├── LICENSE ├── tests ├── testthat.R └── testthat │ ├── test-growth-form.R │ └── test-lookup.R ├── R ├── sysdata.rda ├── utils.R ├── lookup.R └── growth_form.R ├── .Rbuildignore ├── NAMESPACE ├── .travis.yml ├── .gitignore ├── database_assembly_information ├── combine │ └── combine.R ├── functions │ ├── makeTables.R │ └── family_analysis.R ├── data_with_sources │ └── references_database.csv └── original_references │ └── references_database.csv ├── inst └── CITATION ├── DESCRIPTION ├── man ├── growth_form_lookup_table.Rd └── growth_form.Rd ├── README.rmd └── README.md /LICENSE: -------------------------------------------------------------------------------- 1 | YEAR: 2018 2 | COPYRIGHT HOLDER: William Cornwell 3 | -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- 1 | library(testthat) 2 | 3 | test_check("growthform") 4 | -------------------------------------------------------------------------------- /R/sysdata.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/traitecoevo/growthform/HEAD/R/sysdata.rda -------------------------------------------------------------------------------- /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^\.travis\.yml$ 2 | ^.*\.Rproj$ 3 | ^\.Rproj\.user$ 4 | ^createlookup\.R$ 5 | ^plantListAcceptedNames$ 6 | ^remake\.yml$ 7 | ^remake_sources\.yml$ 8 | ^source_data$ 9 | ^Makefile$ 10 | ^plant_lookup\.csv$ 11 | ^\.remake$ 12 | ^README\.rmd$ 13 | ^growth_form\.csv$ 14 | ^database_assembly_information$ -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | export(get_most_recent_growth_form) 4 | export(growth_form) 5 | export(growth_form_del) 6 | export(growth_form_lookup_table) 7 | export(growth_form_version_current_github) 8 | export(growth_form_version_current_local) 9 | export(growth_form_versions) 10 | import(datastorr) 11 | -------------------------------------------------------------------------------- /tests/testthat/test-growth-form.R: -------------------------------------------------------------------------------- 1 | context("growthform") 2 | 3 | 4 | test_that("table sane", { 5 | library(growthform) 6 | lookup <- growthform::growth_form() 7 | expect_that(ncol(lookup), equals(4L)) 8 | expect_that(lookup, is_a("data.frame")) 9 | expect_that(any(is.na(lookup$support)), is_false()) 10 | expect_that(any(duplicated(lookup$sp)), is_false()) 11 | }) 12 | -------------------------------------------------------------------------------- /tests/testthat/test-lookup.R: -------------------------------------------------------------------------------- 1 | context("growthform") 2 | 3 | test_that("lookup sane", { 4 | library(growthform) 5 | checkingPinus<-growthform::growth_form_lookup_table("Pinus ponderosa") 6 | expect_that(checkingPinus$sp, equals("Pinus ponderosa")) 7 | expect_that(checkingPinus$support, equals("F")) 8 | expect_that(any(duplicated(checkingPinus$sp)), is_false()) 9 | }) 10 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: R 2 | sudo: false 3 | latex: false 4 | r_build_args: '--no-manual' 5 | 6 | r_github_packages: 7 | - ropenscilabs/datastorr 8 | - jimhester/covr 9 | 10 | after_success: 11 | - Rscript -e 'library(covr); codecov()' 12 | 13 | after_failure: 14 | - ./travis-tool.sh dump_logs 15 | 16 | notifications: 17 | email: 18 | on_success: change 19 | on_failure: change 20 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .DS_Store 5 | conflicts.csv 6 | new_fixes.csv 7 | .Rapp.history 8 | 9 | *.DS_Store 10 | rawData/.DS_Store 11 | *.Rproj 12 | 13 | data/observations.csv 14 | 15 | output/growthFormData.csv 16 | output/synonym_fixes.csv 17 | taxonomicResources/spermatophyta_synonyms_PLANTLIST.csv 18 | output/spelling_fixes.csv 19 | output/syn_fixes_done.csv 20 | output/spelling_fixes_done.csv 21 | output/conflicts.csv 22 | output/uniqueSpeciesGFData.csv 23 | 24 | .remake/ 25 | 26 | output/ 27 | figures/ 28 | tables/ -------------------------------------------------------------------------------- /database_assembly_information/combine/combine.R: -------------------------------------------------------------------------------- 1 | library(tidyverse) 2 | 3 | gf<-read_csv("database_assembly_information/data_with_sources/consensus_species_growthform.csv") 4 | wood<-read_csv("database_assembly_information/data_with_sources/GlobalWoodinessDatabase.csv") 5 | nfix<-read_csv("database_assembly_information/data_with_sources/Werner_NFix.csv") 6 | 7 | 8 | wood<-rename(wood,sp=gs) 9 | nfix<-rename(nfix,sp=Species) 10 | 11 | left_join(gf,wood) %>% 12 | left_join(nfix) %>% 13 | select(sp,support,woodiness,Data_fixing) %>% 14 | rename(nfixing=Data_fixing) %>% 15 | write_csv("growth_form.csv") 16 | 17 | 18 | -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- 1 | citHeader("To cite growthform data in publications, please use:") 2 | 3 | citEntry(entry = "Article", 4 | author = "G. Taseski and C. J. Beloe and R. V. Gallagher and J. Y. Chan and R. L. Dalrymple and W. K. Cornwell", 5 | title = "A global growth form database for 143,616 vascular plant species", 6 | year = "2018", 7 | journal = "Ecology", 8 | url = "https://doi.org/10.1002/ecy.2614", 9 | textVersion = "Taseski, G. , Beloe, C. J., Gallagher, R. V., Chan, J. Y., Dalrymple, R. L. and Cornwell, W. K. (2019), A global growth form database for 143,616 vascular plant species. Ecology. Accepted Author Manuscript. https://doi.org/10.1002/ecy.2614" 10 | ) -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: growthform 2 | Title: Global Plant Growth Form: a dynamically-updating versioned growth form data for vascular plants 3 | Version: 0.2.3 4 | Description: A growth form database for >145,000 species of vascular plants. 5 | BugReports: https://github.com/traitecoevo/global_plant_growth_form/issues 6 | Depends: R (>= 3.1.0) 7 | License: MIT + file LICENSE 8 | LazyData: true 9 | Authors@R: as.person(c("Will Cornwell [aut, cre]")) 10 | Maintainer: Will Cornwell 11 | Imports: 12 | datastorr (>= 0.0.3) 13 | Suggests: 14 | testthat 15 | Remotes: 16 | github::ropenscilabs/datastorr 17 | RoxygenNote: 6.0.1 18 | -------------------------------------------------------------------------------- /R/utils.R: -------------------------------------------------------------------------------- 1 | vlapply <- function(X, FUN, ...) { 2 | vapply(X, FUN, logical(1), ...) 3 | } 4 | viapply <- function(X, FUN, ...) { 5 | vapply(X, FUN, integer(1), ...) 6 | } 7 | vnapply <- function(X, FUN, ...) { 8 | vapply(X, FUN, numeric(1), ...) 9 | } 10 | vcapply <- function(X, FUN, ...) { 11 | vapply(X, FUN, character(1), ...) 12 | } 13 | 14 | pastec <- function(...) { 15 | paste(..., collapse=", ") 16 | } 17 | 18 | split_genus <- function(str) { 19 | str_split <- strsplit(str, "[_ ]+") 20 | vcapply(str_split, "[[", 1L) 21 | } 22 | 23 | last <- function(x) { 24 | x[[length(x)]] 25 | } 26 | 27 | is_version <- function(version) { 28 | !inherits(try(numeric_version(version), silent=TRUE), "try-error") 29 | } 30 | -------------------------------------------------------------------------------- /database_assembly_information/functions/makeTables.R: -------------------------------------------------------------------------------- 1 | 2 | make.source.table<-function(data.out){ 3 | out<-sort(table(data.out$source),decreasing = TRUE) 4 | write.csv(out,"output/source.table.csv",quote=FALSE) 5 | } 6 | 7 | 8 | output.good.data<-function(all.data){ 9 | library(dplyr) 10 | number.of.levels<-summarize(group_by(all.data,sp),num.val=length(unique(support))) 11 | problems<-number.of.levels$sp[number.of.levels$num.val>1] 12 | no.prob<-number.of.levels$sp[number.of.levels$num.val==1] 13 | filter(all.data,sp%in%no.prob) %>% 14 | arrange(sp)->out 15 | return(out) 16 | } 17 | 18 | output.unique.species.dataset<-function(all.data){ 19 | good.data<-output.good.data(all.data) 20 | dropped.source<-select(good.data,sp,support) 21 | unique.spp <- dropped.source[!duplicated(dropped.source),] 22 | return(unique.spp) 23 | } 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /man/growth_form_lookup_table.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/lookup.R 3 | \name{growth_form_lookup_table} 4 | \alias{growth_form_lookup_table} 5 | \title{Build a lookup table for a set of species, connecting the species names to growth form} 6 | \usage{ 7 | growth_form_lookup_table(species_list, lookup_table = NULL, version = NULL) 8 | } 9 | \arguments{ 10 | \item{species_list}{Character vector of species bionomials Genus and species may be seperated by " " 11 | or "_"} 12 | 13 | \item{lookup_table}{Any growth form lookup table, but by default \code{\link{growth_form}}} 14 | 15 | \item{version}{Version number. The default will load the most 16 | recent version on your computer or the most recent version known 17 | to the package if you have never downloaded the data before. 18 | With \code{growth_form_del}, specifying \code{version=NULL} 19 | will delete \emph{all} data sets.} 20 | } 21 | \description{ 22 | Build a lookup table for a set of species, connecting the species names to growth form 23 | } 24 | -------------------------------------------------------------------------------- /R/lookup.R: -------------------------------------------------------------------------------- 1 | ##' Build a lookup table for a set of species, connecting the species names to growth form 2 | ##' 3 | ##' 4 | ##' @title Build a lookup table for a set of species, connecting the species names to growth form 5 | ##' @param species_list Character vector of species bionomials Genus and species may be seperated by " " 6 | ##' or "_" 7 | ##' @param lookup_table Any growth form lookup table, but by default \code{\link{growth_form}} 8 | ##' @param version Version number. The default will load the most 9 | ##' recent version on your computer or the most recent version known 10 | ##' to the package if you have never downloaded the data before. 11 | ##' With \code{growth_form_del}, specifying \code{version=NULL} 12 | ##' will delete \emph{all} data sets. 13 | ##' @export 14 | 15 | growth_form_lookup_table <- function(species_list, lookup_table=NULL,version=NULL){ 16 | if (is.null(lookup_table)) { 17 | lookup_table <- growth_form(version) 18 | } 19 | species_list <- gsub("_"," ",species_list) 20 | 21 | out<-lookup_table[lookup_table$sp %in% species_list,] 22 | row.names(out)<-NULL 23 | return(out) 24 | } 25 | -------------------------------------------------------------------------------- /man/growth_form.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/growth_form.R 3 | \name{growth_form} 4 | \alias{growth_form} 5 | \alias{growth_form_versions} 6 | \alias{growth_form_version_current_local} 7 | \alias{growth_form_version_current_github} 8 | \alias{get_most_recent_growth_form} 9 | \alias{growth_form_del} 10 | \title{Plant growthform lookup table} 11 | \usage{ 12 | growth_form(version = NULL) 13 | 14 | growth_form_versions(local = TRUE) 15 | 16 | growth_form_version_current_local(local = TRUE) 17 | 18 | growth_form_version_current_github(local = FALSE) 19 | 20 | get_most_recent_growth_form() 21 | 22 | growth_form_del(version) 23 | } 24 | \arguments{ 25 | \item{version}{Version number. The default will load the most 26 | recent version on your computer or the most recent version known 27 | to the package if you have never downloaded the data before. 28 | With \code{growth_form_del}, specifying \code{version=NULL} 29 | will delete \emph{all} data sets.} 30 | 31 | \item{local}{Type of version to return: options are "local" 32 | (versions installed locally) or "github" (versions available on 33 | github). With any luck, "github" is a superset of "local". For 34 | \code{growth_form_version_current}, if "local" is given, but there 35 | are no local versions, then we do check for the most recent 36 | github version.} 37 | } 38 | \description{ 39 | Lookup table for plant growth form 40 | } 41 | \details{ 42 | These data are then currated--please flag any errors or potential additions on github 43 | are at https://github.com/wcornwell/growthformdatabase 44 | } 45 | \examples{ 46 | # 47 | # see the format of the resource 48 | # 49 | head(growth_form()) 50 | 51 | } 52 | -------------------------------------------------------------------------------- /R/growth_form.R: -------------------------------------------------------------------------------- 1 | ##' Lookup table for plant growth form 2 | ##' 3 | ##' 4 | ##' These data are then currated--please flag any errors or potential additions on github 5 | ##' are at https://github.com/wcornwell/growthformdatabase 6 | ##' 7 | ##' @title Plant growthform lookup table 8 | ##' 9 | ##' @param version Version number. The default will load the most 10 | ##' recent version on your computer or the most recent version known 11 | ##' to the package if you have never downloaded the data before. 12 | ##' With \code{growth_form_del}, specifying \code{version=NULL} 13 | ##' will delete \emph{all} data sets. 14 | ##' 15 | ##' 16 | ##' 17 | ##' @export 18 | ##' @import datastorr 19 | ##' @examples 20 | ##' # 21 | ##' # see the format of the resource 22 | ##' # 23 | ##' head(growth_form()) 24 | ##' 25 | 26 | growth_form <- function(version=NULL) { 27 | d <- growth_form_get(version) 28 | return(d) 29 | } 30 | 31 | ## This one is the important part; it defines the three core bits of 32 | ## information we need; 33 | ## 1. the repository name (wcornwell/taxonlookup) 34 | ## 2. the file to download growth_form.csv) 35 | ## 3. the function to read the file, given a filename (read_csv) 36 | growth_form_info <- function() { 37 | datastorr::github_release_info(repo="traitecoevo/growthform", 38 | filename="growth_form.csv", 39 | read=read_csv) 40 | } 41 | 42 | ## Below here are wrappers around the storr functions but with our 43 | ## information object. We could actually save growth_form_info() as 44 | ## an *object* in the package, but I prefer this approach. 45 | growth_form_get <- function(version=NULL) { 46 | datastorr::github_release_get(growth_form_info(), version) 47 | } 48 | 49 | ##' @export 50 | ##' @rdname growth_form 51 | ##' @param local Type of version to return: options are "local" 52 | ##' (versions installed locally) or "github" (versions available on 53 | ##' github). With any luck, "github" is a superset of "local". For 54 | ##' \code{growth_form_version_current}, if "local" is given, but there 55 | ##' are no local versions, then we do check for the most recent 56 | ##' github version. 57 | 58 | growth_form_versions <- function(local=TRUE) { 59 | datastorr::github_release_get(growth_form_info(), local) 60 | } 61 | 62 | ##' @export 63 | ##' @rdname growth_form 64 | growth_form_version_current_local <- function(local=TRUE) { 65 | datastorr::github_release_version_current(growth_form_info(), local=local) 66 | } 67 | 68 | ##' @export 69 | ##' @rdname growth_form 70 | growth_form_version_current_github <- function(local=FALSE) { 71 | datastorr::github_release_version_current(growth_form_info(), local=local) 72 | } 73 | 74 | ##' @export 75 | ##' @rdname growth_form 76 | get_most_recent_growth_form <- function(){ 77 | datastorr::github_release_get(info=growth_form_info() 78 | , version=growth_form_version_current_github()) 79 | } 80 | 81 | 82 | ##' @export 83 | ##' @rdname growth_form 84 | growth_form_del <- function(version) { 85 | datastorr::github_release_del(growth_form_info(), version) 86 | } 87 | 88 | read_csv <- function(...) { 89 | utils::read.csv(..., stringsAsFactors=FALSE) 90 | } 91 | 92 | growth_form_release <- function(description, ...) { 93 | datastorr::github_release_create(growth_form_info(), 94 | description=description, ...) 95 | } 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | -------------------------------------------------------------------------------- /database_assembly_information/functions/family_analysis.R: -------------------------------------------------------------------------------- 1 | 2 | insert.family.names<-function(names.df){ 3 | require(taxonlookup) 4 | lookUp<-plant_lookup() 5 | genera<-taxonlookup:::split_genus(as.character(names.df$sp)) 6 | names.df<-data.frame(sp=names.df$sp,support=names.df$support, 7 | plant.list.accepted=names.df$plant.list.accepted, 8 | genus=genera,stringsAsFactors = FALSE) 9 | names.df$family<-lookUp$family[match(genera,lookUp$genus)] 10 | names.df$group<-lookUp$group[match(genera,lookUp$genus)] 11 | return(names.df) 12 | } 13 | 14 | major.clade.mapping<-function(unique.species.with.families){ 15 | require(taxonlookup) 16 | ao<-add_higher_order() 17 | unique.species.with.families$genus<-taxonlookup:::split_genus(unique.species.with.families$sp) 18 | unique.species.with.families$group<-ao$group[match(unique.species.with.families$genus,ao$genus)] 19 | unique.species.with.families$family<-ao$family[match(unique.species.with.families$genus,ao$genus)] 20 | unique.species.with.families$Mono<-ao$Monocotyledoneae[match(unique.species.with.families$genus,ao$genus)] 21 | unique.species.with.families$Eud<-ao$Eudicotyledoneae[match(unique.species.with.families$genus,ao$genus)] 22 | unique.species.with.families$major.clade<-unique.species.with.families$group 23 | unique.species.with.families$major.clade[unique.species.with.families$Eud==""&unique.species.with.families$Mono==""&unique.species.with.families$group=="Angiosperms"]<-"BasalAngiosperms" 24 | unique.species.with.families$major.clade[unique.species.with.families$Eud=="Eudicotyledoneae"]<-"Eudicot" 25 | unique.species.with.families$major.clade[unique.species.with.families$Mono=="Monocotyledoneae"]<-"Monocot" 26 | out<-dplyr::select(unique.species.with.families,sp,support,genus,family,group,major.clade) 27 | return(out) 28 | } 29 | 30 | do.family.sampling.analysis<-function(names.df){ 31 | good.names<-plant_lookup(include_counts = TRUE) 32 | plantList<-summarize(group_by(good.names,family),num.sp=sum(number.of.species)) 33 | data<-summarize(group_by(names.df,family),num.sp=length(sp)) 34 | out<-merge(plantList,data,by="family",all=TRUE) 35 | out$num.sp.y[is.na(out$num.sp.y)]<-0 36 | out$num.sp.x[is.na(out$num.sp.x)]<-0 37 | names(out)[2]<-"plant.list.species" 38 | names(out)[3]<-"data.set.species" 39 | out$percentage<-out$data.set.species/out$plant.list.species 40 | return(arrange(out,percentage)) 41 | } 42 | 43 | do.family.gf.analysis<-function(unique.species.with.families,gf.code){ 44 | require(dplyr) 45 | good.names<-plant_lookup(include_counts = TRUE) 46 | good.names<-dplyr::filter(good.names,group!="Bryophytes") 47 | plantList<-summarize(group_by(good.names,family),num.sp=sum(number.of.species)) 48 | data<-summarize(group_by(unique.species.with.families,family),num.sp.yes=sum(support==gf.code),num.sp.no=sum(support!=gf.code),major.clade=major.clade[1]) 49 | out<-merge(plantList,data,by="family",all=TRUE) 50 | out$num.sp.yes[is.na(out$num.sp.yes)]<-0 51 | out$num.sp.no[is.na(out$num.sp.no)]<-0 52 | out$percent<-out$num.sp.yes/(out$num.sp.yes+out$num.sp.no) 53 | return(out) 54 | } 55 | 56 | 57 | make.figures<-function(df){ 58 | library(treemap) 59 | unique.species.with.families<-insert.family.names(df) 60 | unique.species.with.families<-major.clade.mapping(unique.species.with.families) 61 | climbers<-do.family.gf.analysis(unique.species.with.families,"C") 62 | 63 | pdf("figures/climbers_in_gf_database_by_family.pdf",width=8.5,height=11) 64 | treemap(climbers, 65 | index=c("major.clade","family"), 66 | vSize="num.sp", 67 | vColor="percent", 68 | type="manual", 69 | palette=brewer.pal(9,"PuBuGn"), 70 | range=c(0,1), 71 | title.legend="Proportion of species that are climbers", 72 | title="Distribution of climbers among clades of vascular plants") 73 | dev.off() 74 | 75 | epi<-do.family.gf.analysis(unique.species.with.families,"E") 76 | 77 | pdf("figures/epiphytes_in_gf_database_by_family.pdf",width=8.5,height=11) 78 | treemap(epi, 79 | index=c("major.clade","family"), 80 | vSize="num.sp", 81 | vColor="percent", 82 | type="manual", 83 | palette=brewer.pal(9,"PuBuGn"), 84 | range=c(0,1), 85 | title.legend="Proportion of species that are epiphytes", 86 | title="Distribution of epiphytes among clades of vascular plants") 87 | dev.off() 88 | 89 | } 90 | 91 | # climbers<-do.family.gf.analysis(unique.species.with.families,"C") 92 | # 93 | # pdf("climbers_in_gf_database_by_family.pdf",width=8.5,height=11) 94 | # treemap(climbers, 95 | # index=c("family"), 96 | # vSize="num.sp", 97 | # vColor="percent", 98 | # type="manual", 99 | # palette=brewer.pal(9,"PuBuGn"), 100 | # range=c(0,1), 101 | # title="Proportion of climbers ") 102 | # dev.off() 103 | # 104 | # epiphytes<-do.family.gf.analysis(unique.species.with.families,"E") 105 | # 106 | # pdf("epiphytes_in_gf_database_by_family.pdf",width=8.5,height=11) 107 | # treemap(epiphytes, 108 | # index=c("family"), 109 | # vSize="num.sp", 110 | # vColor="percent", 111 | # type="manual", 112 | # palette=brewer.pal(9,"PuBuGn"), 113 | # range=c(0,1), 114 | # title="Proportion of epiphytes ") 115 | # dev.off() 116 | 117 | 118 | 119 | 120 | output.family.summary<-function(plant.list.names){ 121 | plant.list.names$support<-as.factor(plant.list.names$support) 122 | table(plant.list.names$support) 123 | fam.ss<-tapply(plant.list.names$support,INDEX=plant.list.names$family,FUN=table) 124 | write.csv(do.call(rbind,fam.ss),"output/familySummary.csv",row.names=T) 125 | } 126 | 127 | 128 | output.major.clade.summary<-function(plant.list.names){ 129 | library(Gmisc) 130 | plant.list.names<-major.clade.mapping(plant.list.names) 131 | out<-getDescriptionStatsBy(plant.list.names$support,plant.list.names$major.clade) 132 | print(htmlTable(out),"help.html") 133 | write.csv(out,"output/majorCladeSummary.csv",row.names=T) 134 | } 135 | 136 | -------------------------------------------------------------------------------- /README.rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: github_document 3 | --- 4 | 5 | # growthform: a versioned lookup table for the growth form of vascular plants 6 | 7 | [![Build Status](https://travis-ci.org/traitecoevo/growthform.png?branch=master)](https://travis-ci.org/traitecoevo/taxonlookup) 8 | [![codecov.io](https://codecov.io/github/traitecoevo/growthform/coverage.svg?branch=master)](https://codecov.io/github/traitecoevo/growthform?branch=master) 9 | [![DOI](https://zenodo.org/badge/161406874.svg)](https://zenodo.org/badge/latestdoi/161406874) 10 | 11 | 12 | **Problem:** You have a list of species from anywhere in the world. You've fixed the names, but you'd like to know something about the species' growth forms. 13 | 14 | **Solution:** We've put together a growing list of growth forms, currently (>140,000 species). This list lives in this github repository. If you want the whole list, head to [our github releases tab and download the whole thing](https://github.com/traitecoevo/growthform/releases). If you want the ones that correspond to your list, load your list into R and follow the steps below. This package combines three separate giant database assembly efforts to build large lists of plant growth forms (see sources below). 15 | 16 | ## How to use this package 17 | 18 | ### Install the required packages 19 | 20 | ```{r, message=FALSE,results=FALSE} 21 | #install.packages("devtools") # if necessary 22 | devtools::install_github("ropenscilabs/datastorr") 23 | devtools::install_github("traitecoevo/growthform") 24 | ``` 25 | 26 | ### Load the growthform package 27 | 28 | ```{r} 29 | library(growthform) 30 | ``` 31 | 32 | ### Find the growth form for your species list 33 | 34 | Once the package is installed, this can be done with one line of code, making sure you have nice clean and standard species names with proper capitalization and no extra spaces. Words that are not a valid species name will currently return nothing. Species that are in one of the databases but not the others will reture `NA` for that column. 35 | 36 | ```{r, message=FALSE} 37 | growth_form_lookup_table(c("Acacia longifolia","Quercus agrifolia", 38 | "Clematis lasiantha","Hedera helix", 39 | "Ficus tremula","Najas flexilis", "Not a species")) 40 | ``` 41 | 42 | For the `support` column,: "F" is for free standing; "C" is for climber; "E" is for epiphyte, "P" is for parasite; "M" is for (holo)-mycoheterotroph; "A" is for aquatic; and "H" is for hemiepiphyte. 43 | 44 | For the `woodiness` column,: "W" is for woody; "H" is for herbaceous. 45 | 46 | For the `nfixing` column,: "yes" is for yes it forms n-fixing nodules; "no" is for no it doesn't. There are many species that presumably do not form N-fixing nodules based on their phylogentic position, but if no one has checked, they will show up as NA in this database. 47 | 48 | If you want a tree versus shrub split, [others have tackled that difficult problem](https://www.bbc.com/news/science-environment-39492977). 49 | 50 | That's it, really. Below is information about the data sources and the versioned data distribution system (which we think is really cool), feel free to check it out, but you don't need to read the rest of this to use the package. 51 | 52 | ### Citing these data 53 | 54 | For the `support` column please cite: 55 | 56 | **Taseski, G. , Beloe, C. J., Gallagher, R. V., Chan, J. Y., Dalrymple, R. L. and Cornwell, W. K.** (2019), A global growth form database for 143,616 vascular plant species. *Ecology*. Accepted Author Manuscript. https://doi.org/10.1002/ecy.2614 57 | 58 | For the `woodiness` column please cite: 59 | 60 | **Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM, Ordonez A** (2014) Three keys to the radiation of angiosperms into freezing environments. *Nature* 506(7486): 89–92. https://doi.org/10.1038/nature12872 61 | 62 | For the `nfixing` column please cite: 63 | 64 | **Werner GDA, Cornwell WK, Sprent JI, Kattge J, Kiers ET** (2014) A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. *Nature Communications* 5: 4087. https://doi.org/10.1038/ncomms5087 65 | 66 | ### Errors and more data 67 | 68 | If you find something to correct or a new amazing dataset to add to this, please raise an [issue](https://github.com/traitecoevo/growthform/issues). We'd like this to keep growing and getting better with time and use. 69 | 70 | ### Reproducing a specific version 71 | 72 | If you are publishing a paper with this library, or you want the results of your analysis to be reproducible for any other reason, include the version number in your call to lookup table. This will always pull the specific version of the taxonomy lookup that you used. If you leave this out, on a new machine the library will download the most recent version of the database rather than the specific one that you used. 73 | 74 | ```{r} 75 | growth_form_lookup_table(c("Acacia longifolia", "Quercus agrifolia"),version="0.2.3") 76 | ``` 77 | 78 | 79 | ---------------------- 80 | 81 | ## Data sources 82 | 83 | All this relies on the botanists that orginially classified these species in the field, but unfortunately they are too many to list here. Check [here](https://github.com/traitecoevo/growthform/tree/master/database_assembly_information/original_references) for a complete list of where these data come from. 84 | 85 | 86 | ## Details about the data distribution system 87 | 88 | This is designed to be a living database--it will update as taxonomy and data changes (which they always will). These updates will correspond with changes to the version number of this resource, and each version of the database will be available via [Github Releases](http://docs.travis-ci.com/user/deployment/releases/). If you use this resource for published analysis, please note the version number in your publication. This will allow anyone in the future to go back and find **exactly** the same version of the data that you used. 89 | 90 | Because Releases can be altered after the fact, we use [zenodo-github integration](https://guides.github.com/activities/citable-code/) to mint a DOI for each release. This will both give a citable DOI and help with the longevity of each version of the database. (Read more about this [here](https://www.software.ac.uk/blog/2016-09-26-making-code-citable-zenodo-and-github).) 91 | 92 | ### Details about the data distribution system 93 | 94 | 95 | You can download and load the data into `R` using the `growth_form()` function: 96 | 97 | ```{r} 98 | head(growth_form()) 99 | ``` 100 | 101 | To get the version number of the dataset run: 102 | 103 | ```{r} 104 | growth_form_version_current_local() 105 | ``` 106 | 107 | For the most current version on Github run: 108 | 109 | ```{r} 110 | growth_form_version_current_github() 111 | ``` 112 | 113 | For most uses, the latest release should be sufficient, and this is all that is necessary to use the data. 114 | 115 | # Living database 116 | 117 | ## Development version 118 | 119 | We will periodically release development versions of the database using github releases. We'll check these automatically using [travis-ci](http://travis-ci.org). As taxonomy is a moving target, we expect that the lookup to change with time. 120 | 121 | # Notes for making a release using this *living dataset* design 122 | 123 | * Update the `DESCRIPTION` file to **increase** the version number. Now that we are past version 1.0.0, we will use [semantic versioning](http://semver.org/) so be aware of when to change what number. 124 | * Rebuild datafile 125 | * Commit code changes and `DESCRIPTION` and push to GitHub 126 | * With R in the package directory, run 127 | 128 | ```{r hmm, eval=FALSE} 129 | growthform:::growth_form_release("") 130 | ``` 131 | 132 | where `""` is a brief description of new features of the release. 133 | 134 | * Check that it works by running `growthform::growth_form()` 135 | * Update the Zenodo badge on the readme 136 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | growthform: a versioned lookup table for the growth form of vascular plants 3 | =========================================================================== 4 | 5 | [![Build Status](https://travis-ci.org/traitecoevo/growthform.png?branch=master)](https://travis-ci.org/traitecoevo/taxonlookup) [![codecov.io](https://codecov.io/github/traitecoevo/growthform/coverage.svg?branch=master)](https://codecov.io/github/traitecoevo/growthform?branch=master) [![DOI](https://zenodo.org/badge/161406874.svg)](https://zenodo.org/badge/latestdoi/161406874) 6 | 7 | **Problem:** You have a list of species from anywhere in the world. You've fixed the names, but you'd like to know something about the species' growth forms. 8 | 9 | **Solution:** We've put together a growing list of growth forms, currently (>140,000 species). This list lives in this github repository. If you want the whole list, head to [our github releases tab and download the whole thing](https://github.com/traitecoevo/growthform/releases). If you want the ones that correspond to your list, load your list into R and follow the steps below. This package combines three separate giant database assembly efforts to build large lists of plant growth forms (see sources below). 10 | 11 | How to use this package 12 | ----------------------- 13 | 14 | ### Install the required packages 15 | 16 | ``` r 17 | #install.packages("devtools") # if necessary 18 | devtools::install_github("ropenscilabs/datastorr") 19 | devtools::install_github("traitecoevo/growthform") 20 | ``` 21 | 22 | ### Load the growthform package 23 | 24 | ``` r 25 | library(growthform) 26 | ``` 27 | 28 | ### Find the growth form for your species list 29 | 30 | Once the package is installed, this can be done with one line of code, making sure you have nice clean and standard species names with proper capitalization and no extra spaces. Words that are not a valid species name will currently return nothing. Species that are in one of the databases but not the others will reture `NA` for that column. 31 | 32 | ``` r 33 | growth_form_lookup_table(c("Acacia longifolia","Quercus agrifolia", 34 | "Clematis lasiantha","Hedera helix", 35 | "Ficus tremula","Najas flexilis", "Not a species")) 36 | ``` 37 | 38 | ## sp support woodiness nfixing 39 | ## 1 Acacia longifolia F W Yes 40 | ## 2 Clematis lasiantha C W No 41 | ## 3 Ficus tremula H W 42 | ## 4 Hedera helix C W No 43 | ## 5 Najas flexilis A H 44 | ## 6 Quercus agrifolia F W No 45 | 46 | For the `support` column,: "F" is for free standing; "C" is for climber; "E" is for epiphyte, "P" is for parasite; "M" is for (holo)-mycoheterotroph; "A" is for aquatic; and "H" is for hemiepiphyte. 47 | 48 | For the `woodiness` column,: "W" is for woody; "H" is for herbaceous. 49 | 50 | For the `nfixing` column,: "yes" is for yes it forms n-fixing nodules; "no" is for no it doesn't. There are many species that presumably do not form N-fixing nodules based on their phylogentic position, but if no one has checked, they will show up as NA in this database. 51 | 52 | If you want a tree versus shrub split, [others have tackled that difficult problem](https://www.bbc.com/news/science-environment-39492977). 53 | 54 | That's it, really. Below is information about the data sources and the versioned data distribution system (which we think is really cool), feel free to check it out, but you don't need to read the rest of this to use the package. 55 | 56 | ### Citing these data 57 | 58 | For the `support` column please cite: 59 | 60 | **Taseski, G. , Beloe, C. J., Gallagher, R. V., Chan, J. Y., Dalrymple, R. L. and Cornwell, W. K.** (2019), A global growth form database for 143,616 vascular plant species. *Ecology*. Accepted Author Manuscript. 61 | 62 | For the `woodiness` column please cite: 63 | 64 | **Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM, Ordonez A** (2014) Three keys to the radiation of angiosperms into freezing environments. *Nature* 506(7486): 89–92. 65 | 66 | For the `nfixing` column please cite: 67 | 68 | **Werner GDA, Cornwell WK, Sprent JI, Kattge J, Kiers ET** (2014) A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. *Nature Communications* 5: 4087. 69 | 70 | ### Errors and more data 71 | 72 | If you find something to correct or a new amazing dataset to add to this, please raise an [issue](https://github.com/traitecoevo/growthform/issues). We'd like this to keep growing and getting better with time and use. 73 | 74 | ### Reproducing a specific version 75 | 76 | If you are publishing a paper with this library, or you want the results of your analysis to be reproducible for any other reason, include the version number in your call to lookup table. This will always pull the specific version of the taxonomy lookup that you used. If you leave this out, on a new machine the library will download the most recent version of the database rather than the specific one that you used. 77 | 78 | ``` r 79 | growth_form_lookup_table(c("Acacia longifolia", "Quercus agrifolia"),version="0.2.3") 80 | ``` 81 | 82 | ## sp support woodiness nfixing 83 | ## 1 Acacia longifolia F W Yes 84 | ## 2 Quercus agrifolia F W No 85 | 86 | ------------------------------------------------------------------------ 87 | 88 | Data sources 89 | ------------ 90 | 91 | All this relies on the botanists that orginially classified these species in the field, but unfortunately they are too many to list here. Check [here](https://github.com/traitecoevo/growthform/tree/master/database_assembly_information/original_references) for a complete list of where these data come from. 92 | 93 | Details about the data distribution system 94 | ------------------------------------------ 95 | 96 | This is designed to be a living database--it will update as taxonomy and data changes (which they always will). These updates will correspond with changes to the version number of this resource, and each version of the database will be available via [Github Releases](http://docs.travis-ci.com/user/deployment/releases/). If you use this resource for published analysis, please note the version number in your publication. This will allow anyone in the future to go back and find **exactly** the same version of the data that you used. 97 | 98 | Because Releases can be altered after the fact, we use [zenodo-github integration](https://guides.github.com/activities/citable-code/) to mint a DOI for each release. This will both give a citable DOI and help with the longevity of each version of the database. (Read more about this [here](https://www.software.ac.uk/blog/2016-09-26-making-code-citable-zenodo-and-github).) 99 | 100 | ### Details about the data distribution system 101 | 102 | You can download and load the data into `R` using the `growth_form()` function: 103 | 104 | ``` r 105 | head(growth_form()) 106 | ``` 107 | 108 | ## sp support woodiness nfixing 109 | ## 1 Aa achalensis F 110 | ## 2 Aa argyrolepis F 111 | ## 3 Aa aurantiaca F 112 | ## 4 Aa calceata F 113 | ## 5 Aa colombiana F 114 | ## 6 Aa denticulata F 115 | 116 | To get the version number of the dataset run: 117 | 118 | ``` r 119 | growth_form_version_current_local() 120 | ``` 121 | 122 | ## [1] "0.2.3" 123 | 124 | For the most current version on Github run: 125 | 126 | ``` r 127 | growth_form_version_current_github() 128 | ``` 129 | 130 | ## [1] "0.2.3" 131 | 132 | For most uses, the latest release should be sufficient, and this is all that is necessary to use the data. 133 | 134 | Living database 135 | =============== 136 | 137 | Development version 138 | ------------------- 139 | 140 | We will periodically release development versions of the database using github releases. We'll check these automatically using [travis-ci](http://travis-ci.org). As taxonomy is a moving target, we expect that the lookup to change with time. 141 | 142 | Notes for making a release using this *living dataset* design 143 | ============================================================= 144 | 145 | - Update the `DESCRIPTION` file to **increase** the version number. 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