added initial draft

_freeze/posts/mid-domain-effect/index/execute-results/html.json

@@ -0,0 +1,16 @@
+{
+  "hash": "0bfb805344fc884011935eedffdf9cb4",
+  "result": {
+    "markdown": "---\ntitle: \"Mid-domain Effect\"\n\nauthor:\n  - name: Abhishek Kumar\n    url: https://akumar.netlify.app\n    affiliation: Panjab University, Chandigarh\n    affiliation_url: https://puchd.ac.in\n    orcid: 0000-0003-2252-7623\n\ndate: 2023-03-21\n\nbibliography: refs.bib\n\ndraft: true\n\ngoogle-scholar: true\n  \nformat: \n  html: \n    default-image-extension: svg\n---\n\n\n## Introduction\n\n\n::: {.cell}\n\n```{.r .cell-code}\nmin.elev <- 300\nmax.elev <- 1500\ndomain <- c(min.elev, max.elev)\n\nplot(domain, c(0, domain[2]-domain[1]), \n     ylab=\"Range Size\", xlab=\"Range Midpoint\", type=\"n\")\n```\n\n::: {.cell-output-display}\n![](index_files/figure-html/unnamed-chunk-1-1.png){width=672}\n:::\n\n```{.r .cell-code}\npool.distris <-runif(200, 0, domain[2]-domain[1])\nhist(pool.distris)\n```\n\n::: {.cell-output-display}\n![](index_files/figure-html/unnamed-chunk-1-2.png){width=672}\n:::\n\n```{.r .cell-code}\nplot(domain, c(0,domain[2]-domain[1]), type=\"n\", \n     ylab=\"Range Size\", xlab=\"Range Midpoint\")\npolygon(x=c(domain[1], domain[1]+(domain[2]-domain[1])/2, domain[2]), \n        y=c(0, domain[2]-domain[1], 0), col=\"grey90\", border=\"grey80\")\n```\n\n::: {.cell-output-display}\n![](index_files/figure-html/unnamed-chunk-1-3.png){width=672}\n:::\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\nfirst.range.size <-pool.distris[1]\nfirst.range.size\n```\n\n::: {.cell-output .cell-output-stdout}\n```\n[1] 540.6791\n```\n:::\n\n```{.r .cell-code}\nfirst.midpoint <-runif(1, domain[1]+( first.range.size/2), \n                       domain[2]-( first.range.size/2))\nfirst.midpoint\n```\n\n::: {.cell-output .cell-output-stdout}\n```\n[1] 1200.342\n```\n:::\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\nmidpoints <- lapply(\n  1:length(pool.distris),\n  function(x, pool.distris, domain){\n    runif(1, domain[1] + (pool.distris[x]/2), domain[2] - (pool.distris[x]/2))\n  },\n  pool.distris=pool.distris, domain=domain\n)\n\nmidpoints <- unlist(midpoints)\nhist(midpoints)\n```\n\n::: {.cell-output-display}\n![](index_files/figure-html/unnamed-chunk-3-1.png){width=672}\n:::\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\ncurrent.distris <- t(apply(\n  cbind(midpoints, pool.distris), 1,\n  function(x){\n    c(x[1] - (x[2]/2), x[1] + (x[2]/2))\n  }\n))\n\n\ncolnames(current.distris) <- c(\"lower_distri_limit\", \"upper_distri_limit\")\nhead(current.distris)\n```\n\n::: {.cell-output .cell-output-stdout}\n```\n     lower_distri_limit upper_distri_limit\n[1,]           909.6816          1450.3607\n[2,]           877.2127          1335.5652\n[3,]           598.5993          1324.4294\n[4,]           441.2734           978.3033\n[5,]           309.7641          1482.1332\n[6,]           943.1608          1461.2516\n```\n:::\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\nplot(domain, c(0, domain[2] - domain[1]), type=\"n\", \n     ylab = \"Range Size\", xlab = \"Range Midpoint\")\npolygon(x=c(domain[1], domain[1]+(domain[2]-domain[1])/2, domain[2]), \n        y=c(0, domain[2]-domain[1], 0), col=\"grey90\", border=\"grey80\")\n\napply(\n  current.distris, 1, \n  function(x){\n    lines(x = c(x[1], x[2]), y = rep(x[2] - x[1], 2), col=\"darkorange\", lwd=2)\n  }\n)\n```\n\n::: {.cell-output .cell-output-stdout}\n```\nNULL\n```\n:::\n\n```{.r .cell-code}\npoints(pool.distris ~ midpoints, cex=1, col=\"darkorange3\", pch=16)\n```\n\n::: {.cell-output-display}\n![](index_files/figure-html/unnamed-chunk-5-1.png){width=672}\n:::\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\n# The number of cells to be used\ndomain.cells <-20  \n\n# this will create a matrix with the upper and lower limits that define the cells \n\ncells.limits <- seq(domain[1], domain[2], length.out = domain.cells + 1)\ncells <- matrix(0, domain.cells, 3)\ncolnames(cells) <- c(\"lower_cell_limit\", \"upper_cell_limit\", \"richness\")\ncells[,1] <- cells.limits[1:domain.cells]\ncells[,2] <- cells.limits[2:(domain.cells + 1)]\n\n# this will create a composition matrix where rows are cells and columns are species. A 1 means the species is present in the cell, a 0 means it is absent.\nfinal.composition <- matrix(0, domain.cells, length(pool.distris))\ncolnames(final.composition) <- rownames(current.distris)\nrownames(final.composition) <- 1:domain.cells\n\nfor (j in 1:nrow(current.distris)) {\n  WhichCells <- intersect(which(cells[,1] < current.distris[j,2]), \n                          which(cells[,2] > current.distris[j,1]))\n  final.composition[WhichCells, j] <- 1\n}\n\n# this calculates the number of species in each cell\ncells[,3] <- rowSums(final.composition)\n```\n:::\n\n::: {.cell}\n\n```{.r .cell-code}\ncell.midpoints <- cells[,1] + ((cells[,2]-cells[,1])/2)\nplot(cells[,\"richness\"] ~ cell.midpoints, ylim=c(0, max(cells[,3])), \n     ylab=\"Species Richness\", xlab=\"Domain\", \n     pch=21, bg=\"grey60\", col=\"grey30\", cex=1.5)\n```\n\n::: {.cell-output-display}\n![](index_files/figure-html/unnamed-chunk-7-1.png){width=672}\n:::\n:::\n",
+    "supporting": [
+      "index_files"
+    ],
+    "filters": [
+      "rmarkdown/pagebreak.lua"
+    ],
+    "includes": {},
+    "engineDependencies": {},
+    "preserve": {},
+    "postProcess": true
+  }
+}

_freeze/posts/siwalik-alien-flora/index/execute-results/html.json

@@ -0,0 +1,18 @@
+{
+  "hash": "ad34e652f2cae7da8ba7a7641dd28be9",
+  "result": {
+    "markdown": "---\ntitle: \"Alien Flora of Indian Siwaliks\"\nauthor: \"Abhishek Kumar\"\n---\n\n::: {.cell}\n::: {.cell-output-display}\n```{=html}\n<div id=\"htmlwidget-e5161a653e726e9100f2\" style=\"width:100%;height:auto;\" class=\"datatables html-widget\"></div>\n<script type=\"application/json\" data-for=\"htmlwidget-e5161a653e726e9100f2\">{\"x\":{\"filter\":\"none\",\"vertical\":false,\"data\":[[\"1\",\"2\",\"3\",\"4\",\"5\"],[\"Ageratum conyzoides\",\"Lantana camara\",\"Parthenium hysterophorus\",\"Chromolaena odorata\",\"Tagetes minuta\"],[\"Invasive\",\"Invasive\",\"Invasive\",\"Invasive\",\"Invasive\"],[null,null,null,null,null]],\"container\":\"<table class=\\\"display\\\">\\n  <thead>\\n    <tr>\\n      <th> <\\/th>\\n      <th>Search<\\/th>\\n      <th>InvasionStatus<\\/th>\\n      <th>Origin<\\/th>\\n    <\\/tr>\\n  <\\/thead>\\n<\\/table>\",\"options\":{\"columnDefs\":[{\"orderable\":false,\"targets\":0}],\"order\":[],\"autoWidth\":false,\"orderClasses\":false}},\"evals\":[],\"jsHooks\":[]}</script>\n```\n:::\n:::\n",
+    "supporting": [],
+    "filters": [
+      "rmarkdown/pagebreak.lua"
+    ],
+    "includes": {
+      "include-in-header": [
+        "<script src=\"../../site_libs/htmlwidgets-1.5.4/htmlwidgets.js\"></script>\r\n<link href=\"../../site_libs/datatables-css-0.0.0/datatables-crosstalk.css\" rel=\"stylesheet\" />\r\n<script src=\"../../site_libs/datatables-binding-0.26/datatables.js\"></script>\r\n<script src=\"../../site_libs/jquery-3.6.0/jquery-3.6.0.min.js\"></script>\r\n<link href=\"../../site_libs/dt-core-1.12.1/css/jquery.dataTables.min.css\" rel=\"stylesheet\" />\r\n<link href=\"../../site_libs/dt-core-1.12.1/css/jquery.dataTables.extra.css\" rel=\"stylesheet\" />\r\n<script src=\"../../site_libs/dt-core-1.12.1/js/jquery.dataTables.min.js\"></script>\r\n<link href=\"../../site_libs/crosstalk-1.2.0/css/crosstalk.min.css\" rel=\"stylesheet\" />\r\n<script src=\"../../site_libs/crosstalk-1.2.0/js/crosstalk.min.js\"></script>\r\n"
+      ]
+    },
+    "engineDependencies": {},
+    "preserve": {},
+    "postProcess": true
+  }
+}