readme.md

In andrewdolman/phytotraitr: An R data package for phytoplankton traits

phytotraitr

This package contains a compilation of compilations of published phytoplankton trait data.

Contents:

• Nutrient uptake traits from Edwards et al (2015)
• Thermal traits from Chen (2015)
• Cell and natural unit biovolumes from Kremer et al (2014)

Chen B. (2015) Patterns of thermal limits of phytoplankton. Journal of Plankton Research 37, 285-292.

Edwards K.F., Klausmeier C.A. & Litchman E. (2015) Nutrient utilization traits of phytoplankton. Ecology 96, 2311-2311.

Kremer C.T., Gillette J.P., Rudstam L.G., Brettum P. & Ptacnik R. (2014) A compendium of cell and natural unit biovolumes for >1200 freshwater phytoplankton species. Ecology 95, 2984.

Installation

phytotraitr is not available from CRAN.

You can install directly from github with:

# install.packages("devtools")
devtools::install_github("andrewdolman/phytotraitr")

Usage

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 |

Minimum and maximum P cell quotas for freshwater taxa

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

Consistency

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.

Full list of dataframes

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 | |

andrewdolman/phytotraitr documentation built on May 10, 2019, 10:31 a.m.