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Add code and data for each species in the CAPS table #2
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@jrfep
jrfep committed Oct 10, 2022
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257 changes: 257 additions & 0 deletions R/Read-table-traits-per-species.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "ebcf7b28-b2b2-4fff-89b9-692f55207cee",
"metadata": {},
"source": [
"# Fire response traits in plants from field samples\n",
"\n",
"This script contains examples of R code to query tables in the database\n",
"\n",
"## Load libraries"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "f24bd72f-1086-4c75-a7b8-395ac8eb79ce",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Loading required package: DBI\n",
"\n",
"\n",
"Attaching package: ‘dplyr’\n",
"\n",
"\n",
"The following objects are masked from ‘package:stats’:\n",
"\n",
" filter, lag\n",
"\n",
"\n",
"The following objects are masked from ‘package:base’:\n",
"\n",
" intersect, setdiff, setequal, union\n",
"\n",
"\n",
"Loading required package: tidyr\n",
"\n"
]
}
],
"source": [
"library(RPostgreSQL)\n",
"library(ggplot2)\n",
"##library(forcats)\n",
"library(dplyr)\n",
"#library(data.table)\n",
"require(tidyr)"
]
},
{
"cell_type": "markdown",
"id": "108e8a20-008a-45c8-8941-80f815b790f1",
"metadata": {},
"source": [
"## Connect to the database"
]
},
{
"cell_type": "markdown",
"id": "9cf99ffd-c436-4c2f-b575-71f6e5b25db2",
"metadata": {},
"source": [
"Read database credentials"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "5759a6bf-b2c5-42e2-80a0-3cf57cdc897f",
"metadata": {},
"outputs": [],
"source": [
"if (file.exists(\"../secrets/database.ini\")) {\n",
" tmp <- readLines(\"../secrets/database.ini\")[-1]\n",
" tmp <- strsplit(tmp,'=',fixed=2)\n",
" dbinfo <- unlist(lapply(tmp,function(x) x[2]))\n",
" names(dbinfo) <- unlist(lapply(tmp,function(x) x[1]))\n",
" dbinfo <- data.frame(t(dbinfo),stringsAsFactors=F)\n",
" rm(tmp)\n",
"} else {\n",
" cat(\"No database information found\")\n",
"}"
]
},
{
"cell_type": "markdown",
"id": "8ade77df-7be2-493f-bb25-6e9e0b6fa6cb",
"metadata": {},
"source": [
"Connection to the postgresql server (remember to update .pgpass file)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "f50fdfe2-2932-46fe-a483-f2bc29714bc6",
"metadata": {},
"outputs": [],
"source": [
"drv <- dbDriver(\"PostgreSQL\") ## \n",
"con <- dbConnect(drv, dbname = dbinfo$database,\n",
" host = dbinfo$host, port = dbinfo$port,\n",
" user = dbinfo$user)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "e7a36330-4a00-4a82-8566-71fa84b48ef9",
"metadata": {},
"outputs": [],
"source": [
"qry <- \n",
"'SELECT family, genus, \"speciesID\", \n",
"count(distinct q.record_id) as nquadrat, \n",
"count(distinct g8.record_id) as germ8, \n",
"count(distinct r2.record_id) as rect2,\n",
"count(distinct g1.record_id) as germ1, \n",
"count(distinct gw1.record_id) as grow1, \n",
"count(distinct r4.record_id) as repr4, \n",
"count(distinct s5.record_id) as surv5, \n",
"count(distinct s6.record_id) as surv6, \n",
"count(distinct s7.record_id) as surv7, \n",
"count(distinct d1.record_id) as disp1, \n",
"count(distinct r3a.record_id) as repr3a, \n",
"count(distinct r3.record_id) as repr3, \n",
"count(distinct s4.record_id) as surv4, \n",
"count(distinct s1.record_id) as surv1\n",
"FROM species.caps \n",
"LEFT JOIN species_traits s \n",
" ON \"speciesCode_Synonym\"=s.species_code::text \n",
"LEFT JOIN form.quadrat_samples q \n",
" ON \"speciesCode_Synonym\"=q.species_code::text \n",
"LEFT JOIN litrev.germ8 g8 ON \"speciesCode_Synonym\"=g8.species_code::text \n",
"LEFT JOIN litrev.rect2 r2 ON \"speciesCode_Synonym\"=r2.species_code::text \n",
"LEFT JOIN litrev.germ1 g1 ON \"speciesCode_Synonym\"=g1.species_code::text \n",
"LEFT JOIN litrev.grow1 gw1 ON \"speciesCode_Synonym\"=gw1.species_code::text \n",
"LEFT JOIN litrev.repr4 r4 ON \"speciesCode_Synonym\"=r4.species_code::text \n",
"LEFT JOIN litrev.surv5 s5 ON \"speciesCode_Synonym\"=s5.species_code::text \n",
"LEFT JOIN litrev.surv6 s6 ON \"speciesCode_Synonym\"=s6.species_code::text \n",
"LEFT JOIN litrev.surv7 s7 ON \"speciesCode_Synonym\"=s7.species_code::text \n",
"LEFT JOIN litrev.disp1 d1 ON \"speciesCode_Synonym\"=d1.species_code::text \n",
"LEFT JOIN litrev.repr3a r3a ON \"speciesCode_Synonym\"=r3a.species_code::text \n",
"LEFT JOIN litrev.repr3 r3 ON \"speciesCode_Synonym\"=r3.species_code::text \n",
"LEFT JOIN litrev.surv4 s4 ON \"speciesCode_Synonym\"=s4.species_code::text \n",
"LEFT JOIN litrev.surv1 s1 ON \"speciesCode_Synonym\"=s1.species_code::text \n",
"\n",
"GROUP BY fam'"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "906884e5-92c3-46c6-aba7-c5a7d6fada17",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"'data.frame':\t368 obs. of 17 variables:\n",
" $ fam : chr \"Acanthaceae\" \"Acrobolbaceae\" \"Actinidiaceae\" \"Adoxaceae\" ...\n",
" $ nspp : num 79 6 1 10 12 67 3 15 19 4 ...\n",
" $ litrev : num 16 0 0 3 1 30 1 5 0 0 ...\n",
" $ quadrat: num 1 0 0 1 0 0 1 0 0 0 ...\n",
" $ germ8 : num 0 0 0 0 0 0 0 0 0 0 ...\n",
" $ rect2 : num 2 0 0 0 0 2 0 0 0 0 ...\n",
" $ germ1 : num 2 0 0 0 0 1 0 0 0 0 ...\n",
" $ grow1 : num 0 0 0 0 0 0 0 0 0 0 ...\n",
" $ repr4 : num 0 0 0 0 0 0 0 0 0 0 ...\n",
" $ surv5 : num 4 0 0 0 0 4 0 0 0 0 ...\n",
" $ surv6 : num 0 0 0 0 0 0 0 0 0 0 ...\n",
" $ surv7 : num 0 0 0 0 0 0 0 0 0 0 ...\n",
" $ disp1 : num 12 0 0 3 0 26 1 5 0 0 ...\n",
" $ repr3a : num 2 0 0 0 0 0 0 0 0 0 ...\n",
" $ repr3 : num 1 0 0 0 0 2 0 0 0 0 ...\n",
" $ surv4 : num 4 0 0 0 0 0 0 0 0 0 ...\n",
" $ surv1 : num 16 0 0 3 1 29 1 4 0 0 ...\n"
]
}
],
"source": [
"my.table<- dbGetQuery(con, qry)\n",
"str(my.table)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "5b64901b-b582-402f-9ba9-c01ba064f135",
"metadata": {},
"outputs": [],
"source": [
"saveRDS(file='../data/Summary-traits-family.rds',my.table)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "f6c75c45-cf6c-4711-ba3e-1edede998c92",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"TRUE"
],
"text/latex": [
"TRUE"
],
"text/markdown": [
"TRUE"
],
"text/plain": [
"[1] TRUE"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"dbDisconnect(con)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "913933a6-a64c-4a30-9756-f2539840d9a9",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "R",
"language": "R",
"name": "ir"
},
"language_info": {
"codemirror_mode": "r",
"file_extension": ".r",
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "3.6.3"
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"nbformat_minor": 5
}
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