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: | no |
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
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(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
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(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
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(stemHeights, file = file.path(tempdir(), "stemHeights.csv"))