R/taxon.response.r
taxon.response.RdThe output of this function to return 1.Weighted Average, 2. cdf_Abundance based, 3. cdf_ presence/absence based; 4. ecdf weighted, 5. cdf weight new; 6. Linear logistic regression, 7. quadratic logistic 8. GAM 5~7 using full data range; 9~11. repeat 6~8 but uses observed range for each single taxon; 12 Count. 13. Raw quantiles
taxon.response(spdata, envdata, sp.siteid = "Sample.ID", species = "GENUS", sp.abndid = "RA", env.siteid = "Sample.ID", xvar = "COND", cutoff = 30, region = "all", lim = "CDF", coord = NULL, mtype = 3, dense.N = 201, plot.pdf = F, add.map = F, statename = NULL, add.lab = F, main = "Capture Probability of Macroinvertebrate Taxon Along Conductivity Gradient", mar = c(5, 4, 3, 2), xlabs = expression(paste("Conductivity ( ", mu, "S/cm)")), log.x = TRUE, rounder = 0, taus = c(0, 95, 100), nbin = 61, wd = getwd())
| spdata | Species data. |
|---|---|
| envdata | Environmental data. |
| sp.siteid | Site/sample id column for spdata; default = "Sample.ID" |
| species | ; default = "GENUS" |
| sp.abndid | Name of column for species relative abundance within sample; default = "RA" |
| env.siteid | Site/sample id column for envdata; default = "Sample.ID" |
| xvar | xvariable, could be column index or name; default = "COND" |
| cutoff | a required minimum sample size for calculation; default = 30 |
| region | Region (e.g., ecoregion or bioregion) used to create directory for PDF output; default = "all" |
| lim | if lim == "GAM", add gam plot xc95 otherwise, add "CDF"; default ="CDF" |
| coord | ; default = NULL |
| mtype | could be 1 to 3, indicating which regression model to use; default = 3 |
| dense.N | is the number of areas to cut into in the calculation of area under the curve; default = 201 |
| plot.pdf | to decide if we want species vs. env plots options "none", "pdf", "tiff"; default = F |
| add.map | to decide if a map should be added before plots; default =F |
| statename | ; default = NULL |
| add.lab | ; default = F |
| main | Plot title (main); default = "Capture Probability of Macroinvertebrate Taxon Along Conductivity Gradient" |
| mar | ; default = c(5,4,3, 2) |
| xlabs | ; default = expression(paste("Conductivity ( ", mu, "S/cm)")) |
| log.x | if xvar should be logtransformated; default = TRUE |
| rounder | xvar rounder, default = 0. |
| taus | determine the output the percentile of env variable; default = c(0,95,100) |
| nbin | Number of bins; default = 61. |
| wd | Working directory for saving files. |
data frame and PDFS of CDF and GAM plots saved to the specified directory in subfolders ("cdf" and "gam")
# Environmental Variables varlist <- c("lgX3daymax", "lgMAF", "lgFallrate", "lgHigh1fall", "RBI", "lgX3daymin") varnames <- c("3-day Max", "Mean Annual Flow", "Fall Rate", "High 1 Fall", "RBI", "3-Day Min") # select variable vari <- 1 mydata <- envdata.all[!is.na(envdata.all[,varlist[vari]]),] # run function whole.values <- taxon.response(spdata = species, envdata = mydata, sp.siteid = "BenSampID", species = "OTU", sp.abndid = "RA", env.siteid = "BenSampID", xvar = varlist[vari], cutoff = 20, region = "tol_all", lim ="GAM", coord = c("BioSta_Long", "BioSta_Lat"), mtype = 3, dense.N = 201, plot.pdf = T, add.map = F, statename = NULL, add.lab = F, main = paste("Macroinvertebrates Response to", varnames[vari]), mar = c(5,4,3,2), xlabs= varnames[vari], log.x = F, rounder = 3, taus = c(0,50,100), nbin = 51, wd = getwd()) # view results View(whole.values)