wdata_org: Function for manipulating scoresheets and obtaining...

In elizabethastroud/FIBS-R-Package: Classification of unknown cases (e.g. archaeobotanical data or other modern weed survey data) using linear discriminant analysis to understand farming regimes

Function for manipulating scoresheets and obtaining functional trait data for wmodel.LDA

Description

Changes archaeobotanical data or other cases the investigator wishes to classify, such as survey data from other farming regimes, into presence/absence data and extracts the functional data for the listed species, and calculates the average of each functional attribute for each sample.

Usage

wdata_org(dataframe, samples, codes,codename, model, fl_pr=NULL, sp_av=NULL, vg_pr=NULL)

Arguments

dataframe	The data set to be transformed. Data should be arranged with each sample as a column and each species as rows. One column needs to contain the species codes of the taxa (see LOCATION for list of taxa and corresponding codes).
samples	The column number in which the sample data starts
codes	The column number containing the species codes
codename	The name of the column containing the species codes
model	The model being used; 1, 2 or 3 - this will determine which functional attributes are used
fl_pr	The flowering period data for the species (needs to be set up as two columns: one containing species codes and one containing flowering data labelled FLOWPER). This is only required for model 1 and model 3
sp_av	The averaged species data of composite taxa - this can be the ouput of ave_wdata
vg_pr	Modified vegetative proprogation values - all values VEGPROP values need to be re-entered if this argument is used

Value

A data frame containing the averaged functional attributes values for each sample. Which attributes are returned will be dependant on the model entered:

model 1:	SLA, ARNODE, LOGCANH, LOGCAND, FLOWPER
model 2:	SLA, ARNODE, LOGCANH, LOGCAND
model 3:	FLOWPER, VEGPROP

Author(s)

Elizabeth Stroud

References

PAPER REFERENCE

Examples

## Random data
species<-c("Chenopodium album" , "Anthemis cotula", "Brassica rapa ssp campestris",
  "Raphanus raphanistrum", "Agrostemma githago" , "Poa annua" )
code<-c("chenalb", "anthcot", "brasrap","raphrap","agrogit", "poa_ann")
s.1246<-sample(1:3, 6, replace=TRUE)
s.46178<-sample(1:5, 6, replace=TRUE)
s.1<-sample(0:8, 6, replace=TRUE)
s.23<-sample(0:3, 6, replace=TRUE)
s.987<-sample(3:9, 6, replace=TRUE)
dataset<-data.frame(species,code,s.1246,s.46178,s.1,s.23,s.987)
code<-c("chenalb", "anthcot", "brasrap","raphrap","agrogit", "poa_ann")
FLOWPER<-sample(3:9, 6, replace=TRUE)
x<-data.frame(code,FLOWPER)

## Use
results<-wdata_org(dataset, samples=3, codes=2, codename="code", model=1, fl_pr=x)

elizabethastroud/FIBS-R-Package documentation built on Sept. 26, 2024, 6:40 p.m.