In jakehosen/stardom_aqualog: PARAFAC Analysis of EEMs from DOM

This report was created using the R package staRdom version r packageVersion("staRdom"), (r packageDescription("staRdom")$Author, r unlist(strsplit(packageDescription("staRdom")$Date,"-"))[1])

Model summary

pfmodel

Results

Components

comp_load <- eempf_comp_load_plot(pfmodel)
comp_load[[1]]

Loadings

comp_load[[2]]

if(class(try(library(kableExtra),silent=TRUE)) != "try-error" & class(try(library(knitr),silent=TRUE)) != "try-error") {
  pfmodel$A %>%
    kable(format = "html", booktabs = T) %>%
    kable_styling(bootstrap_options = c("striped", "hover"), full_width = FALSE) #%>%
  #kable_styling(font_size = 5) %>%
  #row_spec(0, angle = -45) #%>%
  #landscape()
} else {
  pfmodel$A
}

Data summary

if(!is.null(eem_list)){
  if(class(try(library(kableExtra),silent=TRUE)) != "try-error" & class(try(library(knitr),silent=TRUE)) != "try-error") {
    eem_list %>%
      summary() %>%
      kable(format = "html", booktabs = T) %>%
      kable_styling(bootstrap_options = c("striped", "hover"), full_width = FALSE) #%>%
    #kable_styling(font_size = 5) %>%
    #row_spec(0, angle = -45) #%>%
    #landscape()
  } else {
    eem_list %>%
      summary()
  } } else{
    cat("Due to missing EEM data this check was skipped!", fill=TRUE)
  }

Model performance

if(performance[1] != FALSE){
  performance
} else {
  cat("Performance test was skipped.")
}

Leverage of samples and wavelengths

cpl <- eempf_leverage(pfmodel)
eempf_leverage_plot(cpl)

Check input data

if(!is.null(eem_list) & !is.null(abs_data)){
  eem_checkdata(eem_list,abs_data,meta,metacolumns = metacolumns, error = FALSE)
} else {
  cat("Due to missing EEM and absorbance data this check was skipped!", fill=TRUE)
}

Split-half analysis

if(class(splithalf) == "list" & class(splithalf[[1]][[1]]) == "parafac"){
  if(class(try(library(kableExtra),silent=TRUE)) != "try-error" & class(try(library(knitr),silent=TRUE)) != "try-error") {
    tcc %>%
      kable(format = "html", booktabs = T) %>%
      kable_styling(bootstrap_options = c("striped", "hover"), full_width = FALSE) #%>%
    #kable_styling(font_size = 5) %>%
    #row_spec(0, angle = -45) #%>%
    #landscape()
  } else {
    tcc
  }
}

if(class(splithalf) == "list" & class(splithalf[[1]][[1]]) == "parafac"){
  splithalf_plot(splithalf)
} else {
  cat("Split-half analysis was skipped.", fill=TRUE)
}

Sample loadings and residuals

if(residuals){
  eempf_residuals_plot(pfmodel,eem_list,spp=spp)
} else {
  cat("Plotting loadings and residuals was skipped.", fill=TRUE)
}

jakehosen/stardom_aqualog documentation built on May 14, 2019, 3:06 a.m.