe06d28b1ba8fdb2f36ec7bb079fac81bac0d" +uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" +version = "0.5.2" + [[Zlib_jll]] deps = ["Libdl", "Pkg"] git-tree-sha1 = "fdd89e5ab270ea0f2a0174bd9093e557d06d4bfa" diff --git a/Project.toml b/Project.toml index 9689abf..0a867f6 100644 --- a/Project.toml +++ b/Project.toml @@ -7,6 +7,7 @@ version = "0.1.0" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" +Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004" LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" From f1f79fa7f8f7dbf20c11c490d363400c6cf71cbe Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Mon, 5 Oct 2020 13:45:25 -0700 Subject: [PATCH 05/17] fixed build error --- Manifest.toml | 31 ------------------------------- 1 file changed, 31 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 25941d7..9fbd635 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,6 +1,5 @@ # This file is machine-generated - editing it directly is not advised - [[AbstractFFTs]] deps = ["LinearAlgebra"] git-tree-sha1 = "051c95d6836228d120f5f4b984dd5aba1624f716" @@ -217,17 +216,10 @@ uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" version = "0.21.7" [[DataStructures]] -<<<<<<< HEAD deps = ["InteractiveUtils", "OrderedCollections"] git-tree-sha1 = "88d48e133e6d3dd68183309877eac74393daa7eb" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" version = "0.17.20" -======= -deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "db07bb22795762895b60e44d62b34b16c982a687" -uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.7" ->>>>>>> 81c4572e1bf87c33a021111e2fc366a69de59cee [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -243,7 +235,6 @@ deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" [[DiffEqBase]] -<<<<<<< HEAD deps = ["ArrayInterface", "ChainRulesCore", "ConsoleProgressMonitor", "DataStructures", "Distributed", "DocStringExtensions", "FunctionWrappers", "IterativeSolvers", "IteratorInterfaceExtensions", "LabelledArrays", "LinearAlgebra", "Logging", "LoggingExtras", "MuladdMacro", "Parameters", "Printf", "ProgressLogging", "RecipesBase", "RecursiveArrayTools", "RecursiveFactorization", "Requires", "Roots", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "TableTraits", "TerminalLoggers", "TreeViews", "ZygoteRules"] git-tree-sha1 = "4dde9a142bc3780f0216e564673f477ec6f6a6df" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" @@ -254,12 +245,6 @@ deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticAr git-tree-sha1 = "a4ed8a740484627ea41b47f7e1a25dd909a28353" uuid = "01453d9d-ee7c-5054-8395-0335cb756afa" version = "1.7.0" -======= -deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributed", "DocStringExtensions", "FunctionWrappers", "IterativeSolvers", "IteratorInterfaceExtensions", "LabelledArrays", "LinearAlgebra", "Logging", "MuladdMacro", "Parameters", "Printf", "RecipesBase", "RecursiveArrayTools", "RecursiveFactorization", "Requires", "Roots", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "TableTraits", "Tables", "TreeViews", "ZygoteRules"] -git-tree-sha1 = "2457d3b710e2767a8eab5d4d7983ae6a902e9335" -uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.48.0" ->>>>>>> 81c4572e1bf87c33a021111e2fc366a69de59cee [[DiffResults]] deps = ["StaticArrays"] @@ -641,15 +626,12 @@ deps = ["AbstractFFTs", "AbstractMCMC", "AxisArrays", "Compat", "Distributions", git-tree-sha1 = "9238e22fa1d5d81b8a7af87aee27c02aba773788" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" version = "4.2.2" -<<<<<<< HEAD [[MKL_jll]] deps = ["IntelOpenMP_jll", "Libdl", "Pkg"] git-tree-sha1 = "eb540ede3aabb8284cb482aa41d00d6ca850b1f8" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" version = "2020.2.254+0" -======= ->>>>>>> 81c4572e1bf87c33a021111e2fc366a69de59cee [[MLJModelInterface]] deps = ["Random", "ScientificTypes"] @@ -710,17 +692,10 @@ uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" version = "0.2.2" [[NLSolversBase]] -<<<<<<< HEAD deps = ["Calculus", "DiffEqDiffTools", "DiffResults", "Distributed", "ForwardDiff"] git-tree-sha1 = "f1b8ed89fa332f410cfc7c937682eb4d0b361521" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.5.0" -======= -deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "39d6bc45e99c96e6995cbddac02877f9b61a1dd1" -uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.7.1" ->>>>>>> 81c4572e1bf87c33a021111e2fc366a69de59cee [[NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -792,15 +767,9 @@ version = "1.3.1" [[OrdinaryDiffEq]] deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "GenericSVD", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -<<<<<<< HEAD git-tree-sha1 = "e6806009a3a5e74c5a6d44365c15b967daa7f798" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" version = "5.42.3" -======= -git-tree-sha1 = "226c9645949a827d3c8f0a629ff4606d5e4010f5" -uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "5.42.10" ->>>>>>> 81c4572e1bf87c33a021111e2fc366a69de59cee [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"] From 687a76c4a704f074f3eb76f90587ce9386e9b187 Mon Sep 17 00:00:00 2001 From: Aaron Meyer <2065146+aarmey@users.noreply.github.com> Date: Mon, 5 Oct 2020 17:09:22 -0700 Subject: [PATCH 06/17] Update testChains.jl --- test/testChains.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/testChains.jl b/test/testChains.jl index 1c1118c..ea51f78 100644 --- a/test/testChains.jl +++ b/test/testChains.jl @@ -2,4 +2,4 @@ using MCMCChains @testset "Test Chains Package." begin chn = read("../chain-file-10_1.jls", Chains) -end \ No newline at end of file +end From 68295195b09e9e97184c7c7739c4e3ee3bcf7146 Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Thu, 8 Oct 2020 16:43:03 -0700 Subject: [PATCH 07/17] added sampling file --- sampling.jl | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 sampling.jl diff --git a/sampling.jl b/sampling.jl new file mode 100644 index 0000000..49979ec --- /dev/null +++ b/sampling.jl @@ -0,0 +1,14 @@ +import TAMode +using Test +using Turing + +f = open("log.txt", "w") +redirect_stdout(f) +redirect_stderr(f) + +@testset "Test sampling." begin + samp = sample(TAMode.A549model, NUTS(0.65), 500) + write("chain-file-10_1.jls", samp) +end + +close(f) \ No newline at end of file From b98a9bb4842e322147331e838b68fdfe8d8b042a Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Fri, 23 Oct 2020 18:06:08 -0700 Subject: [PATCH 08/17] recursivearraytools notebook --- recursive.ipynb | 72 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 recursive.ipynb diff --git a/recursive.ipynb b/recursive.ipynb new file mode 100644 index 0000000..b371242 --- /dev/null +++ b/recursive.ipynb @@ -0,0 +1,72 @@ +{ + "metadata": { + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5-final" + }, + "orig_nbformat": 2, + "kernelspec": { + "name": "julia-1.5", + "display_name": "Julia 1.5.2" + } + }, + "nbformat": 4, + "nbformat_minor": 2, + "cells": [ + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "using Pkg\n", + "Pkg.instantiate()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "output_type": "error", + "ename": "LoadError", + "evalue": "ArgumentError: Package TAMode not found in current path:\n- Run `import Pkg; Pkg.add(\"TAMode\")` to install the TAMode package.\n", + "traceback": [ + "ArgumentError: Package TAMode not found in current path:\n- Run `import Pkg; Pkg.add(\"TAMode\")` to install the TAMode package.\n", + "", + "Stacktrace:", + " [1] require(::Module, ::Symbol) at ./loading.jl:893", + " [2] include_string(::Function, ::Module, ::String, ::String) at ./loading.jl:1091", + " [3] execute_code(::String, ::String) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/execute_request.jl:27", + " [4] execute_request(::ZMQ.Socket, ::IJulia.Msg) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/execute_request.jl:86", + " [5] #invokelatest#1 at ./essentials.jl:710 [inlined]", + " [6] invokelatest at ./essentials.jl:709 [inlined]", + " [7] eventloop(::ZMQ.Socket) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/eventloop.jl:8", + " [8] (::IJulia.var\"#15#18\")() at ./task.jl:356" + ] + } + ], + "source": [ + "using TAMode\n", + "using RecursiveArrayTools\n", + "using LabelledArrays" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ] +} \ No newline at end of file From 3b160f19ba5221a1a4098d300fb546efaa0c6cb8 Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Sat, 24 Oct 2020 10:10:43 -0700 Subject: [PATCH 09/17] update recursive notebook --- recursive.ipynb | 118 ++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 108 insertions(+), 10 deletions(-) diff --git a/recursive.ipynb b/recursive.ipynb index b371242..3ac889e 100644 --- a/recursive.ipynb +++ b/recursive.ipynb @@ -23,28 +23,128 @@ "cells": [ { "cell_type": "code", - "execution_count": 2, + "execution_count": 20, "metadata": {}, - "outputs": [], + "outputs": [ + { + "output_type": "stream", + "name": "stderr", + "text": [ + "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", + "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Project.toml`\n", + "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Manifest.toml`\n", + "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", + "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Project.toml`\n", + "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Manifest.toml`\n", + "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", + "\u001b[32m\u001b[1mUpdating\u001b[22m\u001b[39m `~/.julia/environments/v1.5/Project.toml`\n", + " \u001b[90m [90137ffa] \u001b[39m\u001b[92m+ StaticArrays v0.12.4\u001b[39m\n", + "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Manifest.toml`\n" + ] + } + ], "source": [ "using Pkg\n", - "Pkg.instantiate()\n" + "Pkg.instantiate()\n", + "Pkg.add(\"RecursiveArrayTools\")\n", + "Pkg.add(\"LabelledArrays\")\n", + "Pkg.add(\"StaticArrays\")\n", + "using RecursiveArrayTools\n", + "using LabelledArrays\n", + "using StaticArrays\n" + ] + }, + { + "source": [ + "larr = SLVector(binding=[1, 2, 3, 3], vRev = [1, 2, 3, 4, 5, 6], expression = 2, xFwd6 = 5)\n", + "arrPart = ArrayPartition(larr)\n", + "for x in arrPart\n", + " println(x)\n", + "end\n", + "println()\n", + "for y in arrPart.x\n", + " println(y)\n", + "end" + ], + "cell_type": "code", + "metadata": {}, + "execution_count": 17, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "[1, 2, 3, 3]\n[1, 2, 3, 4, 5, 6]\n2\n5\n\n4-element SLArray{Tuple{4},Any,1,4,(:binding, :vRev, :expression, :xFwd6)} with indices SOneTo(4):\n :binding => [1, 2, 3, 3]\n :vRev => [1, 2, 3, 4, 5, 6]\n :expression => 2\n :xFwd6 => 5\n" + ] + } + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "text/plain": [ + "([1, 2, 3, 3], [1, 2, 3, 4, 5, 6], 2, 5)" + ] + }, + "metadata": {}, + "execution_count": 9 + } + ], + "source": [ + "binding=[1, 2, 3, 3] \n", + "vRev = [1, 2, 3, 4, 5, 6]\n", + "expression = 2\n", + "xFwd6 = 5\n", + "arrPart2 = ArrayPartition(binding, vRev, expression, xFwd6)" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "123312345625\n", + "[1, 2, 3, 3]\n", + "[1, 2, 3, 4, 5, 6]\n", + "2\n", + "5\n" + ] + } + ], + "source": [ + "for x in arrPart2\n", + " print(x)\n", + "end\n", + "println()\n", + "for y=1:4\n", + " println(arrPart2.x[y])\n", + "end\n", + "# don't think I can access the labelled values so I'm not sure how to use labelled arrays" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 22, "metadata": {}, "outputs": [ { "output_type": "error", "ename": "LoadError", - "evalue": "ArgumentError: Package TAMode not found in current path:\n- Run `import Pkg; Pkg.add(\"TAMode\")` to install the TAMode package.\n", + "evalue": "TypeError: in Type, in parameter, expected Type, got a value of type Tuple{DataType,DataType}", "traceback": [ - "ArgumentError: Package TAMode not found in current path:\n- Run `import Pkg; Pkg.add(\"TAMode\")` to install the TAMode package.\n", + "TypeError: in Type, in parameter, expected Type, got a value of type Tuple{DataType,DataType}", "", "Stacktrace:", - " [1] require(::Module, ::Symbol) at ./loading.jl:893", + " [1] top-level scope at In[22]:1", " [2] include_string(::Function, ::Module, ::String, ::String) at ./loading.jl:1091", " [3] execute_code(::String, ::String) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/execute_request.jl:27", " [4] execute_request(::ZMQ.Socket, ::IJulia.Msg) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/execute_request.jl:86", @@ -56,9 +156,7 @@ } ], "source": [ - "using TAMode\n", - "using RecursiveArrayTools\n", - "using LabelledArrays" + "arrayPart{T} = ArrayPartition{T, (MVector{4, T}, MVector{6, T})}\n" ] }, { From 59d7364eb27c9844a9b8c7a1cdf2629867e10f65 Mon Sep 17 00:00:00 2001 From: Aaron Meyer Date: Sun, 25 Oct 2020 09:17:57 -0700 Subject: [PATCH 10/17] Fixed? --- recursive.ipynb | 85 +++++++++++++------------------------------------ 1 file changed, 22 insertions(+), 63 deletions(-) diff --git a/recursive.ipynb b/recursive.ipynb index 3ac889e..637b3b4 100644 --- a/recursive.ipynb +++ b/recursive.ipynb @@ -23,41 +23,21 @@ "cells": [ { "cell_type": "code", - "execution_count": 20, + "execution_count": 3, "metadata": {}, - "outputs": [ - { - "output_type": "stream", - "name": "stderr", - "text": [ - "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Project.toml`\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Manifest.toml`\n", - "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Project.toml`\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Manifest.toml`\n", - "\u001b[32m\u001b[1m Resolving\u001b[22m\u001b[39m package versions...\n", - "\u001b[32m\u001b[1mUpdating\u001b[22m\u001b[39m `~/.julia/environments/v1.5/Project.toml`\n", - " \u001b[90m [90137ffa] \u001b[39m\u001b[92m+ StaticArrays v0.12.4\u001b[39m\n", - "\u001b[32m\u001b[1mNo Changes\u001b[22m\u001b[39m to `~/.julia/environments/v1.5/Manifest.toml`\n" - ] - } - ], + "outputs": [], "source": [ "using Pkg\n", - "Pkg.instantiate()\n", - "Pkg.add(\"RecursiveArrayTools\")\n", - "Pkg.add(\"LabelledArrays\")\n", - "Pkg.add(\"StaticArrays\")\n", "using RecursiveArrayTools\n", "using LabelledArrays\n", - "using StaticArrays\n" + "using StaticArrays" ] }, { "source": [ - "larr = SLVector(binding=[1, 2, 3, 3], vRev = [1, 2, 3, 4, 5, 6], expression = 2, xFwd6 = 5)\n", - "arrPart = ArrayPartition(larr)\n", + "larr = SLVector(expression = 2, xFwd6 = 5)\n", + "narr = SLVector(A=1, B=2, C=3, D=4)\n", + "arrPart = ArrayPartition(larr, narr)\n", "for x in arrPart\n", " println(x)\n", "end\n", @@ -68,13 +48,27 @@ ], "cell_type": "code", "metadata": {}, - "execution_count": 17, + "execution_count": 4, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ - "[1, 2, 3, 3]\n[1, 2, 3, 4, 5, 6]\n2\n5\n\n4-element SLArray{Tuple{4},Any,1,4,(:binding, :vRev, :expression, :xFwd6)} with indices SOneTo(4):\n :binding => [1, 2, 3, 3]\n :vRev => [1, 2, 3, 4, 5, 6]\n :expression => 2\n :xFwd6 => 5\n" + "2\n", + "5\n", + "1\n", + "2\n", + "3\n", + "4\n", + "\n", + "2-element SLArray{Tuple{2},Int64,1,2,(:expression, :xFwd6)} with indices SOneTo(2):\n", + " :expression => 2\n", + " :xFwd6 => 5\n", + "4-element SLArray{Tuple{4},Int64,1,4,(:A, :B, :C, :D)} with indices SOneTo(4):\n", + " :A => 1\n", + " :B => 2\n", + " :C => 3\n", + " :D => 4\n" ] } ] @@ -130,41 +124,6 @@ "end\n", "# don't think I can access the labelled values so I'm not sure how to use labelled arrays" ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": {}, - "outputs": [ - { - "output_type": "error", - "ename": "LoadError", - "evalue": "TypeError: in Type, in parameter, expected Type, got a value of type Tuple{DataType,DataType}", - "traceback": [ - "TypeError: in Type, in parameter, expected Type, got a value of type Tuple{DataType,DataType}", - "", - "Stacktrace:", - " [1] top-level scope at In[22]:1", - " [2] include_string(::Function, ::Module, ::String, ::String) at ./loading.jl:1091", - " [3] execute_code(::String, ::String) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/execute_request.jl:27", - " [4] execute_request(::ZMQ.Socket, ::IJulia.Msg) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/execute_request.jl:86", - " [5] #invokelatest#1 at ./essentials.jl:710 [inlined]", - " [6] invokelatest at ./essentials.jl:709 [inlined]", - " [7] eventloop(::ZMQ.Socket) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/eventloop.jl:8", - " [8] (::IJulia.var\"#15#18\")() at ./task.jl:356" - ] - } - ], - "source": [ - "arrayPart{T} = ArrayPartition{T, (MVector{4, T}, MVector{6, T})}\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ] } \ No newline at end of file From f25d0642ec85613d4731f74b08edccabe91f70aa Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Mon, 9 Nov 2020 18:45:56 -0800 Subject: [PATCH 11/17] labelled arrays notebook update --- recursive.ipynb | 28 +++++++++++----------------- 1 file changed, 11 insertions(+), 17 deletions(-) diff --git a/recursive.ipynb b/recursive.ipynb index 637b3b4..01f66f2 100644 --- a/recursive.ipynb +++ b/recursive.ipynb @@ -23,7 +23,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 3, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -44,7 +44,8 @@ "println()\n", "for y in arrPart.x\n", " println(y)\n", - "end" + "end\n", + "print(arrPart.x[1].expression)" ], "cell_type": "code", "metadata": {}, @@ -54,21 +55,7 @@ "output_type": "stream", "name": "stdout", "text": [ - "2\n", - "5\n", - "1\n", - "2\n", - "3\n", - "4\n", - "\n", - "2-element SLArray{Tuple{2},Int64,1,2,(:expression, :xFwd6)} with indices SOneTo(2):\n", - " :expression => 2\n", - " :xFwd6 => 5\n", - "4-element SLArray{Tuple{4},Int64,1,4,(:A, :B, :C, :D)} with indices SOneTo(4):\n", - " :A => 1\n", - " :B => 2\n", - " :C => 3\n", - " :D => 4\n" + "2\n5\n1\n2\n3\n4\n\n2-element SLArray{Tuple{2},Int64,1,2,(:expression, :xFwd6)} with indices SOneTo(2):\n :expression => 2\n :xFwd6 => 5\n4-element SLArray{Tuple{4},Int64,1,4,(:A, :B, :C, :D)} with indices SOneTo(4):\n :A => 1\n :B => 2\n :C => 3\n :D => 4\n2" ] } ] @@ -97,6 +84,13 @@ "arrPart2 = ArrayPartition(binding, vRev, expression, xFwd6)" ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "code", "execution_count": 14, From 170a21a32c99a5880addb839ba39565b800469b7 Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Mon, 9 Nov 2020 18:46:13 -0800 Subject: [PATCH 12/17] labelled arrays notebook update --- recursive.ipynb | 260 ++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 254 insertions(+), 6 deletions(-) diff --git a/recursive.ipynb b/recursive.ipynb index 01f66f2..adc0c30 100644 --- a/recursive.ipynb +++ b/recursive.ipynb @@ -23,7 +23,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -49,13 +49,28 @@ ], "cell_type": "code", "metadata": {}, - "execution_count": 4, + "execution_count": 3, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ - "2\n5\n1\n2\n3\n4\n\n2-element SLArray{Tuple{2},Int64,1,2,(:expression, :xFwd6)} with indices SOneTo(2):\n :expression => 2\n :xFwd6 => 5\n4-element SLArray{Tuple{4},Int64,1,4,(:A, :B, :C, :D)} with indices SOneTo(4):\n :A => 1\n :B => 2\n :C => 3\n :D => 4\n2" + "2\n", + "5\n", + "1\n", + "2\n", + "3\n", + "4\n", + "\n", + "2-element SLArray{Tuple{2},Int64,1,2,(:expression, :xFwd6)} with indices SOneTo(2):\n", + " :expression => 2\n", + " :xFwd6 => 5\n", + "4-element SLArray{Tuple{4},Int64,1,4,(:A, :B, :C, :D)} with indices SOneTo(4):\n", + " :A => 1\n", + " :B => 2\n", + " :C => 3\n", + " :D => 4\n", + "2" ] } ] @@ -86,10 +101,20 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 20, "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "ArrayPartition{Int64,Tuple{SLArray{Tuple{2},Int64,1,2,(:expression, :xFwd6)},SLArray{Tuple{4},Int64,1,4,(:A, :B, :C, :D)}}}" + ] + } + ], + "source": [ + "print(typeof(arrPart))" + ] }, { "cell_type": "code", @@ -118,6 +143,229 @@ "end\n", "# don't think I can access the labelled values so I'm not sure how to use labelled arrays" ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "text/plain": [ + "ArrayPartition{T,Tuple{SLArray{Tuple{3},T,1,3,(:AM, :MT, :AT)},SLArray{Tuple{3},T,1,3,(:AM, :MT, :AT)}}} where T" + ] + }, + "metadata": {}, + "execution_count": 12 + } + ], + "source": [ + "bind{T} = LabelledArrays.@SLVector T (:AM, :MT, :AT)\n", + "bPart{T} = ArrayPartition{T, Tuple{bind{T}, bind{T}}}" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "text/plain": [ + "ArrayPartition{T,Tuple{SLArray{Tuple{10},T,1,10,(:xRev1, :xRev2, :xRev3, :xRev4, :xRev5, :xRev6, :xRev7, :xRev8, :xRev9, :xRev10)},SLArray{Tuple{2},T,1,2,(:xFwd15, :xFwd16)}}} where T" + ] + }, + "metadata": {}, + "execution_count": 10 + } + ], + "source": [ + "#hetRates{T}\n", + "xRev10{T} = LabelledArrays.@SLVector T (:xRev1, :xRev2, :xRev3, :xRev4, :xRev5, :xRev6, :xRev7, :xRev8, :xRev9, :xRev10)\n", + "hetArr{T} = LabelledArrays.@SLVector T (:xFwd15, :xFwd16)\n", + "\n", + "hetRates{T} = ArrayPartition{T,\n", + " Tuple{\n", + " xRev10{T},\n", + " hetArr{T}\n", + " }\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "text/plain": [ + "SLArray{Tuple{3},ArrayPartition{T,Tuple{SLArray{Tuple{10},T,1,10,(:xRev1, :xRev2, :xRev3, :xRev4, :xRev5, :xRev6, :xRev7, :xRev8, :xRev9, :xRev10)},SLArray{Tuple{2},T,1,2,(:xFwd15, :xFwd16)}}},1,3,(:AM, :MT, :AT)} where T" + ] + }, + "metadata": {}, + "execution_count": 11 + } + ], + "source": [ + "TAMsType{T} = LabelledArrays.@SLVector TAMrates{T} (:Axl, :MerTK, :Tyro3)\n", + "hetRType{T} = LabelledArrays.@SLVector hetRates{T} (:AM, :MT, :AT)" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "output_type": "execute_result", + "data": { + "text/plain": [ + "ArrayPartition{T,Tuple{SLArray{Tuple{3},ArrayPartition{T,Tuple{SLArray{Tuple{4},T,1,4,(:bind1, :bind2, :bind3, :bind4)},SLArray{Tuple{6},T,1,6,(:xRev1, :xRev2, :xRev3, :xRev4, :xRev5, :xRev6)},SLArray{Tuple{2},T,1,2,(:expression, :xFwd6)}}},1,3,(:Axl, :MerTK, :Tyro3)},SLArray{Tuple{7},T,1,7,(:internalize, :pYinternalize, :fElse, :kRec, :kDeg, :xFwd, :gasCur)},SLArray{Tuple{3},ArrayPartition{T,Tuple{SLArray{Tuple{10},T,1,10,(:xRev1, :xRev2, :xRev3, :xRev4, :xRev5, :xRev6, :xRev7, :xRev8, :xRev9, :xRev10)},SLArray{Tuple{2},T,1,2,(:xFwd15, :xFwd16)}}},1,3,(:AM, :MT, :AT)}}} where T" + ] + }, + "metadata": {}, + "execution_count": 14 + } + ], + "source": [ + "#Rates{T}\n", + "RatesArr{T} = LabelledArrays.@SLVector T (:internalize, :pYinternalize, :fElse, :kRec, :kDeg, :xFwd, :gasCur)\n", + "\n", + "Rates{T} = ArrayPartition{T,\n", + " Tuple{\n", + " TAMsType{T},\n", + " RatesArr{T},\n", + " hetRType{T}\n", + " }\n", + "}" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "4-element SLArray{Tuple{4},Int64,1,4,(:bind1, :bind2, :bind3, :bind4)} with indices SOneTo(4):\n :bind1 => 0\n :bind2 => 1\n :bind3 => 2\n :bind4 => 3\n6-element SLArray{Tuple{6},Int64,1,6,(:xRev1, :xRev2, :xRev3, :xRev4, :xRev5, :xRev6)} with indices SOneTo(6):\n :xRev1 => 4\n :xRev2 => 5\n :xRev3 => 6\n :xRev4 => 7\n :xRev5 => 8\n :xRev6 => 9\n2-element SLArray{Tuple{2},Int64,1,2,(:expression, :xFwd6)} with indices SOneTo(2):\n :expression => 20\n :xFwd6 => 30\nPrinting binding values...\n0123\nPrinting xRev elements\n456789\nPrinting expression and xFwd6...\n2030\n" + ] + } + ], + "source": [ + "###################### Version 1 #####################\n", + "#TAMrates1{T}\n", + "binding{T} = LabelledArrays.@SLVector T (:bind1, :bind2, :bind3, :bind4)\n", + "xRev6{T} = LabelledArrays.@SLVector T (:xRev1, :xRev2, :xRev3, :xRev4, :xRev5, :xRev6)\n", + "TAMarr{T} = LabelledArrays.@SLVector T (:expression, :xFwd6)\n", + "\n", + "TAMrates1{T} = ArrayPartition{T, \n", + " Tuple{\n", + " binding{T}, \n", + " xRev6{T}, \n", + " TAMarr{T}\n", + " }\n", + "}\n", + "\n", + "### Construction\n", + "\n", + "test = TAMrates1{Int64}((binding{Int64}(0,1,2,3), xRev6{Int64}(4,5,6,7,8,9), TAMarr{Int64}(20, 30)))\n", + "\n", + "### Accessing\n", + "\n", + "## In general to access each subarray in the array partition, use array_partition_name.x\n", + "## x is suscriptable so for TAMrates, x[1] is the binding vector, x[2] is the xRev vector, x[3] is the labelled array with expression and xFwd6\n", + "\n", + "for x in test.x\n", + " println(x)\n", + "end\n", + "\n", + "##access by label elements\n", + "println(\"Printing binding values...\")\n", + "println(test.x[1].bind1, test.x[1].bind2, test.x[1].bind3, test.x[1].bind4)\n", + "println(\"Printing xRev elements\")\n", + "println(test.x[2].xRev1, test.x[2].xRev2, test.x[2].xRev3, test.x[2].xRev4, test.x[2].xRev5, test.x[2].xRev6)\n", + "println(\"Printing expression and xFwd6...\")\n", + "println(test.x[3].expression, test.x[3].xFwd6)\n", + "\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "output_type": "error", + "ename": "LoadError", + "evalue": "type Tuple has no field binding", + "traceback": [ + "type Tuple has no field binding", + "", + "Stacktrace:", + " [1] getproperty(::Tuple{SLArray{Tuple{4},Int64,1,4,(:bind1, :bind2, :bind3, :bind4)},SLArray{Tuple{6},Int64,1,6,(:xRev1, :xRev2, :xRev3, :xRev4, :xRev5, :xRev6)},SLArray{Tuple{2},Int64,1,2,(:expression, :xFwd6)}}, ::Symbol) at ./Base.jl:33", + " [2] top-level scope at In[13]:2", + " [3] include_string(::Function, ::Module, ::String, ::String) at ./loading.jl:1091", + " [4] execute_code(::String, ::String) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/execute_request.jl:27", + " [5] execute_request(::ZMQ.Socket, ::IJulia.Msg) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/execute_request.jl:86", + " [6] #invokelatest#1 at ./essentials.jl:710 [inlined]", + " [7] invokelatest at ./essentials.jl:709 [inlined]", + " [8] eventloop(::ZMQ.Socket) at /home/sumedhak/.julia/packages/IJulia/rWZ9e/src/eventloop.jl:8", + " [9] (::IJulia.var\"#15#18\")() at ./task.jl:356" + ] + } + ], + "source": [ + "#we can't access the binding or xRev vector by name with this structure because x isn't a labelled tuple\n", + "\n", + "println(test.x.binding) \n", + "println(test.x[binding])" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Accessing by label...\n[1, 2, 3, 4] 2 5\nPrinting directly from arrayPart...\n[1, 2, 3, 4]\n2\n5\n" + ] + } + ], + "source": [ + "## Ideally, we want to be able to do something like test.x[1].binding the same way we do from expression and xFwd6 which are single values\n", + "\n", + "#This allows for such access\n", + "arr = SLVector(binding = [1,2,3,4], expression = 2, xFwd6 = 5)\n", + "arrayPart = ArrayPartition(arr)\n", + "\n", + "#Accessing\n", + "println(\"Accessing by label...\")\n", + "println(arrayPart.x[1].binding, \" \", arrayPart.x[1].expression, \" \", arrayPart.x[1].xFwd6)\n", + "\n", + "\n", + "# the problem is that the binding vector elements aren't treated separately in the array partition which is what I think we want for improving efficiency\n", + "println(\"Printing directly from arrayPart...\")\n", + "for x in arrayPart\n", + " println(x)\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ] } \ No newline at end of file From 4ed013bbb3940fda1523e64df66334b2e0b5e5a7 Mon Sep 17 00:00:00 2001 From: Aaron Meyer Date: Mon, 9 Nov 2020 19:55:55 -0800 Subject: [PATCH 13/17] Fix Manifest --- Manifest.toml | 108 +++++++++++++------------------------------------- 1 file changed, 27 insertions(+), 81 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 8fcd2f1..7d3cb9c 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -71,12 +71,6 @@ git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9" uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" version = "1.0.0" -[[AxisAlgorithms]] -deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] -git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9" -uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" -version = "1.0.0" - [[AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] git-tree-sha1 = "f31f50712cbdf40ee8287f0443b57503e34122ef" @@ -116,18 +110,6 @@ git-tree-sha1 = "2ac27f59196a68070e132b25713f9a5bbc5fa0d2" uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" version = "0.8.3" -[[Calculus]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" -uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" -version = "0.5.1" - -[[CategoricalArrays]] -deps = ["DataAPI", "Future", "JSON", "Missings", "Printf", "Statistics", "StructTypes", "Unicode"] -git-tree-sha1 = "2ac27f59196a68070e132b25713f9a5bbc5fa0d2" -uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" -version = "0.8.3" - [[ChainRules]] deps = ["ChainRulesCore", "ChainRulesTestUtils", "Compat", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"] git-tree-sha1 = "f6265a7e32d2c82e9462a06e0d5066284c29b89e" @@ -148,9 +130,9 @@ version = "0.5.3" [[CodeTracking]] deps = ["InteractiveUtils", "UUIDs"] -git-tree-sha1 = "8ad457cfeb0bca98732c97958ef81000a543e73e" +git-tree-sha1 = "ce725fcc331618c422e5561a5183baab6a00482c" uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" -version = "1.0.5" +version = "1.0.4" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"] @@ -287,10 +269,10 @@ deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "9c41285c57c6e0d73a21ed4b65f6eec34805f937" +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "StaticArrays", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "501c11d708917ca09ce357bed163dbaf0f30229f" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.23.8" +version = "0.23.12" [[DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "DiffRules", "Distributions", "FillArrays", "ForwardDiff", "LinearAlgebra", "NaNMath", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsBase", "StatsFuns", "ZygoteRules"] @@ -311,10 +293,10 @@ uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" version = "0.9.6" [[EarCut_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "92d8f9f208637e8d2d28c664051a00569c01493d" +deps = ["Libdl", "Pkg"] +git-tree-sha1 = "eabac56550a7d7e0be499125673fbff560eb8b20" uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.1.5+1" +version = "2.1.5+0" [[EllipsisNotation]] git-tree-sha1 = "65dad386e877850e6fce4fc77f60fe75a468ce9d" @@ -357,18 +339,6 @@ git-tree-sha1 = "f10c3009373a2d5c4349b8a2932d8accb892892d" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" version = "3.3.9+6" -[[FFTW]] -deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"] -git-tree-sha1 = "8b7c16b56936047ca41bf25effa137ae0b381ae8" -uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.2.4" - -[[FFTW_jll]] -deps = ["Libdl", "Pkg"] -git-tree-sha1 = "6c975cd606128d45d1df432fb812d6eb10fee00b" -uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.9+5" - [[FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" uuid = "9aa1b823-49e4-5ca5-8b0f-3971ec8bab6a" @@ -560,9 +530,9 @@ version = "0.21.1" [[JuliaInterpreter]] deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"] -git-tree-sha1 = "899ae4c83ad6f4fa36f31d735c758bb756c03254" +git-tree-sha1 = "8f1c59bbca30b0d293f4b2436af49ef4c9c4d601" uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a" -version = "0.8.3" +version = "0.8.2" [[Juno]] deps = ["Base64", "Logging", "Media", "Profile"] @@ -595,9 +565,9 @@ version = "1.3.0" [[Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "a8bea922a4678d5d2314b2fc97df0170a2271126" +git-tree-sha1 = "73292a3259e0141521753065c1df0f91c7e4d5e6" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.14.3" +version = "0.14.2" [[LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] @@ -626,9 +596,9 @@ version = "0.4.2" [[LightGraphs]] deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "6f85a35d2377cb2db1bc448ed0d6340d2bb1ea64" +git-tree-sha1 = "a0d4bcea4b9c056da143a5ded3c2b7f7740c2d41" uuid = "093fc24a-ae57-5d10-9952-331d41423f4d" -version = "1.3.3" +version = "1.3.0" [[LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -669,9 +639,9 @@ version = "0.8.26" [[LoweredCodeUtils]] deps = ["JuliaInterpreter"] -git-tree-sha1 = "6f681c69f95cf2b9b04328bea3f03122b750d34e" +git-tree-sha1 = "92b9819125eac5013c99070f696ec0ec5fc66436" uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b" -version = "1.2.5" +version = "1.2.4" [[MCMCChains]] deps = ["AbstractFFTs", "AbstractMCMC", "AxisArrays", "Compat", "Distributions", "Formatting", "IteratorInterfaceExtensions", "LinearAlgebra", "MLJModelInterface", "NaturalSort", "PrettyTables", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase", "TableTraits", "Tables"] @@ -685,12 +655,6 @@ git-tree-sha1 = "eb540ede3aabb8284cb482aa41d00d6ca850b1f8" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" version = "2020.2.254+0" -[[MKL_jll]] -deps = ["IntelOpenMP_jll", "Libdl", "Pkg"] -git-tree-sha1 = "eb540ede3aabb8284cb482aa41d00d6ca850b1f8" -uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2020.2.254+0" - [[MLJModelInterface]] deps = ["Random", "ScientificTypes"] git-tree-sha1 = "a63e200c4d8bfb3820db9849cc1950a91ddad761" @@ -751,10 +715,10 @@ uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" version = "0.2.2" [[NLSolversBase]] -deps = ["Calculus", "DiffEqDiffTools", "DiffResults", "Distributed", "ForwardDiff"] -git-tree-sha1 = "f1b8ed89fa332f410cfc7c937682eb4d0b361521" +deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] +git-tree-sha1 = "39d6bc45e99c96e6995cbddac02877f9b61a1dd1" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.5.0" +version = "7.7.1" [[NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -764,9 +728,9 @@ version = "4.4.1" [[NNlib]] deps = ["Libdl", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "a8180fd1445e31c0b1add98dae8da694ac2c23fd" +git-tree-sha1 = "1ef04283efe283be08e2d0de842f5e5286dd0b7a" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.7.6" +version = "0.7.5" [[NaNMath]] git-tree-sha1 = "c84c576296d0e2fbb3fc134d3e09086b3ea617cd" @@ -808,12 +772,6 @@ git-tree-sha1 = "9db77584158d0ab52307f8c04f8e7c08ca76b5b3" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.3+4" -[[Optim]] -deps = ["Compat", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "c05aa6b694d426df87ff493306c1c5b4b215e148" -uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "0.22.0" - [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "f9d57f4126c39565e05a2b0264df99f497fc6f37" @@ -827,9 +785,9 @@ version = "1.3.2" [[OrdinaryDiffEq]] deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "GenericSVD", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "4aa8e19a72d6b69ca139de2696d25d9f710ca246" +git-tree-sha1 = "50724f6881234caa4f928473f50ce966b08aa4ed" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "5.44.0" +version = "5.43.0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse", "Test"] @@ -877,18 +835,6 @@ git-tree-sha1 = "b1333d4eced1826e15adbdf01a4ecaccca9d353c" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" version = "0.5.3" -[[PooledArrays]] -deps = ["DataAPI"] -git-tree-sha1 = "b1333d4eced1826e15adbdf01a4ecaccca9d353c" -uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" -version = "0.5.3" - -[[PositiveFactorizations]] -deps = ["LinearAlgebra", "Test"] -git-tree-sha1 = "127c47b91990c101ee3752291c4f45640eeb03d1" -uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" -version = "0.2.3" - [[PrettyTables]] deps = ["Crayons", "Formatting", "Parameters", "Reexport", "Tables"] git-tree-sha1 = "8458dc04a493ae5c2fed3796c1d3117972c69694" @@ -976,9 +922,9 @@ version = "1.0.3" [[Revise]] deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"] -git-tree-sha1 = "3afd4b8001d03475369e6eb55c00bf15609b9289" +git-tree-sha1 = "bfe3d98de018f96d472029b00f6a14478a042171" uuid = "295af30f-e4ad-537b-8983-00126c2a3abe" -version = "3.1.7" +version = "3.1.6" [[Richardson]] deps = ["LinearAlgebra"] @@ -1064,9 +1010,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SparseDiffTools]] deps = ["Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "LightGraphs", "LinearAlgebra", "Requires", "SparseArrays", "VertexSafeGraphs"] -git-tree-sha1 = "1d93f44332d3270963d7f4d87217367397cb8746" +git-tree-sha1 = "69de355cb5e2b9a0e89f383c1762bba5ae70b580" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "1.10.1" +version = "1.10.0" [[SpecialFunctions]] deps = ["OpenSpecFun_jll"] From 6b8e5200ba69a68db0dba2a9123263bed9b931bf Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Mon, 23 Nov 2020 11:48:25 -0800 Subject: [PATCH 14/17] added flatten and unflatten functions --- src/types.jl | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/src/types.jl b/src/types.jl index d11b149..a701376 100644 --- a/src/types.jl +++ b/src/types.jl @@ -55,3 +55,27 @@ mutable struct Lsrates{T} curL::MVector{2, T} xFwd::T end + +function flatten(d::Union{TAMrates{T}, hetRates{T}, Rates{T}, comprates{T}, Lsrates{T}, TAMsType{T}, hetRType{T}}) where{T} + arr::ArrayPartition{T} + if d isa TAMrates{T} + arr = ArrayPartition(d.binding, d.xRev, d.expression, d.xFwd6) + elseif d isa hetRates{T} + arr = ArrayPartition(d.xRev, d.xFwd15, d.xFwd16) + elseif d isa Rates{T} + arr = ArrayPartition(flatten(d.TAMs), d.internalize, d.pYinternalize, d.fElse, d.kRec, d.kDeg, d.xFwd, d.gasCur, flatten(d.hetR)) + elseif d isa comprates{T} + arr = ArrayPartition(flatten(d.TAMs), d.diff, d.gasPart, d.gasCur, d.xFwd, flatten(d.hetR)) + elseif d isa Lsrates{T} + arr = ArrayPartition(d.GBinding, d.PBinding, d.xRev, d.xFwd27, d.xFwd29, d.kRec, d.kDeg, d.fElse, d.internalize, d.pYinternalize, d.expression, d.curL, d.xFwd) + elseif d isa TAMsType{T} + arr = ArrayPartition(flatten(d.Axl), flatten(d.MerTK), flatten(d.Tyro3)) + elseif d isa hetRates{T} + arr = ArrayPartition(flatten(d.AM), flatten(d.MT), flatten(d.TM)) + return arr +end + +#works for TAMrates, hetRates, LsRates +function unflatten(a::ArrayPartition{T}, type::DataType) where{T} + return type(a.x...) +end From 424a3da6e290ed205430e15982a7d9de68456942 Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Sat, 28 Nov 2020 13:28:43 -0800 Subject: [PATCH 15/17] updated Manifest --- Manifest.toml | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 9505c8c..a614986 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -136,9 +136,9 @@ version = "0.5.3" [[CodeTracking]] deps = ["InteractiveUtils", "UUIDs"] -git-tree-sha1 = "ce725fcc331618c422e5561a5183baab6a00482c" +git-tree-sha1 = "8ad457cfeb0bca98732c97958ef81000a543e73e" uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" -version = "1.0.4" +version = "1.0.5" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"] @@ -299,10 +299,10 @@ uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" version = "0.9.7" [[EarCut_jll]] -deps = ["Libdl", "Pkg"] -git-tree-sha1 = "eabac56550a7d7e0be499125673fbff560eb8b20" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "92d8f9f208637e8d2d28c664051a00569c01493d" uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.1.5+0" +version = "2.1.5+1" [[EllipsisNotation]] git-tree-sha1 = "65dad386e877850e6fce4fc77f60fe75a468ce9d" @@ -572,9 +572,9 @@ version = "2.0.1+3" [[JuliaInterpreter]] deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"] -git-tree-sha1 = "8f1c59bbca30b0d293f4b2436af49ef4c9c4d601" +git-tree-sha1 = "899ae4c83ad6f4fa36f31d735c758bb756c03254" uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a" -version = "0.8.2" +version = "0.8.3" [[Juno]] deps = ["Base64", "Logging", "Media", "Profile"] @@ -735,9 +735,9 @@ version = "0.8.26" [[LoweredCodeUtils]] deps = ["JuliaInterpreter"] -git-tree-sha1 = "92b9819125eac5013c99070f696ec0ec5fc66436" +git-tree-sha1 = "6f681c69f95cf2b9b04328bea3f03122b750d34e" uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b" -version = "1.2.4" +version = "1.2.5" [[MCMCChains]] deps = ["AbstractFFTs", "AbstractMCMC", "AxisArrays", "Compat", "Distributions", "Formatting", "IteratorInterfaceExtensions", "LinearAlgebra", "MLJModelInterface", "NaturalSort", "PrettyTables", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase", "TableTraits", "Tables"] @@ -824,9 +824,9 @@ version = "4.4.1" [[NNlib]] deps = ["Libdl", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "1ef04283efe283be08e2d0de842f5e5286dd0b7a" +git-tree-sha1 = "a8180fd1445e31c0b1add98dae8da694ac2c23fd" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.7.5" +version = "0.7.6" [[NaNMath]] git-tree-sha1 = "c84c576296d0e2fbb3fc134d3e09086b3ea617cd" @@ -1042,9 +1042,9 @@ version = "1.0.3" [[Revise]] deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"] -git-tree-sha1 = "bfe3d98de018f96d472029b00f6a14478a042171" +git-tree-sha1 = "3afd4b8001d03475369e6eb55c00bf15609b9289" uuid = "295af30f-e4ad-537b-8983-00126c2a3abe" -version = "3.1.6" +version = "3.1.7" [[Richardson]] deps = ["LinearAlgebra"] @@ -1130,9 +1130,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SparseDiffTools]] deps = ["Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "LightGraphs", "LinearAlgebra", "Requires", "SparseArrays", "VertexSafeGraphs"] -git-tree-sha1 = "69de355cb5e2b9a0e89f383c1762bba5ae70b580" +git-tree-sha1 = "1d93f44332d3270963d7f4d87217367397cb8746" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "1.10.0" +version = "1.10.1" [[SpecialFunctions]] deps = ["OpenSpecFun_jll"] @@ -1462,4 +1462,4 @@ version = "3.0.0+3" deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" +version = "0.9.1+5" \ No newline at end of file From fde4a354b5719ba23896f41df2bea29fdc51e244 Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Sat, 28 Nov 2020 14:35:57 -0800 Subject: [PATCH 16/17] bug fix --- src/types.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/types.jl b/src/types.jl index a701376..f1214f9 100644 --- a/src/types.jl +++ b/src/types.jl @@ -72,6 +72,7 @@ function flatten(d::Union{TAMrates{T}, hetRates{T}, Rates{T}, comprates{T}, Lsra arr = ArrayPartition(flatten(d.Axl), flatten(d.MerTK), flatten(d.Tyro3)) elseif d isa hetRates{T} arr = ArrayPartition(flatten(d.AM), flatten(d.MT), flatten(d.TM)) + end return arr end From 811211b95d1306e81ad7fbba849179a4f420b173 Mon Sep 17 00:00:00 2001 From: sumedha-k Date: Sat, 28 Nov 2020 17:59:00 -0800 Subject: [PATCH 17/17] update to manifest --- Manifest.toml | 88 +++++++++++++++++++++++++-------------------------- 1 file changed, 44 insertions(+), 44 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index a614986..526802d 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -88,9 +88,9 @@ version = "0.5.0" [[Bijectors]] deps = ["ArgCheck", "Compat", "Distributions", "LinearAlgebra", "MappedArrays", "NNlib", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics", "StatsFuns"] -git-tree-sha1 = "3e2637ad074d5e626da6298632e05e57cc4ff27f" +git-tree-sha1 = "9a0f332a5873e81c420477ad9cea001c7484e3d0" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.8.7" +version = "0.8.8" [[BinaryProvider]] deps = ["Libdl", "Logging", "SHA"] @@ -118,15 +118,15 @@ version = "0.8.3" [[ChainRules]] deps = ["ChainRulesCore", "ChainRulesTestUtils", "Compat", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"] -git-tree-sha1 = "f6265a7e32d2c82e9462a06e0d5066284c29b89e" +git-tree-sha1 = "118fad132f286ac9df765e0dda94ddba2f0fb279" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "0.7.32" +version = "0.7.33" [[ChainRulesCore]] deps = ["LinearAlgebra", "MuladdMacro", "SparseArrays"] -git-tree-sha1 = "aebbda0a7c644bd8739b34f2a1b1e48f114aab49" +git-tree-sha1 = "007f084f0136c0e2d87d3ac53e9d8eab06cec27f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "0.9.17" +version = "0.9.19" [[ChainRulesTestUtils]] deps = ["ChainRulesCore", "Compat", "FiniteDifferences", "LinearAlgebra", "Random", "Test"] @@ -222,10 +222,10 @@ uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.4.0" [[DataFrames]] -deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "ecd850f3d2b815431104252575e7307256121548" +deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "20159837c2e5e196793a313cd700b8199fd8f985" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "0.21.8" +version = "0.22.1" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -260,9 +260,9 @@ version = "1.0.2" [[DiffRules]] deps = ["NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "eb0c34204c8410888844ada5359ac8b96292cfd1" +git-tree-sha1 = "214c3fcac57755cfda163d91c58893a8723f93e9" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.0.1" +version = "1.0.2" [[Distances]] deps = ["LinearAlgebra", "Statistics"] @@ -282,9 +282,9 @@ version = "0.23.12" [[DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "DiffRules", "Distributions", "FillArrays", "ForwardDiff", "LinearAlgebra", "NaNMath", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsBase", "StatsFuns", "ZygoteRules"] -git-tree-sha1 = "309458fa6cd189cb080a349130918ace2bce0256" +git-tree-sha1 = "f9348ae225e7168a04f7cec7a562bd0d86657e53" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" -version = "0.6.9" +version = "0.6.11" [[DocStringExtensions]] deps = ["LibGit2", "Markdown", "Pkg", "Test"] @@ -373,9 +373,9 @@ version = "2.7.1" [[FiniteDifferences]] deps = ["ChainRulesCore", "LinearAlgebra", "Printf", "Random", "Richardson"] -git-tree-sha1 = "5ef56eea8b65c2ed2d11bd394629892201369b23" +git-tree-sha1 = "e62dc2e6c482bbbe97e79f875063285257daa142" uuid = "26cc04aa-876d-5657-8c51-4c34ba976000" -version = "0.11.2" +version = "0.11.3" [[FixedPointNumbers]] deps = ["Statistics"] @@ -735,15 +735,15 @@ version = "0.8.26" [[LoweredCodeUtils]] deps = ["JuliaInterpreter"] -git-tree-sha1 = "6f681c69f95cf2b9b04328bea3f03122b750d34e" +git-tree-sha1 = "9af25a91bda16307caff2a50f9c744c432b8bc1b" uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b" -version = "1.2.5" +version = "1.2.6" [[MCMCChains]] deps = ["AbstractFFTs", "AbstractMCMC", "AxisArrays", "Compat", "Distributions", "Formatting", "IteratorInterfaceExtensions", "LinearAlgebra", "MLJModelInterface", "NaturalSort", "PrettyTables", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase", "TableTraits", "Tables"] -git-tree-sha1 = "878a89e412ec091baccfad98da59dc230a2f1e04" +git-tree-sha1 = "1915b448ec72dcd7adc87e957500976e1c07cd62" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "4.2.4" +version = "4.3.1" [[MKL_jll]] deps = ["IntelOpenMP_jll", "Libdl", "Pkg"] @@ -823,15 +823,15 @@ uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" version = "4.4.1" [[NNlib]] -deps = ["Libdl", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "a8180fd1445e31c0b1add98dae8da694ac2c23fd" +deps = ["Compat", "Libdl", "LinearAlgebra", "Pkg", "Requires", "Statistics"] +git-tree-sha1 = "1ae42464fea5258fd2ff49f1c4a40fc41cba3860" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.7.6" +version = "0.7.7" [[NaNMath]] -git-tree-sha1 = "c84c576296d0e2fbb3fc134d3e09086b3ea617cd" +git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.4" +version = "0.3.5" [[NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] @@ -881,9 +881,9 @@ version = "1.3.2" [[OrdinaryDiffEq]] deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "ExponentialUtilities", "FastClosures", "FiniteDiff", "ForwardDiff", "GenericSVD", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "NLsolve", "RecursiveArrayTools", "Reexport", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "7ea4d187575fb5256409d755819afb66e1812f2b" +git-tree-sha1 = "e782c1ff432a6ba8677b6fced19a92a6878a5c68" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "5.45.0" +version = "5.45.1" [[PCRE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -933,9 +933,9 @@ version = "1.0.7" [[Plots]] deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"] -git-tree-sha1 = "892484bb5c9feefb46a3e3064721d4e50d02e5cf" +git-tree-sha1 = "173c7250ccd7c98615b04c669eb13fa7fab494b0" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.9.0" +version = "1.9.1" [[PooledArrays]] deps = ["DataAPI"] @@ -944,10 +944,10 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" version = "0.5.3" [[PrettyTables]] -deps = ["Crayons", "Formatting", "Parameters", "Reexport", "Tables"] -git-tree-sha1 = "8458dc04a493ae5c2fed3796c1d3117972c69694" +deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] +git-tree-sha1 = "237170206bf38a66fee4d845f4ae57f63788eeb0" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "0.9.1" +version = "0.10.1" [[Printf]] deps = ["Unicode"] @@ -976,10 +976,10 @@ uuid = "784f63db-0788-585a-bace-daefebcd302b" version = "2019.1.0+2" [[Qt_jll]] -deps = ["Fontconfig_jll", "Glib_jll", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] -git-tree-sha1 = "b3979580c712b167a131bd1a4152a840d6df89cb" +deps = ["Artifacts", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] +git-tree-sha1 = "72244a8e084251aea25968c61bbf5c001aaa7d5a" uuid = "ede63266-ebff-546c-83e0-1c6fb6d0efc8" -version = "5.15.0+3" +version = "5.15.1+0" [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] @@ -1036,15 +1036,15 @@ version = "0.2.0" [[Requires]] deps = ["UUIDs"] -git-tree-sha1 = "2fc2e1ab606a5dca7bbad9036a694553c3a57926" +git-tree-sha1 = "e05c53ebc86933601d36212a93b39144a2733493" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.0.3" +version = "1.1.1" [[Revise]] deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"] -git-tree-sha1 = "3afd4b8001d03475369e6eb55c00bf15609b9289" +git-tree-sha1 = "637d03a5262b9f1d334cd63aaf092297fbc4f168" uuid = "295af30f-e4ad-537b-8983-00126c2a3abe" -version = "3.1.7" +version = "3.1.9" [[Richardson]] deps = ["LinearAlgebra"] @@ -1086,9 +1086,9 @@ uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" version = "0.5.5" [[ScientificTypes]] -git-tree-sha1 = "b06fff5c17a20aa69494a3d9da62d9c88ec6b764" +git-tree-sha1 = "1d3f5f8bdf5dd0c9951eb9c595ee08a728aec331" uuid = "321657f4-b219-11e9-178b-2701a2544e81" -version = "1.1.0" +version = "1.1.1" [[Scratch]] deps = ["Dates"] @@ -1158,9 +1158,9 @@ version = "0.33.2" [[StatsFuns]] deps = ["Rmath", "SpecialFunctions"] -git-tree-sha1 = "04a5a8e6ab87966b43f247920eab053fd5fdc925" +git-tree-sha1 = "3b9f665c70712af3264b61c27a7e1d62055dafd1" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.5" +version = "0.9.6" [[StructArrays]] deps = ["Adapt", "DataAPI", "Tables"] @@ -1220,9 +1220,9 @@ version = "0.3.0" [[Turing]] deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedVI", "Bijectors", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker", "ZygoteRules"] -git-tree-sha1 = "0ee8eae03fc19c1ce36d6e598dffa2b523d4a8e2" +git-tree-sha1 = "d35cab4bd3f1d8feec9eea4855ee481ff310e4f4" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.14.10" +version = "0.14.11" [[UUIDs]] deps = ["Random", "SHA"]