TR8: A Tool for Downloading Functional Traits Data for Plant Species

植物の機能形質データのダウンロードツール

> library(TR8)


            Please remember to always cite the appropriate sources of traits data (see ?bib).

> data("ECOFLORA_df")
> data("available_tr8")

バージョン: 0.9.14

関数名 概略
ECOFLORA_df ECOFLORA_df: local lookup table for Ecoflora species' url(s)
Ecoflora-class Class '"Ecoflora"': Class containing traits from Ecological Flora of the british Isles
LEDA_df LEDA_df : local (partial) copy of the LEDA traitbase website.
TR8-package TR8: a tool for retrieving functional traits data for plant species.
Tr8-class Class '"Tr8"'
available_tr8 A dataframe containing the traits available for download.
available_traits available_traits shows which traits are available for download
biolflor Retrieve traits data from the BiolFlor website.
biolflor_check biolflor_check
biolflor_clean Removes redundant text in traits collected from Biolflor
biolflor_lookup biolflor_lookup
biolflor_lu biolflor_lu
biolflor_traits-class Class '"biolflor_traits"' for containing traits retrieved from Biolflor
column_conversion column_conversion
column_list column_list
control control
ecoflora Retrieves traits data from Ecoflora website
ellenberg_pignatti-class Class '"ellenberg_pignatti"' to contain ellenberg values for Italian Flora's species
extract extract data from biolflor_traits classes
get_italian_flowering get_italian_flowering leda Extracts functional traits from the LEDA traitbase.
leda_download_to_local_directory A utility to download a local copy of the LEDA data files.
leda_general Function which takes care of downloading the '.txt' files composing the LEDA Traitbase
leda_lookup List with reference variables needed to download traits from LEDA Traitbase
list_of_traits_Biolflor list_of_traits_Biolflor
local_storage A utility to storage a local copy of traits data
luirig luirig
myco myco
pignatti pignatti
pignatti_f Extracts ellenberg values for the Italia Flora as provided by Pignatti et al. (2005)
retrieve_amf retrieve_amf
seed_simplify seed_simplify a function to shorten levels for seed longevity
tr8 'tr8': retrieving functional traits data from various databases.
tr8_config 'tr8_config' a GUI to configure TR8 package.
traits_eco Set of functional traits to be retrieved by Ecoflora.

ECOFLORA_df

Ecoflora webのデータセット

> data("ECOFLORA_df")
> ECOFLORA_df %>% {
+   print(class(.))
+   dplyr::glimpse(.)
+ }

[1] "data.frame"
Observations: 1,879
Variables: 7
$ species      (AsIs) Abies alba, Abies grandis, Abies nordmanniana, A...
$ web_link     (chr) "plant_no=260010060", "plant_no=260010020", "plan...
$ acceptedname (chr) "Abies alba", "Abies grandis", "Abies nordmannian...
$ sourceid     (chr) "iPlant_TNRS", "iPlant_TNRS", "iPlant_TNRS", "iPl...
$ score        (dbl) 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1...
$ matchedname  (chr) "Abies alba", "Abies grandis", "Abies nordmannian...
$ uri          (chr) "http://www.tropicos.org/Name/24900049", "http://...

LEDA_df

> data("LEDA_df")
> LEDA_df %>% {
+   print(class(.))
+   dplyr::glimpse(.)
+ }

available_tr8

> data("available_tr8")
> available_tr8 %>% {
+   print(class(.))
+   dplyr::glimpse(.)
+ }

[1] "data.frame"
Observations: 74
Variables: 3
$ short_code  (chr) "h_max", "h_min", "le_area", "le_long", "phot_path...
$ description (chr) "Maximum height", "Minimum height", "Leaf area", "...
$ db          (chr) "Ecoflora", "Ecoflora", "Ecoflora", "Ecoflora", "E...

column_list

> column_list %>% {
+   print(class(.))
+   print(str(.))
+ }

[1] "list"
List of 74
 $ height_max               : chr [1:3] "h_max" "Maximum height" "Ecoflora"
 $ height_min               : chr [1:3] "h_min" "Minimum height" "Ecoflora"
 $ leaf_area                : chr [1:3] "le_area" "Leaf area" "Ecoflora"
 $ leaf_longevity           : chr [1:3] "le_long" "Leaf longevity" "Ecoflora"
 $ Photosynthetic_pathway   : chr [1:3] "phot_path" "Photosynthetic pathway" "Ecoflora"
 $ life_form                : chr [1:3] "li_form" "Life form" "Ecoflora"
 $ Vegetative_reprod_method : chr [1:3] "reprod_meth" "Vegetative reprod method" "Ecoflora"
 $ Flowering_earliest_month : chr [1:3] "flw_early" "Flowering earliest month" "Ecoflora"
 $ Flowering_latest_month   : chr [1:3] "flw_late" "Flowering latest month" "Ecoflora"
 $ Pollen_vector            : chr [1:3] "poll_vect" "Pollen vector" "Ecoflora"
 $ Seed_weight_mean         : chr [1:3] "seed_wght" "Seed weight mean" "Ecoflora"
 $ Method_of_propagation    : chr [1:3] "propag" "Method of propagation" "Ecoflora"
 $ Ellenberg_light_Eco      : chr [1:3] "ell_light_uk" "Ellenberg light" "Ecoflora"
 $ Ellenberg_moisture_Eco   : chr [1:3] "ell_moist_uk" "Ellenberg moisture" "Ecoflora"
 $ Ellenberg_pH_Eco         : chr [1:3] "ell_pH_uk" "Ellenberg pH" "Ecoflora"
 $ Ellenberg_nitrogen_Eco   : chr [1:3] "ell_N" "Ellenberg nitrogen" "Ecoflora"
 $ Ellenberg_salt_Eco       : chr [1:3] "ell_S" "Ellenberg salt" "Ecoflora"
 $ age_of_first_flowering   : chr [1:3] "age_first_flowering" "Age of first flowering" "LEDA"
 $ branching                : chr [1:3] "branching" "Branching" "LEDA"
 $ bud_bank_seasonality_soil: chr [1:3] "bud_bank_seasonality_soil" "Bud bank seasonality at soil level" "LEDA"
 $ buoyancy                 : chr [1:3] "buoyancy" "Buoyancy" "LEDA"
 $ canopy_height            : chr [1:3] "canopy_height" "Mean canopy height" "LEDA"
 $ dispersal                : chr [1:3] "dispersal" "Dispersal type" "LEDA"
 $ leaf_distribution        : chr [1:3] "leaf_distribution" "Leaf distribution along the stem" "LEDA"
 $ leaf_dmc                 : chr [1:3] "leaf_dmc" "Leaf dry matter content " "LEDA"
 $ leaf_mass                : chr [1:3] "leaf_mass" "Leaf mass" "LEDA"
 $ leaf_size                : chr [1:3] "leaf_size" "Leaf size" "LEDA"
 $ dispersal_morphology     : chr [1:3] "dispersal_morphology" "Dispersal morphology" "LEDA"
 $ growth_form              : chr [1:3] "growth_form" "Growth form" "LEDA"
 $ life_span                : chr [1:3] "life_span" "Life span" "LEDA"
 $ releasing_height         : chr [1:3] "releasing_height" "Releasing height" "LEDA"
 $ sbank                    : chr [1:3] "sbank" "Seed bank" "LEDA"
 $ seed_mass                : chr [1:3] "seed_mass" "Seed mass" "LEDA"
 $ shoot_growth_form        : chr [1:3] "shoot_growth_form" "Shoot growth form" "LEDA"
 $ seed_number_per_shoot    : chr [1:3] "seed_number_per_shoot" "Seed number per shoot" "LEDA"
 $ woodiness                : chr [1:3] "woodiness" "Woodiness" "LEDA"
 $ terminal_velocity        : chr [1:3] "terminal_velocity" "Terminal velocity" "LEDA"
 $ Life form                : chr [1:3] "li_form_B" "Life form" "BiolFlor"
 $ Life span                : chr [1:3] "li_span" "Life span" "BiolFlor"
 $ Rosettes                 : chr [1:3] "ros" "Rosettes" "BiolFlor"
 $ Type of reproduction     : chr [1:3] "reprod_B" "Type of reproduction" "BiolFlor"
 $ Strategy type            : chr [1:3] "strategy" "Strategy type" "BiolFlor"
 $ Pollen vector            : chr [1:3] "poll_vect_B" "Pollen vector" "BiolFlor"
 $ L                        : chr [1:3] "ell_L_it" "Ellenberg value for light in Italy" "Pignatti"
 $ T                        : chr [1:3] "ell_T_it" "Ellenberg value for temperature in Italy" "Pignatti"
 $ C                        : chr [1:3] "ell_C_it" "Ellenberg value for continentality in Italy" "Pignatti"
 $ U                        : chr [1:3] "ell_U_it" "Ellenberg value for humidity in Italy" "Pignatti"
 $ R                        : chr [1:3] "ell_R_it" "Ellenberg value for soil reaction in Italy" "Pignatti"
 $ N                        : chr [1:3] "ell_N_it" "Ellenberg value for nitrogen in Italy" "Pignatti"
 $ S                        : chr [1:3] "ell_S_it" "Ellenberg value for salinity in Italy" "Pignatti"
 $ life_form_P              : chr [1:3] "life_form_P" "Life form for Italian Flora" "Pignatti"
 $ corotipo                 : chr [1:3] "distribution_p" "Distributions of species for the Italian Flora" "Pignatti"
 $ IT_beg_flow              : chr [1:3] "IT_beg_flow" "Beginning of flowering in Italy" "Pignatti"
 $ IT_end_flow              : chr [1:3] "IT_end_flow" "End of flowering in Italy" "Pignatti"
 $ Myco_infection           : chr [1:3] "Myco_infection" "Infection of AMF according to Akhmetzhanova et al." "AMF"
 $ MycoFlor                 : chr [1:3] "MycoFlor" "Infection of AMF according to MycoFlor" "AMF"
 $ inflorescence_fr         : chr [1:3] "inflorescence_fr" "Type of inflorescence" "Catminat"
 $ sex_reprod_fr            : chr [1:3] "sex_reprod_fr" "Type of sexual reproduction" "Catminat"
 $ poll_vect_fr             : chr [1:3] "poll_vect_fr" "Pollen vector" "Catminat"
 $ fruit_type_fr            : chr [1:3] "fruit_type_fr" "Type of fruit" "Catminat"
 $ dissemination_fr         : chr [1:3] "dissemination_fr" "Type of dissemination" "Catminat"
 $ flower_colour_fr         : chr [1:3] "flower_colour_fr" "Flower colour" "Catminat"
 $ ell_L_fr                 : chr [1:3] "ell_L_fr" "Ellenberg values for Light" "Catminat"
 $ elle_T_fr                : chr [1:3] "elle_T_fr" "Ellenberg values for temperature" "Catminat"
 $ ell_C_fr                 : chr [1:3] "ell_C_fr" "Ellenberg values for continentality" "Catminat"
 $ ell_U_atm_fr             : chr [1:3] "ell_U_atm_fr" "Ellenberg values for atmospheric moisture" "Catminat"
 $ ell_U_fr                 : chr [1:3] "ell_U_fr" "Ellenberg values for moisture" "Catminat"
 $ ell_R_fr                 : chr [1:3] "ell_R_fr" "Ellenberg values for soil reaction" "Catminat"
 $ ell_N_fr                 : chr [1:3] "ell_N_fr" "Ellenberg values for nitrogen" "Catminat"
 $ ell_S_fr                 : chr [1:3] "ell_S_fr" "Ellenberg values for salt" "Catminat"
 $ Soil_texture_fr          : chr [1:3] "Soil_texture_fr" "Type of soil texture" "Catminat"
 $ organic_matter_fr        : chr [1:3] "organic_matter_fr" "Organic matter in the soil" "Catminat"
 $ beg_flow_fr              : chr [1:3] "beg_flow_fr" "Beginning of flowering (month)" "Catminat"
 $ end_flow_fr              : chr [1:3] "end_flow_fr" "End of flowering (month)" "Catminat"
NULL

tr8

> tr8(species_list = c("Abies alba"),
+     download_list = c("life_form_P"))

           life_form_P
Abies alba P SCAP (SV)