R/lm_resid.R

In forestmangr: Forest Mensuration and Management

#' @title 
#' Fit linear regressions, with the option of removing outliers using a interactive plot of residuals.
#' @description 
#' With this function it's possible to fit linear regressions by a grouping variable, and evaluate each equation via
#' an interactive plot of residuals, and get a data frame.
#' with each column as a coefficient and quality of fit variables, and other output options. Works with dplyr grouping functions.
#' @details 
#' this function uses lm_table as a basis, but calls a plot of residuals for each fitted model, for the user to evaluate. If
#' one decides to remove any of the points, one can click and drag, and then click on the 'remove points' button. After that,
#' one must simply click 'done' and the coefficients will be printed out.
#' 
#' It's possible to use the \code{output} argument to get a merged table if \code{output="merge"}, that binds
#' the original data frame and the fitted coefficients. 
#' If \code{output="merge_est"} we get a merged table as well, but with y estimated using the coefficients. If the fit is made using groups, this is taken into account, i.e. the estimation is made by group.
#' 
#' If \code{output="nest"}, a data frame with nested columns is provided. This can be used if the user desires to get a customized output.
#'
#' @param df A data frame.
#' @param model A linear regression model, with or without quotes. The variables mentioned in the model must exist in the provided data frame. X and Y sides of the model must be separated by "~".
#' @param output_mode  Selects different output options. Can be either \code{"table"}, \code{"merge"}, \code{"merge_est"} and \code{"nest"}. See details for explanations for each option. Default: \code{"table"}.
#' @param est.name Name of the estimated y value. Used only if \code{est.name = TRUE}. Default: \code{"est"}. 
#' @param keep_model If \code{TRUE}, a column containing lm object(s) is kept in the output. Useful if the user desires to get more information on the regression. Default: \code{FALSE}.
#' @param rmoutliers If \code{TRUE}, outliers are filtered out using the IQR method. Default: \code{FALSE}.
#' @param fct_to_filter Name of a factor or character column to be used as a filter to remove levels. Default: \code{NA}.
#' @param rmlevels Levels of the fct_to_filter variable to be removed from the fit Default: \code{NA}.
#' @param onlyfiteddata If \code{TRUE}, the output data will be the same as the fitted (and possibly filtered) data. Default: \code{FALSE}.
#' @param group_print This argument is only used internally by another function. Please ignore.
#' @return  A data frame. Different data frame options are available using the output argument.
#' 
#' @export
#' @examples 
#' if (interactive() ){
#'   library(forestmangr)
#'   library(dplyr)
#' 
#'   data("exfm19")
#' 
#'   # Fit SH model:
#'   lm_resid(exfm19, log(VWB) ~  log(DBH) + log(TH))
#' 
#' }
#' 
#' @author Sollano Rabelo Braga \email{sollanorb@@gmail.com}
#' @export
lm_resid <- function(df,model,output_mode='table',est.name = "est",
                     keep_model = FALSE,rmoutliers = FALSE,fct_to_filter=NA,
                     rmlevels=NA,onlyfiteddata=FALSE,group_print=NA){
  
  remove_these<-data<-reg<-.<-est<-Coefs<-Qualid<-Res<-NULL
  # copiar nome da variavel Y, com base no modelo
  Y <- all.vars( stats::formula(model)[[2]]) 
  
  # aqui criamos a interface. nothing fancy
  ui <- miniUI::miniPage(
    miniUI::gadgetTitleBar("Drag to select points"),
    
    miniUI::miniContentPanel(
      # The brush="brush" argument means we can listen for
      # brush events on the plot using input$brush.
      shiny::plotOutput("plot", height = "100%", brush = "brush")
    ),
    # adiciona mini botoes
    miniUI::miniButtonBlock(
      shiny::actionButton('rerun','retirar pontos'),
      shiny::actionButton("reset", "restaurar")
    ),
    
  ) # ui end
  
  
  
  server <- function(input, output, session){
    
    if(!any(is.na(group_print))){
      title_group <- paste0(group_print,unique(df[group_print]),collapse = " ")
      print(title_group)
    }
    # criar valor reativo
    vals <- shiny::reactiveValues()
    
    vals$keeprows = rep(TRUE, nrow(df) )
    
    # Toggle points that are clicked
    shiny::observeEvent( input$rerun, {
      
      selected <- shiny::brushedPoints(resid_orig(), input$brush)[[Y]]
      
      vals$keeprows <- xor(vals$keeprows,  df[[Y]] %in% selected )
      
    })
    
    # observar o botao 'restaurar'. se ele rodar,
    # aplicar true pra tudo na coluna keeprows, ou seja,
    # manter todas as colunas
    shiny::observeEvent(input$reset, {
      vals$keeprows <- rep(TRUE, nrow(df) )
    })
    
    # dfok e o dataframe que contem apenas as linhas keeprows,
    # ou seja, apenas as que o usuario nao marcou e retirou.
    # para facilitar o ajuste, será criada uma coluna com keeprows,
    # e ele será utilizado para filtrar na hora de ajustar
    dfok <- shiny::reactive({
      
      dfok <- df
      
      dfok$remove_these = vals$keeprows
      
      if(input$rerun){
        
        dfok$remove_these = vals$keeprows
        
      }
      
      dfok
      
    })
    
    # este e o ajuste com o dataframe original, sem alteracoes. utilizamos o res_table=TRUE
    # para ter como saida a tabela de residuos. sera uzado para fazer o plot com pontos vazios.
    resid_orig <- shiny::reactive({
      
      tab <- lm_table(df, model, output = "merge_est",
                      rmoutliers = rmoutliers,fct_to_filter=fct_to_filter,rmlevels=rmlevels,onlyfiteddata = TRUE) 
      
      resid_plot(tab, Y,'est',res_table = TRUE)
      
    })
    # aqui fazemos o grafico de fato. Sao dois graficos de dispersao,
    # sobrepostos. um com o dado original, outro com o dado filtrado
    output$plot <- shiny::renderPlot({
      
      # aqui, ajustamos o modelo novamente, porem utilizando dfok, nosso dado filtrado.
      dfok <- dfok() %>% 
        dplyr::filter(remove_these) %>% 
        lm_table(model, output = "merge_est",
                       rmoutliers = rmoutliers,fct_to_filter=fct_to_filter,rmlevels=rmlevels,onlyfiteddata = TRUE) 
      # aqui puxamos os residuos dos dados originais
      residorig <- resid_orig()
      # aqui fazemos o grafico com o dfok
      resid_plot(dfok, Y,'est') +  # em seguida adicionamos uma nova camada, com os residuos originais
        ggplot2::geom_point(data=residorig,ggplot2::aes_string( Y,'ERROR'),
                            fill=NA,col="black",alpha=0.75,shape=21) + {
                              if(!any(is.na(group_print)))
                                ggplot2::ggtitle(title_group)
                            } # mudamos o formato para circulo vazio
      # assim serao plotados duas camadas de dispersao, uma com o ajuste customizado, outra com o ajuste real
      
    })
    # out_final e a saida final da funcao. ela precisa ser reativa, pois depende
    # da selecao que o usuario fara dos pontos. # apenas ajustamos o modelo informado com dfok
    # o tipo de saida e definida pelo usuario. apenas betas, df com os dados (merge_est), etc
    out_final <- shiny::reactive({
      #print(dfok())
      lm_table(dfok(), model, 
               #output = "merge_est"
               output=output_mode,
               est.name = est.name, keep_model = keep_model,
               rmoutliers = rmoutliers,fct_to_filter=fct_to_filter,
               rmlevels=rmlevels,onlyfiteddata=onlyfiteddata,
               boolean_filter='remove_these',del_boolean=TRUE
      ) 
      
    })
    # para encerrar e entregar o resultado, o usuario deve clicar no botao done.
    # observamos ele. Caso seja clicado, paramos o app e entregamos out_final
    shiny::observeEvent(input$done, {
      print('reg_ok')
      shiny::stopApp( out_final() )
    })
    
  } # fim do servidor
  
  # como a ideia seria fazer um mini shiny dentro da funcao. acima criamos um servidor e UI.
  # agora no final da funcao, rodamos runGadget. isso faz com que a funcao entregue o shiny.
  # a funcao faz o resto
  shiny::runGadget(ui,server)
  
}