In pratheesh3780/grapesAgri1: Collection of Shiny Apps for Agricultural Research Data Analysis

knitr::opts_chunk$set(echo = TRUE)
library(shiny)
library(shinyWidgets)
library(shinycssloaders)
library(rmarkdown)
library(pastecs)
library(dplyr)
library(reshape2)
library(knitr)
library(magrittr)
library(kableExtra)

RESULT

csvfile <- reactive({
    csvfile <- input$file1
    if (is.null(csvfile)){return(NULL)}
    dt <- read.csv(csvfile$datapath, header=input$header, sep=",",check.names = FALSE)
    dt
  })

################## summary one sample ttest
if(input$req1=='ottest'){
      if(input$submit3 > 0){
      grp1<- subset(csvfile(),select=input$dvar)
      final<-grp1
      res <- stat.desc(final)
      result<-as.data.frame(res)
      rownames(result)[rownames(result) == "nbr.val"] <- "Number of Obs."
      rownames(result)[rownames(result) == "nbr.null"] <- "null values"
      rownames(result)[rownames(result) == "nbr.na"] <- "NA"
      round(result,3)
      kable(result,caption = "Summary Statistics",digits=3) %>% kable_styling() %>% kable_paper("hover", full_width = F)
      }
    }
################# summary
if(input$req1 == 'ttest'||input$req1 == 'wttest'||input$req1=='ftest'||input$req1=='pttest'){
      if(input$submit1 > 0||input$submit2 > 0||input$submit4 > 0||input$submit5 > 0){
      grp1<- subset(csvfile(),select=input$dvar)
      grp2<- subset(csvfile(),select=input$ivar)
      final<-cbind(grp1,grp2)
      res <- pastecs::stat.desc(final)
      result<-as.data.frame(res)
      rownames(result)[rownames(result) == "nbr.val"] <- "Number of Obs."
      rownames(result)[rownames(result) == "nbr.null"] <- "null values"
      rownames(result)[rownames(result) == "nbr.na"] <- "NA"
      round(result,3)
      kable(result,caption = "Summary Statistics",digits=3) %>% kable_styling() %>% kable_paper("hover", full_width = F)
      }
    }
########## two sample ttest
 if(input$req1 == 'ttest'){
      if(input$submit1 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        y<-as.vector(csvfile()[,input$ivar])
        t<-t.test(x, y, alternative = input$alt,
                  var.equal = TRUE,paired = FALSE,na.omit=TRUE)
        t_value<-round(t$statistic,3)
        df<-t$parameter
        Pvalue<-round(t$p.value,6)
        alt.Hypothesis<-t$alternative
        result<-cbind(t_value,df,Pvalue,alt.Hypothesis)
        result<-as.data.frame(result)
         kable(result,caption = "Two sample unpaired t-test",row.names = FALSE) %>% kable_styling() %>% kable_paper("hover", full_width = F)
      }
 }
h3("")
########## note 1
  if(input$req1 == 'ttest'){
      if(input$submit1 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        y<-as.vector(csvfile()[,input$ivar])
        t<-t.test(x, y, alternative = input$alt,
                  var.equal = TRUE,paired = FALSE, na.omit=TRUE)

        if(t$p.value<=0.05){

        cat("Since P-value is < 0.05 we reject the null hypothesis at 5% level of significance.\n(here null hypothesis is: Population mean of group A = Population mean of group B)\n ")

        }
       else if(t$p.value>0.05){

        cat("Since P-value is > 0.05 we don't have enough evidence to reject the null hypothesis at 5% level of significance.\n(here null hypothesis is: Population mean of group A = Population mean of group B)\n")

         }
      }
  }
#############################################welch ttest
 if(input$req1 == 'wttest'){
      if(input$submit2 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        y<-as.vector(csvfile()[,input$ivar])
        t<-t.test(x, y, alternative = input$alt,
                  var.equal = FALSE,paired = FALSE,na.omit=TRUE)
        t_value<-round(t$statistic,3)
        df<-round(t$parameter,2)
        Pvalue<-round(t$p.value,6)
        alt.Hypothesis<-t$alternative
        result<-cbind(t_value,df,Pvalue,alt.Hypothesis)
        result<-as.data.frame(result)
        result
        kable(result,caption = "Welch unpaired t-test",row.names = FALSE) %>% kable_styling() %>% kable_paper("hover", full_width = F)
      }
 }
h3("")
########### note2
 if(input$req1 == 'wttest'){
      if(input$submit2 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        y<-as.vector(csvfile()[,input$ivar])
        t<-t.test(x, y, alternative = input$alt,
                  var.equal = FALSE,paired = FALSE, na.omit=TRUE)

        if(t$p.value<=0.05){
      cat("Since P-value is < 0.05 we reject the null hypothesis at 5% level of significance.\n(here null hypothesis is: Population mean of group A = Population mean of group B)\n ")

        }
        else if(t$p.value>0.05){
         cat("Since P-value is > 0.05 we don't have enough evidence to reject the null hypothesis at 5% level of significance.\n(here null hypothesis is: Population mean of group A = Population mean of group B)\n")

        }
      }
    }
############### one sample ttest
if(input$req1 == 'ottest'){
      if(input$submit3 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        t<-t.test(x, y=NULL, alternative = input$alt,
                  mu = input$mu, na.omit=TRUE)
        t_value<-round(t$statistic,3)
        df<-round(t$parameter,2)
        Pvalue<-round(t$p.value,6)
        alt.Hypothesis<-t$alternative
        result<-cbind(t_value,df,Pvalue,alt.Hypothesis)
        result<-as.data.frame(result)
        kable(result,caption = "One sample t-test",row.names = FALSE) %>% kable_styling() %>% kable_paper("hover", full_width = F)
      }
}
h3("")

############### note 3
if(input$req1 == 'ottest'){
      if(input$submit3 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        t<-t.test(x, y=NULL, alternative = input$alt,
                  mu = input$mu, na.omit=TRUE)
        mu<-as.numeric(input$mu)

        if(t$p.value<=0.05){
          cat("Since P-value is < 0.05.\nwe can reject the null hypothesis at 5 percent level of significance.\n")
        }
        else if(t$p.value>0.05){
          cat("Since P-value is > 0.05.\nwe don't have enough evidence to reject null hypothesis at 5 percent level of significance.\n")
        }
      }
    }
############### F test
if(input$req1 == 'ftest'){
      if(input$submit4 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        y<-as.vector(csvfile()[,input$ivar])
        f<-var.test(x, y, ratio = 1,
                 alternative = input$alt)
        F_value<-round(f$statistic,3)
        df<-as.data.frame(f$parameter)
        Pvalue<-round(f$p.value,6)
        alt.Hypothesis<-f$alternative
        result<-cbind(F_value,t(df),Pvalue,alt.Hypothesis)
        result<-as.data.frame(result)
         kable(result,caption = "F test for Homogenity of Variance",row.names = FALSE) %>% kable_styling() %>% kable_paper("hover", full_width = F)
      }
}
h3("")
##### note 4
if(input$req1 == 'ftest'){
      if(input$submit4 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        y<-as.vector(csvfile()[,input$ivar])
        f<-var.test(x, y, ratio = 1,
                    alternative = input$alt)

        if(f$p.value<=0.05){
          cat("Since P-value is < 0.05 we can reject the null hypothesis at 5 percent level of significance.\n(Here null hypothesis: Variances are Homogenous)\n")
        }
        else if(f$p.value>0.05){
          cat("Since P-value is > 0.05 we don't have enough evidence to reject null hypothesis at 5 percent level of significance. Variance is homogenous.\n(Here null hypothesis: Variances are Homogenous)\n")

        }
      }
    }
############################# Paired t test
if(input$req1 == 'pttest'){
      if(input$submit5 > 0){
      grp1<- subset(csvfile(),select=input$dvar)
      grp2<- subset(csvfile(),select=input$ivar)
      final<-cbind(grp1,grp2)
      ttest <- t.test(final[,1], final[,2], paired = TRUE, alternative = input$alt)
      tvalue<-round(ttest$statistic,3)
      df<-ttest$parameter
      pvalue<-round(ttest$p.value,6)
      meandiff<-round(ttest$estimate,3)
      result1<-cbind(tvalue,df,pvalue,meandiff)
      row.names(result1)<-NULL
       kable(result1,caption = "Paired t test",row.names = FALSE) %>% kable_styling() %>% kable_paper("hover", full_width = F)
      }
}
h3("")
 if(input$req1 == 'pttest'){
      if(input$submit5 > 0){
        x<-as.vector(csvfile()[,input$dvar])
        y<-as.vector(csvfile()[,input$ivar])
        t<-t.test(x, y, alternative = input$alt,
                  var.equal = FALSE,paired = TRUE, na.omit=TRUE)

        if(t$p.value<=0.05){
          cat("Since P-value is < 0.05 we reject the null hypothesis at 5% level of significance.\n(here null hypothesis is: Population mean of group A = Population mean of group B) \n")

        }
        else if(t$p.value>0.05){
         cat("Since P-value is > 0.05 we don't have enough evidence to reject the null hypothesis at 5% level of significance.\n(here null hypothesis is: Population mean of group A = Population mean of group B)\n")

        }
      }
    }

Package: grapesAgri1, Version: 1.0.0

pratheesh3780/grapesAgri1 documentation built on Dec. 7, 2023, 5:49 a.m.