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MNPclimoseq_linetransects.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Mojave C climosequence line-intercept veg data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Creosote line transects\n"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>year</th><th scope=col>season</th><th scope=col>site</th><th scope=col>transect</th><th scope=col>start</th><th scope=col>stop</th><th scope=col>species</th><th scope=col>condition</th><th scope=col>notes</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>2017 </td><td>winter </td><td>Creosote </td><td>1 </td><td>0.00 </td><td>0.81 </td><td>soil </td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>Creosote </td><td>1 </td><td>0.81 </td><td>1.02 </td><td>biocrust </td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>Creosote </td><td>1 </td><td>1.02 </td><td>1.46 </td><td>soil </td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>Creosote </td><td>1 </td><td>1.46 </td><td>3.80 </td><td>creosote </td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>Creosote </td><td>1 </td><td>3.50 </td><td>3.70 </td><td>unk shrub </td><td>dead </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>Creosote </td><td>1 </td><td>3.80 </td><td>3.92 </td><td>unk grass 2</td><td> </td><td>NA </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllllllll}\n",
" year & season & site & transect & start & stop & species & condition & notes\\\\\n",
"\\hline\n",
"\t 2017 & winter & Creosote & 1 & 0.00 & 0.81 & soil & & NA \\\\\n",
"\t 2017 & winter & Creosote & 1 & 0.81 & 1.02 & biocrust & & NA \\\\\n",
"\t 2017 & winter & Creosote & 1 & 1.02 & 1.46 & soil & & NA \\\\\n",
"\t 2017 & winter & Creosote & 1 & 1.46 & 3.80 & creosote & & NA \\\\\n",
"\t 2017 & winter & Creosote & 1 & 3.50 & 3.70 & unk shrub & dead & NA \\\\\n",
"\t 2017 & winter & Creosote & 1 & 3.80 & 3.92 & unk grass 2 & & NA \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" year season site transect start stop species condition notes\n",
"1 2017 winter Creosote 1 0.00 0.81 soil NA \n",
"2 2017 winter Creosote 1 0.81 1.02 biocrust NA \n",
"3 2017 winter Creosote 1 1.02 1.46 soil NA \n",
"4 2017 winter Creosote 1 1.46 3.80 creosote NA \n",
"5 2017 winter Creosote 1 3.50 3.70 unk shrub dead NA \n",
"6 2017 winter Creosote 1 3.80 3.92 unk grass 2 NA "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"422"
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"422"
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"422"
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"[1] 422"
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"metadata": {},
"output_type": "display_data"
}
],
"source": [
"require(dplyr)\n",
"require(tidyr)\n",
"\n",
"veg.raw <- read.csv(\"~/data/gdrive_berkeley/MojaveCarbon/Data/VegTransects//LineTransects_Creosote.csv\", skip=1)\n",
"head(veg.raw)\n",
"\n",
"###cleaning\n",
"###########\n",
"\n",
"`%!in%` <- Negate(`%in%`) \n",
"remove <- c(\"0\", \"LITT\", \"UNKNO\", \"ROCK\", \"SOIL\", \"1SOIL\", \"SOIIL\", \"UNK\", \"SHRUB\", \"BRASS\", \"BFORB\", \"BOER\", \"BOGR\", \"GRASS\")\n",
"\n",
"#veg.raw <- subset(veg.raw, species %!in% remove) \n",
"nrow(veg.raw)\n",
"\n",
"veg.raw <- subset(veg.raw, condition != 'dead')\n",
"\n",
"\n",
"####finding cover value per individual\n",
"#######################################\n",
"veg.raw$cover_cm <- veg.raw$stop - veg.raw$start\n",
"\n",
"#finding largest cover value between seasons \n",
"veg.sum <- data.frame(summarise(group_by(veg.raw, year, species), cover_cm=sum(cover_cm)))\n",
"veg.max <- data.frame(summarise(group_by(veg.sum, year, species), max.cover_cm = max(cover_cm)))\n",
"\n",
"veg.sum$functionaltype <- 'shrub'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('unk grass 2')] <- 'grass'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('soil')] <- 'soil'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('biocrust')] <- 'biocrust'\n",
"\n",
"veg.sum$pct_cover <- veg.sum$cover_cm/250\n",
"\n",
"veg.sum.ft <- data.frame(summarise(group_by(veg.sum, functionaltype), pct_cover=sum(pct_cover)))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Creosote tables by species and functional type\n",
"\n",
"The last number here is total cover"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>year</th><th scope=col>species</th><th scope=col>cover_cm</th><th scope=col>functionaltype</th><th scope=col>pct_cover</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>2017 </td><td>Amsonia </td><td> 1.96 </td><td>shrub </td><td>0.00784 </td></tr>\n",
"\t<tr><td>2017 </td><td>biocrust </td><td> 7.67 </td><td>biocrust </td><td>0.03068 </td></tr>\n",
"\t<tr><td>2017 </td><td>Burro bush </td><td> 21.63 </td><td>shrub </td><td>0.08652 </td></tr>\n",
"\t<tr><td>2017 </td><td>creosote </td><td> 38.32 </td><td>shrub </td><td>0.15328 </td></tr>\n",
"\t<tr><td>2017 </td><td>hopsage </td><td> 0.61 </td><td>shrub </td><td>0.00244 </td></tr>\n",
"\t<tr><td>2017 </td><td>soil </td><td>170.86 </td><td>soil </td><td>0.68344 </td></tr>\n",
"\t<tr><td>2017 </td><td>unk grass 2</td><td> 8.81 </td><td>grass </td><td>0.03524 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllll}\n",
" year & species & cover\\_cm & functionaltype & pct\\_cover\\\\\n",
"\\hline\n",
"\t 2017 & Amsonia & 1.96 & shrub & 0.00784 \\\\\n",
"\t 2017 & biocrust & 7.67 & biocrust & 0.03068 \\\\\n",
"\t 2017 & Burro bush & 21.63 & shrub & 0.08652 \\\\\n",
"\t 2017 & creosote & 38.32 & shrub & 0.15328 \\\\\n",
"\t 2017 & hopsage & 0.61 & shrub & 0.00244 \\\\\n",
"\t 2017 & soil & 170.86 & soil & 0.68344 \\\\\n",
"\t 2017 & unk grass 2 & 8.81 & grass & 0.03524 \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" year species cover_cm functionaltype pct_cover\n",
"1 2017 Amsonia 1.96 shrub 0.00784 \n",
"2 2017 biocrust 7.67 biocrust 0.03068 \n",
"3 2017 Burro bush 21.63 shrub 0.08652 \n",
"4 2017 creosote 38.32 shrub 0.15328 \n",
"5 2017 hopsage 0.61 shrub 0.00244 \n",
"6 2017 soil 170.86 soil 0.68344 \n",
"7 2017 unk grass 2 8.81 grass 0.03524 "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>functionaltype</th><th scope=col>pct_cover</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>biocrust</td><td>0.03068 </td></tr>\n",
"\t<tr><td>grass </td><td>0.03524 </td></tr>\n",
"\t<tr><td>shrub </td><td>0.25008 </td></tr>\n",
"\t<tr><td>soil </td><td>0.68344 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" functionaltype & pct\\_cover\\\\\n",
"\\hline\n",
"\t biocrust & 0.03068 \\\\\n",
"\t grass & 0.03524 \\\\\n",
"\t shrub & 0.25008 \\\\\n",
"\t soil & 0.68344 \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" functionaltype pct_cover\n",
"1 biocrust 0.03068 \n",
"2 grass 0.03524 \n",
"3 shrub 0.25008 \n",
"4 soil 0.68344 "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"0.31656"
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"0.31656"
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"text/markdown": [
"0.31656"
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"text/plain": [
"[1] 0.31656"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"veg.sum\n",
"veg.sum.ft\n",
"1 - sum(veg.sum$pct_cover[veg.sum$species%in%c('soil')])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Joshua tree"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>year</th><th scope=col>season</th><th scope=col>site</th><th scope=col>transect</th><th scope=col>start</th><th scope=col>stop</th><th scope=col>species</th><th scope=col>condition</th><th scope=col>notes</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>2017 </td><td>winter </td><td>JTree </td><td>1 </td><td>0.00 </td><td>0.30 </td><td>soil </td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>JTree </td><td>1 </td><td>0.30 </td><td>0.38 </td><td>unk grass 1</td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>JTree </td><td>1 </td><td>0.38 </td><td>1.10 </td><td>soil </td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>JTree </td><td>1 </td><td>1.10 </td><td>1.28 </td><td>Burro bush </td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>JTree </td><td>1 </td><td>1.38 </td><td>1.50 </td><td>unk grass 1</td><td> </td><td>NA </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>JTree </td><td>1 </td><td>1.50 </td><td>1.67 </td><td>Burro bush </td><td> </td><td>NA </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllllllll}\n",
" year & season & site & transect & start & stop & species & condition & notes\\\\\n",
"\\hline\n",
"\t 2017 & winter & JTree & 1 & 0.00 & 0.30 & soil & & NA \\\\\n",
"\t 2017 & winter & JTree & 1 & 0.30 & 0.38 & unk grass 1 & & NA \\\\\n",
"\t 2017 & winter & JTree & 1 & 0.38 & 1.10 & soil & & NA \\\\\n",
"\t 2017 & winter & JTree & 1 & 1.10 & 1.28 & Burro bush & & NA \\\\\n",
"\t 2017 & winter & JTree & 1 & 1.38 & 1.50 & unk grass 1 & & NA \\\\\n",
"\t 2017 & winter & JTree & 1 & 1.50 & 1.67 & Burro bush & & NA \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" year season site transect start stop species condition notes\n",
"1 2017 winter JTree 1 0.00 0.30 soil NA \n",
"2 2017 winter JTree 1 0.30 0.38 unk grass 1 NA \n",
"3 2017 winter JTree 1 0.38 1.10 soil NA \n",
"4 2017 winter JTree 1 1.10 1.28 Burro bush NA \n",
"5 2017 winter JTree 1 1.38 1.50 unk grass 1 NA \n",
"6 2017 winter JTree 1 1.50 1.67 Burro bush NA "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"630"
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"630"
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"630"
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"[1] 630"
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"metadata": {},
"output_type": "display_data"
}
],
"source": [
"veg.raw <- read.csv(\"~/data/gdrive_berkeley/MojaveCarbon/Data/VegTransects//LineTransects_JTree.csv\", skip=1)\n",
"head(veg.raw)\n",
"\n",
"###cleaning\n",
"###########\n",
"\n",
"`%!in%` <- Negate(`%in%`) \n",
"remove <- c(\"0\", \"LITT\", \"UNKNO\", \"ROCK\", \"SOIL\", \"1SOIL\", \"SOIIL\", \"UNK\", \"SHRUB\", \"BRASS\", \"BFORB\", \"BOER\", \"BOGR\", \"GRASS\")\n",
"\n",
"#veg.raw <- subset(veg.raw, species %!in% remove) \n",
"nrow(veg.raw)\n",
"\n",
"veg.raw <- subset(veg.raw, condition != 'dead')\n",
"\n",
"\n",
"####finding cover value per individual\n",
"#######################################\n",
"veg.raw$cover_cm <- veg.raw$stop - veg.raw$start\n",
"\n",
"#finding largest cover value between seasons \n",
"veg.sum <- data.frame(summarise(group_by(veg.raw, year, species), cover_cm=sum(cover_cm)))\n",
"veg.max <- data.frame(summarise(group_by(veg.sum, year, species), max.cover_cm = max(cover_cm)))\n",
"\n",
"veg.sum$functionaltype <- 'shrub'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('unk grass 1', 'Black grama grass', 'needle grass', 'muhly grass')] <- 'grass'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('joshua tree', 'mojave yucca')] <- 'tree (yucca)'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('forb', 'small mustard(alyssum)')] <- 'forb'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('echinocerius trig', 'pencil cholla', 'silver cholla')] <- 'cacti'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('soil')] <- 'soil'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('biocrust')] <- 'biocrust'\n",
"\n",
"veg.sum$pct_cover <- veg.sum$cover_cm/250\n",
"\n",
"veg.sum.ft <- data.frame(summarise(group_by(veg.sum, functionaltype), pct_cover=sum(pct_cover)))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Joshua tree tables by species and functional type\n",
"\n",
"The last number here is total cover"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>year</th><th scope=col>species</th><th scope=col>cover_cm</th><th scope=col>functionaltype</th><th scope=col>pct_cover</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>2017 </td><td>Black grama grass </td><td> 16.540 </td><td>grass </td><td>0.066160 </td></tr>\n",
"\t<tr><td>2017 </td><td>Burro bush </td><td> 2.110 </td><td>shrub </td><td>0.008440 </td></tr>\n",
"\t<tr><td>2017 </td><td>echinocerius trig </td><td> 0.220 </td><td>cacti </td><td>0.000880 </td></tr>\n",
"\t<tr><td>2017 </td><td>ephedra </td><td> 20.780 </td><td>shrub </td><td>0.083120 </td></tr>\n",
"\t<tr><td>2017 </td><td>forb </td><td> 0.250 </td><td>forb </td><td>0.001000 </td></tr>\n",
"\t<tr><td>2017 </td><td>goldenbush </td><td> 3.360 </td><td>shrub </td><td>0.013440 </td></tr>\n",
"\t<tr><td>2017 </td><td>joshua tree </td><td> 4.340 </td><td>tree (yucca) </td><td>0.017360 </td></tr>\n",
"\t<tr><td>2017 </td><td>lycium cooperi </td><td> 0.260 </td><td>shrub </td><td>0.001040 </td></tr>\n",
"\t<tr><td>2017 </td><td>mojave yucca </td><td> 4.090 </td><td>tree (yucca) </td><td>0.016360 </td></tr>\n",
"\t<tr><td>2017 </td><td>muhly grass </td><td> 6.820 </td><td>grass </td><td>0.027280 </td></tr>\n",
"\t<tr><td>2017 </td><td>needle grass </td><td> 48.481 </td><td>grass </td><td>0.193924 </td></tr>\n",
"\t<tr><td>2017 </td><td>pencil cholla </td><td> 3.600 </td><td>cacti </td><td>0.014400 </td></tr>\n",
"\t<tr><td>2017 </td><td>rubber brush </td><td> 0.170 </td><td>shrub </td><td>0.000680 </td></tr>\n",
"\t<tr><td>2017 </td><td>silver cholla </td><td> 0.730 </td><td>cacti </td><td>0.002920 </td></tr>\n",
"\t<tr><td>2017 </td><td>small mustard(alyssum)</td><td> 0.190 </td><td>forb </td><td>0.000760 </td></tr>\n",
"\t<tr><td>2017 </td><td>soil </td><td>134.449 </td><td>soil </td><td>0.537796 </td></tr>\n",
"\t<tr><td>2017 </td><td>spiny menodora </td><td> 2.570 </td><td>shrub </td><td>0.010280 </td></tr>\n",
"\t<tr><td>2017 </td><td>unk grass 1 </td><td> 2.060 </td><td>grass </td><td>0.008240 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllll}\n",
" year & species & cover\\_cm & functionaltype & pct\\_cover\\\\\n",
"\\hline\n",
"\t 2017 & Black grama grass & 16.540 & grass & 0.066160 \\\\\n",
"\t 2017 & Burro bush & 2.110 & shrub & 0.008440 \\\\\n",
"\t 2017 & echinocerius trig & 0.220 & cacti & 0.000880 \\\\\n",
"\t 2017 & ephedra & 20.780 & shrub & 0.083120 \\\\\n",
"\t 2017 & forb & 0.250 & forb & 0.001000 \\\\\n",
"\t 2017 & goldenbush & 3.360 & shrub & 0.013440 \\\\\n",
"\t 2017 & joshua tree & 4.340 & tree (yucca) & 0.017360 \\\\\n",
"\t 2017 & lycium cooperi & 0.260 & shrub & 0.001040 \\\\\n",
"\t 2017 & mojave yucca & 4.090 & tree (yucca) & 0.016360 \\\\\n",
"\t 2017 & muhly grass & 6.820 & grass & 0.027280 \\\\\n",
"\t 2017 & needle grass & 48.481 & grass & 0.193924 \\\\\n",
"\t 2017 & pencil cholla & 3.600 & cacti & 0.014400 \\\\\n",
"\t 2017 & rubber brush & 0.170 & shrub & 0.000680 \\\\\n",
"\t 2017 & silver cholla & 0.730 & cacti & 0.002920 \\\\\n",
"\t 2017 & small mustard(alyssum) & 0.190 & forb & 0.000760 \\\\\n",
"\t 2017 & soil & 134.449 & soil & 0.537796 \\\\\n",
"\t 2017 & spiny menodora & 2.570 & shrub & 0.010280 \\\\\n",
"\t 2017 & unk grass 1 & 2.060 & grass & 0.008240 \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" year species cover_cm functionaltype pct_cover\n",
"1 2017 Black grama grass 16.540 grass 0.066160 \n",
"2 2017 Burro bush 2.110 shrub 0.008440 \n",
"3 2017 echinocerius trig 0.220 cacti 0.000880 \n",
"4 2017 ephedra 20.780 shrub 0.083120 \n",
"5 2017 forb 0.250 forb 0.001000 \n",
"6 2017 goldenbush 3.360 shrub 0.013440 \n",
"7 2017 joshua tree 4.340 tree (yucca) 0.017360 \n",
"8 2017 lycium cooperi 0.260 shrub 0.001040 \n",
"9 2017 mojave yucca 4.090 tree (yucca) 0.016360 \n",
"10 2017 muhly grass 6.820 grass 0.027280 \n",
"11 2017 needle grass 48.481 grass 0.193924 \n",
"12 2017 pencil cholla 3.600 cacti 0.014400 \n",
"13 2017 rubber brush 0.170 shrub 0.000680 \n",
"14 2017 silver cholla 0.730 cacti 0.002920 \n",
"15 2017 small mustard(alyssum) 0.190 forb 0.000760 \n",
"16 2017 soil 134.449 soil 0.537796 \n",
"17 2017 spiny menodora 2.570 shrub 0.010280 \n",
"18 2017 unk grass 1 2.060 grass 0.008240 "
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>functionaltype</th><th scope=col>pct_cover</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>cacti </td><td>0.018200 </td></tr>\n",
"\t<tr><td>forb </td><td>0.001760 </td></tr>\n",
"\t<tr><td>grass </td><td>0.295604 </td></tr>\n",
"\t<tr><td>shrub </td><td>0.117000 </td></tr>\n",
"\t<tr><td>soil </td><td>0.537796 </td></tr>\n",
"\t<tr><td>tree (yucca)</td><td>0.033720 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" functionaltype & pct\\_cover\\\\\n",
"\\hline\n",
"\t cacti & 0.018200 \\\\\n",
"\t forb & 0.001760 \\\\\n",
"\t grass & 0.295604 \\\\\n",
"\t shrub & 0.117000 \\\\\n",
"\t soil & 0.537796 \\\\\n",
"\t tree (yucca) & 0.033720 \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" functionaltype pct_cover\n",
"1 cacti 0.018200 \n",
"2 forb 0.001760 \n",
"3 grass 0.295604 \n",
"4 shrub 0.117000 \n",
"5 soil 0.537796 \n",
"6 tree (yucca) 0.033720 "
]
},
"metadata": {},
"output_type": "display_data"
},
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"0.462204"
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"[1] 0.462204"
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"metadata": {},
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],
"source": [
"veg.sum\n",
"veg.sum.ft\n",
"1 - sum(veg.sum$pct_cover[veg.sum$species%in%c('soil')])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Pinyon Juniper"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>year</th><th scope=col>season</th><th scope=col>site</th><th scope=col>transect</th><th scope=col>start</th><th scope=col>stop</th><th scope=col>species</th><th scope=col>condition</th><th scope=col>notes</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>2017 </td><td>winter </td><td>PJ </td><td>1 </td><td>0.00 </td><td>0.44 </td><td>soil </td><td> </td><td> </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>PJ </td><td>1 </td><td>0.44 </td><td>0.53 </td><td>Black grama grass</td><td> </td><td> </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>PJ </td><td>1 </td><td>0.53 </td><td>0.79 </td><td>biocrust </td><td> </td><td> </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>PJ </td><td>1 </td><td>0.79 </td><td>0.94 </td><td>soil </td><td> </td><td> </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>PJ </td><td>1 </td><td>0.94 </td><td>1.37 </td><td>buckwheat </td><td> </td><td> </td></tr>\n",
"\t<tr><td>2017 </td><td>winter </td><td>PJ </td><td>1 </td><td>1.37 </td><td>1.44 </td><td>woody debris </td><td> </td><td> </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllllllll}\n",
" year & season & site & transect & start & stop & species & condition & notes\\\\\n",
"\\hline\n",
"\t 2017 & winter & PJ & 1 & 0.00 & 0.44 & soil & & \\\\\n",
"\t 2017 & winter & PJ & 1 & 0.44 & 0.53 & Black grama grass & & \\\\\n",
"\t 2017 & winter & PJ & 1 & 0.53 & 0.79 & biocrust & & \\\\\n",
"\t 2017 & winter & PJ & 1 & 0.79 & 0.94 & soil & & \\\\\n",
"\t 2017 & winter & PJ & 1 & 0.94 & 1.37 & buckwheat & & \\\\\n",
"\t 2017 & winter & PJ & 1 & 1.37 & 1.44 & woody debris & & \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" year season site transect start stop species condition notes\n",
"1 2017 winter PJ 1 0.00 0.44 soil \n",
"2 2017 winter PJ 1 0.44 0.53 Black grama grass \n",
"3 2017 winter PJ 1 0.53 0.79 biocrust \n",
"4 2017 winter PJ 1 0.79 0.94 soil \n",
"5 2017 winter PJ 1 0.94 1.37 buckwheat \n",
"6 2017 winter PJ 1 1.37 1.44 woody debris "
]
},
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"output_type": "display_data"
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"[1] 569"
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],
"source": [
"veg.raw <- read.csv(\"~/data/gdrive_berkeley/MojaveCarbon/Data/VegTransects//LineTransects_PJ.csv\", skip=1)\n",
"head(veg.raw)\n",
"\n",
"###cleaning\n",
"###########\n",
"\n",
"`%!in%` <- Negate(`%in%`) \n",
"remove <- c(\"0\", \"LITT\", \"UNKNO\", \"ROCK\", \"SOIL\", \"1SOIL\", \"SOIIL\", \"UNK\", \"SHRUB\", \"BRASS\", \"BFORB\", \"BOER\", \"BOGR\", \"GRASS\")\n",
"\n",
"veg.raw <- subset(veg.raw, species %!in% remove) \n",
"nrow(veg.raw)\n",
"\n",
"veg.raw <- subset(veg.raw, condition != 'dead')\n",
"\n",
"\n",
"####finding cover value per individual\n",
"#######################################\n",
"veg.raw$cover_cm <- veg.raw$stop - veg.raw$start\n",
"\n",
"#finding largest cover value between seasons \n",
"veg.sum <- data.frame(summarise(group_by(veg.raw, year, species), cover_cm=sum(cover_cm)))\n",
"veg.max <- data.frame(summarise(group_by(veg.sum, year, species), max.cover_cm = max(cover_cm)))\n",
"\n",
"veg.sum$functionaltype <- 'shrub'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('Indian rice grass','Black grama grass','Blue grama grass','needle grass','muhly grass')] <- 'grass'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('juniper')] <- 'tree (Juniper)'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('forb', 'small mustard(alyssum)')] <- 'forb'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('echinocerius trig', 'pencil cholla', 'cholla')] <- 'cacti'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('soil')] <- 'soil'\n",
"veg.sum$functionaltype[veg.sum$species%in%c('biocrust')] <- 'biocrust'\n",
"\n",
"veg.sum$pct_cover <- veg.sum$cover_cm/250\n",
"\n",
"veg.sum.ft <- data.frame(summarise(group_by(veg.sum, functionaltype), pct_cover=sum(pct_cover)))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## PJ tables by species and functional type\n",
"\n",
"The last number here is total cover"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>year</th><th scope=col>species</th><th scope=col>cover_cm</th><th scope=col>functionaltype</th><th scope=col>pct_cover</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>2017 </td><td>banana yucca </td><td> 2.73 </td><td>shrub </td><td>0.01092 </td></tr>\n",
"\t<tr><td>2017 </td><td>big sage </td><td> 21.94 </td><td>shrub </td><td>0.08776 </td></tr>\n",
"\t<tr><td>2017 </td><td>biocrust </td><td> 0.96 </td><td>biocrust </td><td>0.00384 </td></tr>\n",
"\t<tr><td>2017 </td><td>Black grama grass </td><td> 9.81 </td><td>grass </td><td>0.03924 </td></tr>\n",
"\t<tr><td>2017 </td><td>Blue grama grass </td><td> 5.28 </td><td>grass </td><td>0.02112 </td></tr>\n",
"\t<tr><td>2017 </td><td>buckwheat </td><td> 18.77 </td><td>shrub </td><td>0.07508 </td></tr>\n",
"\t<tr><td>2017 </td><td>cholla </td><td> 1.47 </td><td>cacti </td><td>0.00588 </td></tr>\n",
"\t<tr><td>2017 </td><td>cliff rose </td><td> 2.54 </td><td>shrub </td><td>0.01016 </td></tr>\n",
"\t<tr><td>2017 </td><td>desert sage </td><td> 14.17 </td><td>shrub </td><td>0.05668 </td></tr>\n",
"\t<tr><td>2017 </td><td>ephedra </td><td> 14.40 </td><td>shrub </td><td>0.05760 </td></tr>\n",
"\t<tr><td>2017 </td><td>forb </td><td> 1.05 </td><td>forb </td><td>0.00420 </td></tr>\n",
"\t<tr><td>2017 </td><td>four wing salt bush</td><td> 0.38 </td><td>shrub </td><td>0.00152 </td></tr>\n",
"\t<tr><td>2017 </td><td>goldenbush </td><td> 5.11 </td><td>shrub </td><td>0.02044 </td></tr>\n",
"\t<tr><td>2017 </td><td>hopsage </td><td> 3.48 </td><td>shrub </td><td>0.01392 </td></tr>\n",
"\t<tr><td>2017 </td><td>Indian rice grass </td><td> 6.40 </td><td>grass </td><td>0.02560 </td></tr>\n",
"\t<tr><td>2017 </td><td>juniper </td><td> 12.00 </td><td>tree (Juniper) </td><td>0.04800 </td></tr>\n",
"\t<tr><td>2017 </td><td>muhly grass </td><td> 7.70 </td><td>grass </td><td>0.03080 </td></tr>\n",
"\t<tr><td>2017 </td><td>needle grass </td><td> 2.27 </td><td>grass </td><td>0.00908 </td></tr>\n",
"\t<tr><td>2017 </td><td>snakeweed </td><td> 8.29 </td><td>shrub </td><td>0.03316 </td></tr>\n",
"\t<tr><td>2017 </td><td>soil </td><td>111.93 </td><td>soil </td><td>0.44772 </td></tr>\n",
"\t<tr><td>2017 </td><td>unk shrub 1 </td><td> 0.92 </td><td>shrub </td><td>0.00368 </td></tr>\n",
"\t<tr><td>2017 </td><td>woody debris </td><td> 11.12 </td><td>shrub </td><td>0.04448 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllll}\n",
" year & species & cover\\_cm & functionaltype & pct\\_cover\\\\\n",
"\\hline\n",
"\t 2017 & banana yucca & 2.73 & shrub & 0.01092 \\\\\n",
"\t 2017 & big sage & 21.94 & shrub & 0.08776 \\\\\n",
"\t 2017 & biocrust & 0.96 & biocrust & 0.00384 \\\\\n",
"\t 2017 & Black grama grass & 9.81 & grass & 0.03924 \\\\\n",
"\t 2017 & Blue grama grass & 5.28 & grass & 0.02112 \\\\\n",
"\t 2017 & buckwheat & 18.77 & shrub & 0.07508 \\\\\n",
"\t 2017 & cholla & 1.47 & cacti & 0.00588 \\\\\n",
"\t 2017 & cliff rose & 2.54 & shrub & 0.01016 \\\\\n",
"\t 2017 & desert sage & 14.17 & shrub & 0.05668 \\\\\n",
"\t 2017 & ephedra & 14.40 & shrub & 0.05760 \\\\\n",
"\t 2017 & forb & 1.05 & forb & 0.00420 \\\\\n",
"\t 2017 & four wing salt bush & 0.38 & shrub & 0.00152 \\\\\n",
"\t 2017 & goldenbush & 5.11 & shrub & 0.02044 \\\\\n",
"\t 2017 & hopsage & 3.48 & shrub & 0.01392 \\\\\n",
"\t 2017 & Indian rice grass & 6.40 & grass & 0.02560 \\\\\n",
"\t 2017 & juniper & 12.00 & tree (Juniper) & 0.04800 \\\\\n",
"\t 2017 & muhly grass & 7.70 & grass & 0.03080 \\\\\n",
"\t 2017 & needle grass & 2.27 & grass & 0.00908 \\\\\n",
"\t 2017 & snakeweed & 8.29 & shrub & 0.03316 \\\\\n",
"\t 2017 & soil & 111.93 & soil & 0.44772 \\\\\n",
"\t 2017 & unk shrub 1 & 0.92 & shrub & 0.00368 \\\\\n",
"\t 2017 & woody debris & 11.12 & shrub & 0.04448 \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" year species cover_cm functionaltype pct_cover\n",
"1 2017 banana yucca 2.73 shrub 0.01092 \n",
"2 2017 big sage 21.94 shrub 0.08776 \n",
"3 2017 biocrust 0.96 biocrust 0.00384 \n",
"4 2017 Black grama grass 9.81 grass 0.03924 \n",
"5 2017 Blue grama grass 5.28 grass 0.02112 \n",
"6 2017 buckwheat 18.77 shrub 0.07508 \n",
"7 2017 cholla 1.47 cacti 0.00588 \n",
"8 2017 cliff rose 2.54 shrub 0.01016 \n",
"9 2017 desert sage 14.17 shrub 0.05668 \n",
"10 2017 ephedra 14.40 shrub 0.05760 \n",
"11 2017 forb 1.05 forb 0.00420 \n",
"12 2017 four wing salt bush 0.38 shrub 0.00152 \n",
"13 2017 goldenbush 5.11 shrub 0.02044 \n",
"14 2017 hopsage 3.48 shrub 0.01392 \n",
"15 2017 Indian rice grass 6.40 grass 0.02560 \n",
"16 2017 juniper 12.00 tree (Juniper) 0.04800 \n",
"17 2017 muhly grass 7.70 grass 0.03080 \n",
"18 2017 needle grass 2.27 grass 0.00908 \n",
"19 2017 snakeweed 8.29 shrub 0.03316 \n",
"20 2017 soil 111.93 soil 0.44772 \n",
"21 2017 unk shrub 1 0.92 shrub 0.00368 \n",
"22 2017 woody debris 11.12 shrub 0.04448 "
]
},
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"output_type": "display_data"
},
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"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>functionaltype</th><th scope=col>pct_cover</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>biocrust </td><td>0.00384 </td></tr>\n",
"\t<tr><td>cacti </td><td>0.00588 </td></tr>\n",
"\t<tr><td>forb </td><td>0.00420 </td></tr>\n",
"\t<tr><td>grass </td><td>0.12584 </td></tr>\n",
"\t<tr><td>shrub </td><td>0.41540 </td></tr>\n",
"\t<tr><td>soil </td><td>0.44772 </td></tr>\n",
"\t<tr><td>tree (Juniper)</td><td>0.04800 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" functionaltype & pct\\_cover\\\\\n",
"\\hline\n",
"\t biocrust & 0.00384 \\\\\n",
"\t cacti & 0.00588 \\\\\n",
"\t forb & 0.00420 \\\\\n",
"\t grass & 0.12584 \\\\\n",
"\t shrub & 0.41540 \\\\\n",
"\t soil & 0.44772 \\\\\n",
"\t tree (Juniper) & 0.04800 \\\\\n",
"\\end{tabular}\n"
],
"text/plain": [
" functionaltype pct_cover\n",
"1 biocrust 0.00384 \n",
"2 cacti 0.00588 \n",
"3 forb 0.00420 \n",
"4 grass 0.12584 \n",
"5 shrub 0.41540 \n",
"6 soil 0.44772 \n",
"7 tree (Juniper) 0.04800 "
]
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}
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