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_freeze/posts/mid-domain-effect/index/execute-results/html.json
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"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", | ||
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_freeze/posts/siwalik-alien-flora/index/execute-results/html.json
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"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", | ||
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