I have a strange Error and actually don't know how to solve it, even after checking other posts. Everything runs until the Kriging and then I receive the error: Error in (function (classes, fdef, mtable) unable to find an inherited method for function ‘krige’ for signature ‘"formula", "tbl_df"’
The strange thing is that everything worked a few days ago, I did not change anything in the code and now it doesn't run anymore. Some other posts related the problem with the Raster, but I could not find any discrepances. Is there something because of recent updates? I use for example the sp package.
Unfortunately I cannot provide the data I use, hopefully it can be solved without.
How can I solve the issue? Thank you in advance for the help.
homeDir = "D:/Folder/DataXYyear/"
y = 1992
Source = paste("Year", y, ".csv")
File = file.path(homeDir,Source)
GWMeas <- read_csv(File)
GWMeasX <- na.omit(GWMeas)
ggplot(
data = GWMeasX,
mapping = aes(x = X, y = Y, color = level)
) +
geom_point(size = 3) +
scale_color_viridis(option = "B") +
theme_classic()
GWMX_sf <- st_as_sf(GWMeasX, coords = c("X", "Y"), crs = 25832) %>%
cbind(st_coordinates(.))
v_emp_OK <- gstat::variogram(
level~1,
as(GWMX_sf, "Spatial") # switch from {sf} to {sp}
)
v_mod_OK <- automap::autofitVariogram(level~1, as(GWMX_sf, "Spatial"), model = "Sph")$var_model
GWMeasX %>% as.data.frame %>% glimpse
GW.vgm <- variogram(level~1, locations = ~X+Y, data = GWMeasX) # calculates sample variogram values
GW.fit <- fit.variogram(GW.vgm, model=vgm(model = "Gau")) # fit model
sf_GWlevel <- st_as_sf(GWMeasX, coords = c("X", "Y"), crs = 25833)
grd_sf <- sf_GWlevel %>%
st_bbox() %>%
st_as_sfc() %>%
st_make_grid(
cellsize = c(5000, 5000), # 5000m pixel size
what = "centers"
) %>%
st_as_sf() %>%
cbind(., st_coordinates(.))
grid <- as(grd_sf, "Spatial")
gridded(grid) <- TRUE
grid <- as(grid, "SpatialPixels")
createGrid <- function(XY.Spacing)
crs(grid) <- crs(GWMX_sf)
OK3 <- krige(formula = level~1, # variable to interpolate
data = GWMX_sf, # gauge data
newdata = grid, # grid to interpolate on
model = v_mod_OK, # variogram model to use
nmin = 4, # minimum number of points to use for the interpolation
nmax = 20, # maximum number of points to use for the interpolation
maxdist = 120e3 # maximum distance of points to use for the interpolation
)
I tried to add significane level (package:ggpubrto)to my t_test plot (package:rstatix) and got a plot which the lines of significance are in the "pulled" to the right of the plot.
I copy the code from this link [https://www.datanovia.com/en/blog/how-to-perform-multiple-t-test-in-r-for-different-variables/][1] but still got the same plot
here is the code:
library(tidyverse)
library(rstatix)
library(ggpubr)
# Prepare the data and inspect a random sample of the data
mydata <- iris %>%
filter(Species != "setosa") %>%
as_tibble()
mydata %>% sample_n(6)
mydata.long <- mydata %>%
pivot_longer(-Species, names_to = "variables", values_to = "value")
mydata.long %>% sample_n(6)
stat.test <- mydata.long %>%
group_by(variables) %>%
t_test(value ~ Species) %>%
adjust_pvalue(method = "BH") %>%
add_significance()
stat.test
myplot <- ggboxplot(
mydata.long, x = "Species", y = "value",
fill = "Species", palette = "npg", legend = "none",
ggtheme = theme_pubr(border = TRUE)) +
facet_wrap(~variables)
# Add statistical test p-values
stat.test <- stat.test %>% add_xy_position(x = "Species")
myplot + stat_pvalue_manual(stat.test, label = "p.adj.signif")`
[this is the result from the site:][2]
[and this is what i got:][4]
any idea what i did wrong?
My Rstudio version is 1.4.1103
[1]: https://www.datanovia.com/en/blog/how-to-perform-multiple-t-test-in-r-for-different-variables/
[2]: https://i.stack.imgur.com/tzPo6.png
[3]: https://i.stack.imgur.com/1rtAO.jpg
[4]: https://i.stack.imgur.com/MJolk.png
I found it
i changed the "xmin" and "xmax values of "stat.test
Hello I am creating an environmental shiny app in which I want to use a leaflet map to create some simple plots based on openair package(https://rpubs.com/NateByers/Openair).
Aq_measurements() general form
AQ<- (aq_measurements(country = “country”, city = “city”, location = “location”, parameter = “pollutant choice”, date_from = “YYYdateY-MM-DD”, date_to = “YYYY-MM-DD”).
All parameters available in locations dataframe.
worldmet() general form
met <- importNOAA(code = "12345-12345", year = YYYYY:YYYY)
NOAA Code available in locations dataframe
Below I create a sample of my initial data frame:
location = c("100 ail","16th and Whitmore","40AB01 - ANTWERPEN")
lastUpdated = c("2018-02-01 09:30:00", "2018-02-01 03:00:00", "2017-03-07 10:00:00")
firstUpdated = c("2015-09-01 00:00:00","2016-03-06 19:00:00","2016-11-22 15:00:00")
pm25=c("FALSE","FALSE","FALSE")
pm10=c("TRUE","FALSE","FALSE")
no2=c("TRUE","FALSE","FALSE")
latitude=c(47.932907,41.322470,36.809700)
longitude=c(106.92139000,-95.93799000
,-107.65170000)
df = data.frame(location, lastUpdated, firstUpdated,latitude,longitude,pm25,pm10,no2)
As a general idea I want to be able to click on a certain location in the map based on this dataframe. Then I have one selectInput() and 2 dateInput(). The 2 dateInput() should take as inputs the df$firstUpdated and df$lastUpdated respectively. Then the selectInput() should take as inputs the pollutants that exist in the df based on "TRUE"/"FALSE" value. And then the plots should be created. All of these should be triggered by clicking on the map.
Up to now I was not able to achieve this so in order to help you understand I connected the selectInput() and the dateInput() with input$loc which is a selectIpnut() with locations in the first tab as I will not need this when I find the solution.
library(shiny)
library(leaflet)
library(plotly)
library(shinythemes)
library(htmltools)
library(DT)
library(utilr)
library(openair)
library(plotly)
library(dplyr)
library(ggplot2)
library(gissr)
library(ropenaq)
library(worldmet)
# Define UI for application that draws a histogram
ui = navbarPage("ROPENAQ",
tabPanel("CREATE DATAFRAME",
sidebarLayout(
# Sidebar panel for inputs ----
sidebarPanel(
wellPanel(
uiOutput("loc"),
helpText("Choose a Location to create the dataframe.")
)
),
mainPanel(
)
)
),
tabPanel("LEAFLET MAP",
leafletOutput("map"),
wellPanel(
uiOutput("dt"),
uiOutput("dt2"),
helpText("Choose a start and end date for the dataframe creation. Select up to 2 dates")
),
"Select your Pollutant",
uiOutput("pollutant"),
helpText("While all pollutants are listed here, not all pollutants are measured at all locations and all times.
Results may not be available; this will be corrected in further revisions of the app. Please refer to the measurement availability
in the 'popup' on the map."),
hr(),
fluidRow(column(8, plotOutput("tim")),
column(4,plotOutput("polv"))),
hr(),
fluidRow(column(4, plotOutput("win")),
column(8,plotOutput("cal"))),
hr(),
fluidRow(column(12, plotOutput("ser"))
)
)
)
#server.r
# load data
# veh_data_full <- readRDS("veh_data_full.RDS")
# veh_data_time_var_type <- readRDS("veh_data_time_var_type.RDS")
df$location <- gsub( " " , "+" , df$location)
server = function(input, output, session) {
output$pollutant<-renderUI({
selectInput("pollutant", label = h4("Choose Pollutant"),
choices = colnames(df[,6:8]),
selected = 1)
})
#Stores the value of the pollutant selection to pass to openAQ request
###################################
#output$OALpollutant <- renderUI({OALpollutant})
##################################
# create the map, using dataframe 'locations' which is polled daily (using ropenaq)
#MOD TO CONSIDER: addd all available measurements to the popup - true/false for each pollutant, and dates of operation.
output$map <- renderLeaflet({
leaflet(subset(df,(df[,input$pollutant]=="TRUE")))%>% addTiles() %>%
addMarkers(lng = subset(df,(df[,input$pollutant]=="TRUE"))$longitude, lat = subset(df,(df[,input$pollutant]=="TRUE"))$latitude,
popup = paste("Location:", subset(df,(df[,input$pollutant]=="TRUE"))$location, "<br>",
"Pollutant:", input$pollutant, "<br>",
"First Update:", subset(df,(df[,input$pollutant]=="TRUE"))$firstUpdated, "<br>",
"Last Update:", subset(df,(df[,input$pollutant]=="TRUE"))$lastUpdated
))
})
#Process Tab
OAL_site <- reactive({
req(input$map_marker_click)
location %>%
filter(latitude == input$map_marker_click$lat,
longitude == input$map_marker_click$lng)
###########
#call Functions for data retrieval and processing. Might be best to put all data request
#functions into a seperate single function. Need to:
# call importNOAA() to retrieve meteorology data into temporary data frame
# call aq_measurements() to retrieve air quality into a temporary data frame
# merge meteorology and air quality datasets into one working dataset for computations; temporary
# meteorology and air quality datasets to be removed.
# call openAir() functions to create plots from merged file. Pass output to a dashboard to assemble
# into appealing output.
# produce output, either as direct download, or as an emailable PDF.
# delete all temporary files and reset for next run.
})
#fun
output$loc<-renderUI({
selectInput("loc", label = h4("Choose location"),
choices = df$location ,selected = 1
)
})
output$dt<-renderUI({
dateInput('date',
label = 'First Available Date',
value = subset(df$firstUpdated,(df[,1]==input$loc))
)
})
output$dt2<-renderUI({
dateInput('date2',
label = 'Last available Date',
value = subset(df$lastUpdated,(df[,1]==input$loc))
)
})
rt<-reactive({
AQ<- aq_measurements(location = input$loc, date_from = input$dt,date_to = input$dt2,parameter = input$pollutant)
met <- importNOAA(year = 2014:2018)
colnames(AQ)[9] <- "date"
merged<-merge(AQ, met, by="date")
# date output -- reports user-selected state & stop dates in UI
merged$location <- gsub( " " , "+" , merged$location)
merged
})
#DT
output$tim = renderPlot({
timeVariation(rt(), pollutant = "value")
})
}
shinyApp(ui = ui, server = server)
The part of my code that I believe input$MAPID_click should be applied is:
output$map <- renderLeaflet({
leaflet(subset(locations,(locations[,input$pollutant]=="TRUE")))%>% addTiles() %>%
addMarkers(lng = subset(locations,(locations[,input$pollutant]=="TRUE"))$longitude, lat = subset(locations,(locations[,input$pollutant]=="TRUE"))$latitude,
popup = paste("Location:", subset(locations,(locations[,input$pollutant]=="TRUE"))$location, "<br>",
"Pollutant:", input$pollutant, "<br>",
"First Update:", subset(locations,(locations[,input$pollutant]=="TRUE"))$firstUpdated, "<br>",
"Last Update:", subset(locations,(locations[,input$pollutant]=="TRUE"))$lastUpdated
))
})
output$dt<-renderUI({
dateInput('date',
label = 'First Available Date',
value = subset(locations$firstUpdated,(locations[,1]==input$loc))
)
})
output$dt2<-renderUI({
dateInput('date2',
label = 'Last available Date',
value = subset(locations$lastUpdated,(locations[,1]==input$loc))
)
})
rt<-reactive({
AQ<- aq_measurements(location = input$loc, date_from = input$dt,date_to = input$dt2)
met <- importNOAA(year = 2014:2018)
colnames(AQ)[9] <- "date"
merged<-merge(AQ, met, by="date")
# date output -- reports user-selected state & stop dates in UI
merged$location <- gsub( " " , "+" , merged$location)
merged
})
#DT
output$tim = renderPlot({
timeVariation(rt(), pollutant = "value")
})
Here is a minimal example. You click on your marker and you get a plot.
ui = fluidPage(
leafletOutput("map"),
textOutput("temp"),
plotOutput('tim')
)
#server.r
#df$location <- gsub( " " , "+" , df$location)
server = function(input, output, session) {
output$map <- renderLeaflet({
leaflet(df)%>% addTiles() %>% addMarkers(lng = longitude, lat = latitude)
})
output$temp <- renderPrint({
input$map_marker_click$lng
})
output$tim <- renderPlot({
temp <- df %>% filter(longitude == input$map_marker_click$lng)
# timeVariation(temp, pollutant = "value")
print(ggplot(data = temp, aes(longitude, latitude)) + geom_point())
})
}
shinyApp(ui = ui, server = server)
I put all the functions are placed in a class, including the creation of the process of the function and the implementation of the function, in another file to call the function of this class
from multiprocessing import Pool
def initData(self, type):
# create six process to deal with the data
if type == 'train':
data = pd.read_csv('./data/train_merged_8.csv')
elif type == 'test':
data = pd.read_csv('./data/test_merged_2.csv')
modelvec = allWord2Vec('no').getModel()
modelvec_all = allWord2Vec('all').getModel()
modelvec_stop = allWord2Vec('stop').getModel()
p = Pool(6)
count = 0
for i in data.index:
count += 1
p.apply_async(self.valueCal, args=(i, data, modelvec, modelvec_all, modelvec_stop))
if count % 1000 == 0:
print(str(count // 100) + 'h rows of data has been dealed')
p.close()
p.join
def valueCal(self, i, data, modelvec, modelvec_all, modelvec_stop):
# the function run in process
list_con = []
q1 = str(data.get_value(i, 'question1')).split()
q2 = str(data.get_value(i, 'question2')).split()
f1 = self.getF1_union(q1, q2)
f2 = self.getF2_inter(q1, q2)
f3 = self.getF3_sum(q1, q2)
f4_q1 = len(q1)
f4_q2 = len(q2)
f4_rate = f4_q1/f4_q2
q1 = [','.join(str(ve)) for ve in q1]
q2 = [','.join(str(ve)) for ve in q2]
list_con.append('|'.join(q1))
list_con.append('|'.join(q2))
list_con.append(f1)
list_con.append(f2)
list_con.append(f3)
list_con.append(f4_q1)
list_con.append(f4_q2)
list_con.append(f4_rate)
f = open('./data/test.txt', 'a')
f.write('\t'.join(list_con) + '\n')
f.close()
The result appears very soon like this, but I have not even seen the file being created.But when I check the task manager, there are indeed six processes are created and consumed a lot of resources I cpu. And when the program is finished, the file is still not created.
How can i solve this problem?
10h rows of data have been dealed
20h rows of data have been dealed
30h rows of data have been dealed
40h rows of data have been dealed
I would like to load a CSV file with inside a list of variable names such as
"var_A", "var_B", "var_C"
and create in the GUI a list of numeric inputs for each variable name. I guess I need to pass by uiOutput function but no idea to do that. here's a kinda draft of what I'm trying to do
ui <- bootstrapPage(
fileInput('file1', 'Choose CSV File', accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv'))
# list of numeric inputs
#uiOutput("list_numeric_inputs")
)
server <- function(input,output) {
data_set <- reactive({
inFile <- input$file1
if (is.null(inFile))
return(NULL)
data_set<-read.csv(inFile$datapath, header=F)
})
# # list of numeric inputs
# output$list_numeric_inputs <- renderUI({
# # If missing input, return to avoid error later in function
# if(is.null(input$data_set()))
# return()
#
# # Get the data set value for variable name
# for (i in 1:nrow(data_set)) {
# numericInput("...", paste0(data_set[i]), value = 0.)
# }
# })
}
shinyApp(ui, server)
1) Your example not working ( havent inputs for header=input$header,sep=input$sep, quote=input$quote)
2)You havent input$dataset only data_set <- reactive
3) So working one :
library(shiny)
ui <- bootstrapPage(
fileInput('file1', 'Choose CSV File', accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')),
# list of numeric inputs
uiOutput("list_numeric_inputs")
)
server <- function(input,output) {
data_set <- reactive({
inFile <- input$file1
if (is.null(inFile))
return(NULL)
data_set<-read.csv(inFile$datapath,header = F)
})
# list of numeric inputs
output$list_numeric_inputs <- renderUI({
# If missing input, return to avoid error later in function
if(is.null(data_set()))
return()
# Get the data set value for variable name
lapply(data_set(),function(i){
numericInput(paste0(i,"_ID"), i, value = 0.)
}
)
})
}
shinyApp(ui, server)