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Nick Heyek
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Add functionality to view trait data within given dates
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‎experiment-trait-data-visualizer/.DS_Store‎

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‎experiment-trait-data-visualizer/app.R‎

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@@ -9,16 +9,14 @@ options(betydb_key = readLines('~/.betykey', warn = FALSE),
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betydb_api_version = 'beta')
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experiments <- betydb_query(table='experiments')
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traitData <- betydb_query(table='traits', date='~2016-08', limit=2000)
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varIdsObserved <- as.numeric(unique(traitData$variable_id))
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#varIdsObserved <- as.numeric(unique(traitData$variable_id))
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ui <- fluidPage(
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titlePanel("BETYdb Trait Data"),
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sidebarLayout (
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sidebarPanel(
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selectInput('selectedExp', 'Experiment', experiments$name),
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selectInput('selectedVariable','Variable', varIdsObserved)
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selectInput('selectedExp', 'Experiment', experiments$name)
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#selectInput('selectedVariable','Variable', varIdsObserved)
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),
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mainPanel(
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plotOutput('traitPlot')
@@ -27,8 +25,23 @@ ui <- fluidPage(
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)
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server <- function(input, output) {
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output$traitPlot <- renderPlot({
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qplot(as.Date(traitData$date), traitData$mean, main="[Variable] for [Experiment]",
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fullTraitData = data.frame()
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selectedExpRow <- subset(experiments, name==input$selectedExp)
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experimentStartDate <- as.Date(selectedExpRow$start_date)
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experimentEndDate <- as.Date(selectedExpRow$end_date)
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currDate <- experimentStartDate
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while (experimentEndDate - currDate != 0) {
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currTraitData <- betydb_query(table='traits', date=paste0('~', currDate), limit='5')
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fullTraitData <- rbind(fullTraitData, currTraitData)
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currDate <- currDate + days(1)
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}
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qplot(as.Date(fullTraitData$date), fullTraitData$mean, main="[Variable] for [Experiment]",
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xlab="Date", ylab="Unit", geom="auto")
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})
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}

‎experiment-trait-data-visualizer/cache/Cache2017-06-14 09:33:51.log‎

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[1] "Loading data at 2017-06-14 09:33:51"

‎experiment-trait-data-visualizer/cache/Cache2017-06-14 09:34:18.log‎

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[1] "Loading data at 2017-06-14 09:34:18"
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| |====== | 7% | |========= | 10% | |============ | 13% | |=============== | 17% | |================== | 20% | |===================== | 23% | |======================== | 27% | |=========================== | 30% | |============================== | 33% | |================================= | 37% | |==================================== | 40% | |======================================= | 43% | |========================================== | 47%# A tibble: 200 x 32
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id site_id specie_id citation_id cultivar_id treatment_id date
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* <dbl> <dbl> <int> <dbl> <lgl> <lgl> <chr>
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1 6001440138 6000003071 2588 6e+09 NA NA 2016-08-12T17:35:19-05:00
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2 6001039550 6000003250 2588 6e+09 NA NA 2016-08-21T14:11:24-05:00
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3 6001039551 6000003166 2588 6e+09 NA NA 2016-08-21T14:30:08-05:00
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4 6001440156 6000003010 2588 6e+09 NA NA 2016-08-12T17:54:10-05:00
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5 6001039554 6000003327 2588 6e+09 NA NA 2016-08-21T13:48:46-05:00
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6 6001039556 6000003041 2588 6e+09 NA NA 2016-08-21T15:02:56-05:00
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7 6001039557 6000003304 2588 6e+09 NA NA 2016-08-21T13:53:16-05:00
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8 6001440176 6000002769 2588 6e+09 NA NA 2016-08-12T18:53:08-05:00
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9 6001039562 6000003052 2588 6e+09 NA NA 2016-08-21T15:00:29-05:00
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10 6001440185 6000003049 2588 6e+09 NA NA 2016-08-12T17:42:24-05:00
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# ... with 190 more rows, and 25 more variables: dateloc <chr>, time <lgl>, timeloc <chr>,
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# mean <dbl>, n <lgl>, statname <chr>, stat <lgl>, notes <chr>, created_at <chr>,
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# updated_at <chr>, variable_id <dbl>, user_id <dbl>, checked <int>, access_level <int>,
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# entity_id <lgl>, method_id <dbl>, date_year <lgl>, date_month <lgl>, date_day <lgl>,
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# time_hour <lgl>, time_minute <lgl>, `number of associated covariates` <int>, `number of
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# associated variables` <int>, view_url <chr>, edit_url <chr>
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# A tibble: 200 x 32
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id site_id specie_id citation_id cultivar_id treatment_id date
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* <dbl> <dbl> <int> <dbl> <lgl> <lgl> <chr>
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1 6001440138 6000003071 2588 6e+09 NA NA 2016-08-12T17:35:19-05:00
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2 6001039550 6000003250 2588 6e+09 NA NA 2016-08-21T14:11:24-05:00
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3 6001039551 6000003166 2588 6e+09 NA NA 2016-08-21T14:30:08-05:00
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4 6001440156 6000003010 2588 6e+09 NA NA 2016-08-12T17:54:10-05:00
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5 6001039554 6000003327 2588 6e+09 NA NA 2016-08-21T13:48:46-05:00
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6 6001039556 6000003041 2588 6e+09 NA NA 2016-08-21T15:02:56-05:00
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7 6001039557 6000003304 2588 6e+09 NA NA 2016-08-21T13:53:16-05:00
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8 6001440176 6000002769 2588 6e+09 NA NA 2016-08-12T18:53:08-05:00
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9 6001039562 6000003052 2588 6e+09 NA NA 2016-08-21T15:00:29-05:00
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10 6001440185 6000003049 2588 6e+09 NA NA 2016-08-12T17:42:24-05:00
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# ... with 190 more rows, and 25 more variables: dateloc <chr>, time <lgl>, timeloc <chr>,
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# mean <dbl>, n <lgl>, statname <chr>, stat <lgl>, notes <chr>, created_at <chr>,
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# updated_at <chr>, variable_id <dbl>, user_id <dbl>, checked <int>, access_level <int>,
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# entity_id <lgl>, method_id <dbl>, date_year <lgl>, date_month <lgl>, date_day <lgl>,
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# time_hour <lgl>, time_minute <lgl>, `number of associated covariates` <int>, `number of
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# associated variables` <int>, view_url <chr>, edit_url <chr>
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# A tibble: 200 x 32
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id site_id specie_id citation_id cultivar_id treatment_id date
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* <dbl> <dbl> <int> <dbl> <lgl> <lgl> <chr>
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1 6001440138 6000003071 2588 6e+09 NA NA 2016-08-12T17:35:19-05:00
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2 6001039550 6000003250 2588 6e+09 NA NA 2016-08-21T14:11:24-05:00
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3 6001039551 6000003166 2588 6e+09 NA NA 2016-08-21T14:30:08-05:00
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4 6001440156 6000003010 2588 6e+09 NA NA 2016-08-12T17:54:10-05:00
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5 6001039554 6000003327 2588 6e+09 NA NA 2016-08-21T13:48:46-05:00
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6 6001039556 6000003041 2588 6e+09 NA NA 2016-08-21T15:02:56-05:00
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7 6001039557 6000003304 2588 6e+09 NA NA 2016-08-21T13:53:16-05:00
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8 6001440176 6000002769 2588 6e+09 NA NA 2016-08-12T18:53:08-05:00
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9 6001039562 6000003052 2588 6e+09 NA NA 2016-08-21T15:00:29-05:00
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10 6001440185 6000003049 2588 6e+09 NA NA 2016-08-12T17:42:24-05:00
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# ... with 190 more rows, and 25 more variables: dateloc <chr>, time <lgl>, timeloc <chr>,
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# mean <dbl>, n <lgl>, statname <chr>, stat <lgl>, notes <chr>, created_at <chr>,
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# updated_at <chr>, variable_id <dbl>, user_id <dbl>, checked <int>, access_level <int>,
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# entity_id <lgl>, method_id <dbl>, date_year <lgl>, date_month <lgl>, date_day <lgl>,
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# time_hour <lgl>, time_minute <lgl>, `number of associated covariates` <int>, `number of
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# associated variables` <int>, view_url <chr>, edit_url <chr>
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# A tibble: 200 x 32
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id site_id specie_id citation_id cultivar_id treatment_id date
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* <dbl> <dbl> <int> <dbl> <lgl> <lgl> <chr>
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1 6001440138 6000003071 2588 6e+09 NA NA 2016-08-12T17:35:19-05:00
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2 6001039550 6000003250 2588 6e+09 NA NA 2016-08-21T14:11:24-05:00
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3 6001039551 6000003166 2588 6e+09 NA NA 2016-08-21T14:30:08-05:00
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4 6001440156 6000003010 2588 6e+09 NA NA 2016-08-12T17:54:10-05:00
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5 6001039554 6000003327 2588 6e+09 NA NA 2016-08-21T13:48:46-05:00
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6 6001039556 6000003041 2588 6e+09 NA NA 2016-08-21T15:02:56-05:00
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7 6001039557 6000003304 2588 6e+09 NA NA 2016-08-21T13:53:16-05:00
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8 6001440176 6000002769 2588 6e+09 NA NA 2016-08-12T18:53:08-05:00
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9 6001039562 6000003052 2588 6e+09 NA NA 2016-08-21T15:00:29-05:00
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10 6001440185 6000003049 2588 6e+09 NA NA 2016-08-12T17:42:24-05:00
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# ... with 190 more rows, and 25 more variables: dateloc <chr>, time <lgl>, timeloc <chr>,
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# mean <dbl>, n <lgl>, statname <chr>, stat <lgl>, notes <chr>, created_at <chr>,
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# updated_at <chr>, variable_id <dbl>, user_id <dbl>, checked <int>, access_level <int>,
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# entity_id <lgl>, method_id <dbl>, date_year <lgl>, date_month <lgl>, date_day <lgl>,
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# time_hour <lgl>, time_minute <lgl>, `number of associated covariates` <int>, `number of
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# associated variables` <int>, view_url <chr>, edit_url <chr>
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Classes ‘tbl_df’, ‘tbl’ and 'data.frame': 200 obs. of 32 variables:
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$ id : num 6e+09 6e+09 6e+09 6e+09 6e+09 ...
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$ site_id : num 6e+09 6e+09 6e+09 6e+09 6e+09 ...
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$ specie_id : int 2588 2588 2588 2588 2588 2588 2588 2588 2588 2588 ...
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$ citation_id : num 6e+09 6e+09 6e+09 6e+09 6e+09 ...
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$ cultivar_id : logi NA NA NA NA NA NA ...
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$ treatment_id : logi NA NA NA NA NA NA ...
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$ date : chr "2016-08-12T17:35:19-05:00" "2016-08-21T14:11:24-05:00" "2016-08-21T14:30:08-05:00" "2016-08-12T17:54:10-05:00" ...
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$ dateloc : chr "5.0" "5.0" "5.0" "5.0" ...
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$ time : logi NA NA NA NA NA NA ...
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$ timeloc : chr "1.0" "1.0" "1.0" "1.0" ...
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$ mean : num 0.000928 0.000562 0.000611 0.00083 0.000596 ...
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$ n : logi NA NA NA NA NA NA ...
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$ statname : chr "" "" "" "" ...
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$ stat : logi NA NA NA NA NA NA ...
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$ notes : chr "" "" "" "" ...
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$ created_at : chr "2017-05-31T02:13:45-05:00" "2017-05-20T05:42:12-05:00" "2017-05-20T05:42:13-05:00" "2017-05-31T02:14:07-05:00" ...
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$ updated_at : chr "2017-05-31T02:13:45-05:00" "2017-05-20T05:42:12-05:00" "2017-05-20T05:42:13-05:00" "2017-05-31T02:14:07-05:00" ...
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$ variable_id : num 6e+09 6e+09 6e+09 6e+09 6e+09 ...
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$ user_id : num 6e+09 6e+09 6e+09 6e+09 6e+09 ...
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$ checked : int 0 0 0 0 0 0 0 0 0 0 ...
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$ access_level : int 2 2 2 2 2 2 2 2 2 2 ...
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$ entity_id : logi NA NA NA NA NA NA ...
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$ method_id : num 6e+09 6e+09 6e+09 6e+09 6e+09 ...
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$ date_year : logi NA NA NA NA NA NA ...
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$ date_month : logi NA NA NA NA NA NA ...
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$ date_day : logi NA NA NA NA NA NA ...
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$ time_hour : logi NA NA NA NA NA NA ...
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$ time_minute : logi NA NA NA NA NA NA ...
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$ number of associated covariates: int 0 0 0 0 0 0 0 0 0 0 ...
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$ number of associated variables : int 0 0 0 0 0 0 0 0 0 0 ...
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$ view_url : chr "https://terraref.ncsa.illinois.edu/bety/traits/6001440138" "https://terraref.ncsa.illinois.edu/bety/traits/6001039550" "https://terraref.ncsa.illinois.edu/bety/traits/6001039551" "https://terraref.ncsa.illinois.edu/bety/traits/6001440156" ...
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$ edit_url : chr "https://terraref.ncsa.illinois.edu/bety/traits/6001440138/edit" "https://terraref.ncsa.illinois.edu/bety/traits/6001039550/edit" "https://terraref.ncsa.illinois.edu/bety/traits/6001039551/edit" "https://terraref.ncsa.illinois.edu/bety/traits/6001440156/edit" ...
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- attr(*, "metadata")=List of 3
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..$ URI : chr "https://terraref.ncsa.illinois.edu/bety/api/beta/traits.json?key=sS8quPK7nt0ySnTFahzDP9VMlGhBqxIqjUKP6SUx&date="| __truncated__
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..$ timestamp: chr "2017-06-14T09:49:12-05:00"
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..$ count : int 200
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# A tibble: 200 x 32
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id site_id specie_id citation_id cultivar_id treatment_id date
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* <dbl> <dbl> <int> <dbl> <lgl> <lgl> <chr>
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1 6001440138 6000003071 2588 6e+09 NA NA 2016-08-12T17:35:19-05:00
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2 6001039549 6000002690 2588 6e+09 NA NA 2017-01-13T17:25:07-06:00
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3 6001039550 6000003250 2588 6e+09 NA NA 2016-08-21T14:11:24-05:00
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4 6001039551 6000003166 2588 6e+09 NA NA 2016-08-21T14:30:08-05:00
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5 6001039552 6000002678 2588 6e+09 NA NA 2017-01-13T17:27:00-06:00
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6 6001440156 6000003010 2588 6e+09 NA NA 2016-08-12T17:54:10-05:00
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7 6001039554 6000003327 2588 6e+09 NA NA 2016-08-21T13:48:46-05:00
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8 6001039555 6000002689 2588 6e+09 NA NA 2017-01-13T17:25:03-06:00
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9 6001039556 6000003041 2588 6e+09 NA NA 2016-08-21T15:02:56-05:00
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10 6001039557 6000003304 2588 6e+09 NA NA 2016-08-21T13:53:16-05:00
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# ... with 190 more rows, and 25 more variables: dateloc <chr>, time <lgl>, timeloc <chr>,
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# mean <dbl>, n <lgl>, statname <chr>, stat <lgl>, notes <chr>, created_at <chr>,
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# updated_at <chr>, variable_id <dbl>, user_id <dbl>, checked <int>, access_level <int>,
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# entity_id <lgl>, method_id <dbl>, date_year <lgl>, date_month <lgl>, date_day <lgl>,
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# time_hour <lgl>, time_minute <lgl>, `number of associated covariates` <int>, `number of
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# associated variables` <int>, view_url <chr>, edit_url <chr>
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The downloaded binary packages are in
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/var/folders/n6/nzfhhtp10zz9_m2gmd02kj6w0000gn/T//Rtmp3NsL7u/downloaded_packages
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# A tibble: 200 x 32
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id site_id specie_id citation_id cultivar_id treatment_id date
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* <dbl> <dbl> <int> <dbl> <lgl> <lgl> <chr>
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1 6001440138 6000003071 2588 6e+09 NA NA 2016-08-12T17:35:19-05:00
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2 6001039550 6000003250 2588 6e+09 NA NA 2016-08-21T14:11:24-05:00
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3 6001039551 6000003166 2588 6e+09 NA NA 2016-08-21T14:30:08-05:00
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4 6001440156 6000003010 2588 6e+09 NA NA 2016-08-12T17:54:10-05:00
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5 6001039554 6000003327 2588 6e+09 NA NA 2016-08-21T13:48:46-05:00
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6 6001039556 6000003041 2588 6e+09 NA NA 2016-08-21T15:02:56-05:00
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7 6001039557 6000003304 2588 6e+09 NA NA 2016-08-21T13:53:16-05:00
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8 6001440176 6000002769 2588 6e+09 NA NA 2016-08-12T18:53:08-05:00
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9 6001039562 6000003052 2588 6e+09 NA NA 2016-08-21T15:00:29-05:00
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10 6001440185 6000003049 2588 6e+09 NA NA 2016-08-12T17:42:24-05:00
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# ... with 190 more rows, and 25 more variables: dateloc <chr>, time <lgl>, timeloc <chr>,
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# mean <dbl>, n <lgl>, statname <chr>, stat <lgl>, notes <chr>, created_at <chr>,
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# updated_at <chr>, variable_id <dbl>, user_id <dbl>, checked <int>, access_level <int>,
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# entity_id <lgl>, method_id <dbl>, date_year <lgl>, date_month <lgl>, date_day <lgl>,
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# time_hour <lgl>, time_minute <lgl>, `number of associated covariates` <int>, `number of
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# associated variables` <int>, view_url <chr>, edit_url <chr>

‎experiment-trait-data-visualizer/cache/Cache2017-06-14 09:40:31.log‎

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[1] "Loading data at 2017-06-14 09:40:31"

‎experiment-trait-data-visualizer/cache/Cache2017-06-14 09:40:31.rda‎

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