| Type: | Package |
| Title: | Linear Population Growth Scenarios |
| Version: | 0.1.1 |
| Maintainer: | Biman Chakraborty <biman_c@yahoo.com> |
| Description: | Fit linear splines to species time series to detect population growth scenarios based on Hyndman, R J and Mesgaran, M B and Cousens, R D (2015) <doi:10.1007/s10530-015-0962-8>. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.1.1 |
| Imports: | dplyr |
| Depends: | R (≥ 2.10) |
| NeedsCompilation: | no |
| Packaged: | 2022-05-09 12:04:35 UTC; chakrabb |
| Author: | Philipp Robeck [aut], Biman Chakraborty [cre] |
| Repository: | CRAN |
| Date/Publication: | 2022-05-10 10:40:06 UTC |
Frequency and Specimens Data
Description
Example Frequency and Specimens data by year for each species to be used in 'PopulationGrowthR' package
Usage
fdata
Format
An object of class data.frame with 3771 rows and 4 columns.
Frequency plot for a lagphase fit
Description
Frequency plot for a lagphase fit
Usage
freqplot(
fit1,
fit2 = NULL,
fit3 = NULL,
fit4 = NULL,
xlab = "Year",
ylab = "Frequency",
main = fit1$name,
cols = 2:5,
...
)
Arguments
fit1, fit2, fit3, fit4 |
"lagphase" fit objects to plot |
xlab |
Label for the $x$-axis |
ylab |
Label for the $y$-axis |
main |
Title of the plot |
cols |
Colors to be used to draw the lines |
... |
(optional) parameters to pass to plot |
Value
Produces a plot of observed and predicted frequencies for the species against year
Examples
Species = unique(fdata$Species) #List of all species
fit1 = lagfit(fdata, yeardata, species=Species[1])
freqplot(fit1$fit)
Produces plot of the fitted spline function after adjusting for number of Specimens
Description
Produces plot of the fitted spline function after adjusting for number of Specimens
Usage
growthplot(
fit,
ylim = NULL,
xlab = "Year",
ylab = "Adjusted Frequency",
main = fit$name,
...
)
Arguments
fit |
a "lagphase" fit object to plot |
ylim |
vector of size 2 - limits of the $y$-axis |
xlab |
Label for the $x$-axis |
ylab |
Label for the $y$-axis |
main |
Title of the plot |
... |
(optional) parameters to pass to plot |
Value
Produces a plot of the fit with confidence bands
Examples
Species = unique(fdata$Species) #List of all species
fit1 = lagfit(fdata, yeardata, species=Species[1])
growthplot(fit1$fit)
Fits a piecewise glm model with lags
Description
This function fits a piecewise poisson model to the frequency data of different Species. It assumes that the data contains columns Year, Frequency and Specimens.
Usage
lagfit(
data,
yeardata,
species = NULL,
knots = NULL,
zeros = TRUE,
plotlag = FALSE,
plotfreq = FALSE
)
Arguments
data |
a dataframe containing the columns Species (optional), Year, Frequency and Specimens. |
yeardata |
a dataframe containing the columns Year and Specimens giving the total number of Specimens for each Year. |
species |
list of species for which the model is to be fitted. Default is NULL, which fits the model for all species in the data. |
knots |
a list of knots to be used for the piecewise model. Default is NULL, which chooses the optimal model with 0-4 knots. |
zeros |
logical. Specifies whether missing year for the species will be filled with zeros. Default is TRUE. |
plotlag |
logical. If TRUE a plot of the fitted model will be produced for each species. |
plotfreq |
logical. If TRUE frquency plots will be created for each species. |
Value
If the model is fit for a single species following are returned as a list
Species - Species name
Scene - Different scenario of the fit between the knots. A sequence of 0, + or - is returned. A 0 indicates constant, + indicates increasing and a - indicates decreasing.
Lag - Logical. Is there a lag present or not.
Laglength - Length of the first lag. Position of the First Knot - the first year for that species
FirstYear - The first year for that species for which data is available.
EndYear - The first knot position.
fit - the fitted model.
If the number of species is more than one, then a list is returned with following items:
fitdata - dataframe is returned with the items in the above list except for the fitted model.
fitcoefs - list of coefficients for the piecewise fits for each Species
Examples
#Run lagfit for 1 species only
Species = unique(fdata$Species) #List of all species
fit1 = lagfit(fdata, yeardata, species=Species[1])
#Run lagfit for multiple species
fit2 = lagfit(fdata, yeardata, species=Species[1:3])
fitdata = fit2$fitdata #Dataframe containing fits
fitcoefs = fit2$fitcoefs #List containing slopes of the fitted splines
## Not run:
#Run lagfit for the whole dataset
fitall = lagfit(fdata, yeardata)
## End(Not run)
Extract Frequency and Specimen data from the raw data
Description
Extract Frequency and Specimen data from the raw data
Usage
raw2freqdata(rawdata, species = "species", year = "year")
Arguments
rawdata |
a dataframe containing species, year |
species |
name of the column containing species names |
year |
name of the column containing year |
Value
Retirns a list of two dataframes
data - a dataframe conatining Species, Year, Freuqency and Specimens
yeardata - a dataframe containing Year and Specimens
Examples
cleandata = raw2freqdata(rawdata)
fdata = cleandata$data
yeardata = cleandata$yeardata
Raw GBIF Data
Description
Example raw GBIF data used in 'PopulationGrowthR' package
Usage
rawdata
Format
An object of class data.frame with 34088 rows and 50 columns.
Total Specimens Data
Description
Example total Specimens data by year to be used in 'PopulationGrowthR' package
Usage
yeardata
Format
An object of class data.frame with 60 rows and 2 columns.