Help for package NitrogenUptake2016

Type:

Package

Title:

Data and Source Code From: Nitrogen Uptake and Allocation Estimates for Spartina Alterniflora and Distichlis Spicata

Version:

0.2.3

Date:

2018-10-28

Author:

Troy D. Hill, Nathalie R. Sommer, Caroline R. Kanaskie, Emily A. Santos, and Autumn J. Oczkowski

Maintainer:

Troy D. Hill <Hill.Troy@gmail.com>

Description:

Contains data, code, and figures from Hill et al. 2018a (Journal of Experimental Marine Biology and Ecology; <doi:10.1016/j.jembe.2018.07.006>) and Hill et al. 2018b (Data In Brief <doi:10.1016/j.dib.2018.09.133>). Datasets document plant allometry, stem heights, nutrient and stable isotope content, and sediment denitrification enzyme assays. The data and analysis offer an examination of nitrogen uptake and allocation in two salt marsh plant species.

License:

GPL-3

Encoding:

UTF-8

URL:

https://github.com/troyhill/NitrogenUptake2016

LazyData:

true

Depends:

R (≥ 3.0), zoo, car, MASS

RoxygenNote:

6.1.0

Suggests:

knitr, rmarkdown, plyr, reshape2, ggplot2, scales, MuMIn, rsq

VignetteBuilder:

knitr

NeedsCompilation:

Packaged:

2018-10-28 17:21:21 UTC; tdh

Repository:

CRAN

Date/Publication:

2018-10-28 18:20:03 UTC

Data: Nutrient concentrations, stable isotope ratios, and biomass from destructive mesocosm harvests

Description

Data: Nutrient concentrations, stable isotope ratios, and biomass from destructive mesocosm harvests

Usage

CN_mass_data

Format

A dataframe with 1192 observations of 16 variables:

time: Time point of harvest (harvested at one-week intervals)
new.core.id: Unique mesocosm identifier, including species (SA or DS) and mesocosm number
depth_bottom: Depth at bottom of sample (only applicable for belowground data)
sample.type: Sample material; tissue type
interval: Depth interval for sample; indicates the top and bottom depths (e.g., an entry of "5_10" covers the depth interval from 5-10 cm)
pool_label: Label for each pool (combination of "sample.type" and "depth_bottom")
id: Same as "pool_label" but with mesocosm ID included
species: Spartina alterniflora (SA) or Distichlis spicata (DS)
d15n: 15-N isotope ratio in per mille units
n_pct: Nitrogen content, decimal fraction (0.015 = 1.5 percent)
d13c: 13-C isotope ratio in per mille units
c_pct: Carbon content, decimal fraction (0.015 = 1.5 percent)
total_volume_cm3: Total volume of interval (only applicable for belowground data)
depth_top: Depth at top of sample (only applicable for belowground data)
sample.type2: Simplified "sample.type" column; leaf numbers dropped, and belowground stems included as "stems"
g_core: Total mass (grams) in entire pool; corrects for subsampling of depth intervals

References

Hill, T.D., N.R. Sommer, C.R. Kanaskie, E.A. Santos, A.J. Oczkowski. 2018. Data and source code from: Nitrogen uptake and allocation estimates for Spartina alterniflora and Distichlis spicata. Data In Brief. 21: 466-472. https://doi.org/10.1016/j.dib.2018.09.133.

Hill, T.D., N.R. Sommer, C.R. Kanaskie, E.A. Santos, A.J. Oczkowski. 2018. Nitrogen uptake and allocation estimates for Spartina alterniflora and Distichlis spicata. Journal of Experimental Marine Biology and Ecology 507: 53-60. https://doi.org/10.1016/j.jembe.2018.07.006.

Examples

### export to .csv:
write.csv(CN_mass_data, file = file.path(tempdir(), "CN_mass_data.csv"))

Data: Stem masses and heights for plants collected from Colt State Park, Rhode Island, USA, during summer 2016

Description

A dataframe of masses and heights of stems of Spartina alterniflora and Distichlis spicata. Samples were collected from Colt State Park, Bristol, RI, USA, during May-July 2016. Column descriptions:

Usage

allometry

Format

A dataframe with 170 observations of 6 variables:

site: Study location (Colt State Park, RI)
samplingDate: Sampling dates
status: Indicates whether plant was live or dead
height_cm: Stem height, in centimeters, from the sediment surface to the tip of the longest leaf
sample: Biomass, grams
spp: Species (SPAL or DISP)

References

Examples

### export to .csv:
write.csv(allometry, file = file.path(tempdir(), "allometry.csv"))

Convert per mil isotope values to atom percent

Description

Convert per mil isotope values to atom percent

Usage

ap(perMilValues, isotope = "15N")

Arguments

perMilValues

Value to be converted, in per mil notation

isotope

can be 13C or 15N

Value

a numeric value or vector

Examples

ap(10); ap(1000)

Parameterize Box-Cox model for mass-height allometry (based on Lu et al. 2016)

Description

Parameterize Box-Cox model for mass-height allometry (based on Lu et al. 2016)

Usage

bCM(dat, mass = "sample", height = "height_cm", lam.avail = c(-2,
  -1.5, -1, -2/3, -1/2, -1/3, 0, 1/3, 1/2, 2/3, 1, 1.5, 2),
  lam.only = FALSE)

Arguments

dat

dataframe with data

mass

mass column

height

height column

lam.avail

set of possible lambda values

lam.only

if TRUE, lambda is returned. If FALSE, model is returned

Value

if lam.only is FALSE, a model is returned. If lam.only is TRUE, lambda value is returned.

References

Lu, Meng, Caplan, Joshua S., Bakker, Jonathan D., Mozdzer, Thomas J., Drake, Bert G., Megonigal, J. Patrick, and Langley, J. Adam. 2016. Allometry data and equations for coastal marsh plants. Ecology. https://doi.org/10.1002/ecy.1600.

Examples

### get allometry model for each species
CSP <- plyr::dlply(allometry, c("spp"), bCM)
CSP.coef <- plyr::ldply(CSP, stats::coef)
### add lambda value
CSP.coef$lam <- plyr::ddply(allometry, c("spp"), function(df)  
                bCM(df, lam.only = TRUE))[, "V1"]

Data: Denitrification enzyme activity and in vitro N2O production rates

Description

Data: Denitrification enzyme activity and in vitro N2O production rates

Usage

dea

Format

A dataframe with six rows and five columns:

pot: Mesocosm ID; equivalent to "new.core.id" in other datasets
DEA: Denitrification enzyme activity (units = nanomoles N2O / gram dry mass / hour)
IV: "In vitro" N2O production; no nutrient solution added, just filtered seawater (units = nanomoles N2O / gram dry mass / hour)
mcf: Moisture correction factor (1 - gravimetric water content)
bd_gcm3: Bulk density (grams per cubic centimeter)

References

Examples

### export to .csv:
write.csv(dea, file = file.path(tempdir(), "dea.csv"))

Calculate net aboveground primary production

Description

Calculate net aboveground primary production

Usage

nappCalc2(dataset, liveCol = "mass", deadCol = "dead",
  yearCol = "year", siteCol = "pot2", timeCol = "day",
  annualReset = "TRUE", MilnerHughes = "TRUE", EOS = "FALSE",
  EOS_window = 1, summarize = "TRUE")

Arguments

dataset

data

liveCol

live biomass

deadCol

dead biomass

yearCol

year

siteCol

site/plot/experimental unit identifier

timeCol

time column (sequential measurements within each year)

annualReset

should data be reset to zero each year

MilnerHughes

If "TRUE", Milner-Hughes NAPP is calculated

EOS

If "TRUE", end-of-season live biomass is reported

EOS_window

window for EOSL

summarize

If "TRUE", output will be a list with two elements: incremental data and summary data

Value

list

Convert N2O units from nanomoles of N2O per hour to milligrams of N per day

Description

Convert N2O units from nanomoles of N2O per hour to milligrams of N per day

Usage

nmolHr_mgDay(x)

Arguments

x

numeric or integer value(s)

Value

numeric value

Examples

nmolHr_mgDay(dea$DEA)

Calculates standard error

Description

Calculates standard error

Usage

se(x)

Arguments

x

numeric or integer

Value

value

Examples

se(CN_mass_data$n_pct)
plyr::ddply(CN_mass_data, plyr::.(species, pool_label), plyr::summarise, se = se(n_pct))

Data: Stem heights for each mesocosm and each measurement date

Description

A dataframe of Spartina alterniflora and Distichlis spicata stem heights, from the mesocosms used in 15N study. Samples were collected from Colt State Park, Bristol, RI, USA, and grown in the US EPA Atlantic Ecology Division greenhouse.

Usage

stemHeights

Format

A dataframe with 3315 observations of 10 variables:

date: Measurement date
core_num: Mesocosm number
species: Species, either Spartina alterniflora (SA) or Distichlis spicata (DS)
dead_live: Indicates whether plant was live or dead
plant_num: Plants were tagged to permit growth rate calculations; this is the plant tag number
height_cm: Stem height, in centimeters, from the sediment surface to the tip of the longest leaf
id: Unique plant identifier, combining species, mesocosm number, and plant tag number
day: Measurement date expressed in YYYY-MM-DD format (and structured as a POSIXct column in R)
timeSinceLast: Days since last measurement
new.core.id: Mesocosm ID, including species and a unique mesocosm number (time-zero mesocosms re-numbered as mesocosms 13, 14, and 15)

References

Examples

### export to .csv:
write.csv(stemHeights, file = file.path(tempdir(), "stemHeights.csv"))