This package contains a compilation of compilations of published phytoplankton trait data.
phytotraitr is not available from CRAN.
You can install directly from github with:
# install.packages("devtools")
devtools::install_github("andrewdolman/phytotraitr")
Each table has a corresponding *_key table with details about each variable. The first three columns of the keys are also found in the help files for each table.
kable(Edwards_nutrient_traits[1:10,1:6], format = "markdown")
|species |isolate |taxon |system | temperature| irradiance| |:-----------------------|:----------|:------|:----------|-----------:|----------:| |Cyclotella cryptica |SAG 1070-1 |diatom |freshwater | 20.0| 60.00000| |Nitzschia closterium |NA |diatom |marine | 20.0| 60.00000| |Planktothrix agardhii |NA |cyano |freshwater | 24.0| 37.00000| |Planktothrix agardhii |NA |cyano |freshwater | 15.5| 37.00000| |Planktothrix agardhii |NA |cyano |freshwater | 20.5| 37.00000| |Planktothrix agardhii |NA |cyano |freshwater | 25.5| 37.00000| |Planktothrix agardhii |NA |cyano |freshwater | 15.4| 66.40000| |Scenedesmus quadricauda |NA |green |freshwater | 5.0| 16.60578| |Scenedesmus quadricauda |NA |green |freshwater | 10.0| 33.21156| |Scenedesmus quadricauda |NA |green |freshwater | 15.0| 116.24045|
kable(Edwards_nutrient_traits_key[1:6,], format = "markdown")
|Column name |Variable definition |Units |Storage type | |:-----------|:-------------------|:------------------------|:--------------| |species |Species name |text |string | |isolate |Isolate ID |text |string | |taxon |Taxon name |text |string | |system |Freshwater/marine |text |string | |temperature |Culture temperature |°C |floating point | |irradiance |Culture irradiance |µmol photons m^-2^ s^-1^ |floating point |
p <- Edwards_nutrient_traits %>%
filter(system == "freshwater") %>%
select(taxon, qmin_p_c, qmax_p_c) %>%
gather(Trait, Value, -taxon) %>%
filter(complete.cases(Value)) %>%
ggplot(aes(x = taxon, y = Value, colour = Trait)) %>%
+ geom_point(position = position_jitter(width = 0.05)) %>%
+ coord_flip() %>%
+ scale_x_discrete(with(Edwards_nutrient_traits_key,
Edwards_nutrient_traits_key[`Column name`=="taxon","Variable definition"])) %>%
+ scale_y_continuous(paste0("[",
with(Edwards_nutrient_traits_key,
Edwards_nutrient_traits_key[`Column name`=="qmin_p_c","Units"]),
"]"))
p
The data from the separate publications have not been harmonized - i.e. variable names may differ (e.g. species, Species) and they may use different taxonomy.
sets <- data(package = "phytotraitr")
sets <- data.frame(sets[[3]]) %>%
select(Item, Title)
kable(sets, format = "markdown")
|Item |Title | |:------------------------------|:-----------------------------------------------------------------------------------------------------------| |Chen_thermal_traits |Chen (2015) Thermal Traits. | |Chen_thermal_traits_key |Chen (2015) Thermal Traits key | |Chen_thermal_traits_references |Chen (2015) Thermal Traits references. | |Edwards_cell_volumes |Cell volumes of phytoplankton. | |Edwards_cell_volumes_key | | |Edwards_citations |Citation information for nutrient utilization traits. | |Edwards_nutrient_traits |Nutrient utilization traits of phytoplankton. | |Edwards_nutrient_traits_key | | |Kremer_raw |Phytoplankton cell and natural unit biovolumes. Raw biovolume data - pre quality control. | |Kremer_raw_key | | |Kremer_taxa |Phytoplankton cell and natural unit biovolumes. Taxonomic look-up table based on ITIS classifications | |Kremer_taxa_key | | |Kremer_volumes_genus |Phytoplankton cell and natural unit biovolumes. Genus-level biovolume data. | |Kremer_volumes_genus_agg |Phytoplankton cell and natural unit biovolumes. Genus-level aggregated biovolume data and full taxonomy. | |Kremer_volumes_genus_agg_key | | |Kremer_volumes_genus_key | | |Kremer_volumes_species |Phytoplankton cell and natural unit biovolumes. Species-level biovolume data. | |Kremer_volumes_species_agg |Phytoplankton cell and natural unit biovolumes. Species-level aggregated biovolume data and full taxonomy. | |Kremer_volumes_species_agg_key | | |Kremer_volumes_species_key | |
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