To install R/qtl, you need to first install the package. (This needs to be done just once.)
You then load the R/qtl package using the library
function Type (within R):
#git clone https://github.com/juldebar/IndicatorsForFisheries.git
# setwd("/home/tomcat7/IndicatorsForFisheries/") #devtools::build() #install.packages("/home/tomcat7/IndicatorsForFisheries_0.2.tar.gz",type="source", repo=NULL)
install.packages("IndicatorsForFisheries")
#library(IndicatorsForFisheries)
Si besoin remettre les codes du serveur Github (dans un terminal dans le répertoire du package):
git fetch --all git reset --hard origin/master
A noter qu'on peut faire des rapports paramétrés avec knitR: here
This is a short tutorial on how to use NVD3 with rCharts. The source for this tutorial can be found here
## require(knitr) ## require(rmarkdown) ## require(rCharts) options(RCHART_WIDTH = 500, RCHART_HEIGHT = 300) opts_chunk$set(results = 'asis', comment = NA, message = F, tidy = F)
WFS data access
Nombre total de représentations par le biais de cet indicateur: une série temporelle par espèce soit 13 indicateurs pour le moment cf indicateurs précalculés sur le serveur MDST
# require(IndicatorsForFisheries) df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i1i2_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo></ogc:Filter>',withSparql=FALSE) indicator1 <- Atlas_i1_SpeciesByOcean_julien(df=df, yearAttributeName="year", oceanAttributeName="ocean", speciesAttributeName="species", valueAttributeName="value") resultPlot <- ggplot(indicator1$data, aes(x=year, y=value, group=ocean)) + geom_area(aes(fill=ocean), position="stack") + geom_line(position="stack", color="grey20") + scale_fill_manual(name="Ocean", values=indicator1$colors) + xlab("Year") + ylab("Catches in thousand tons") + ggtitle(paste(indicator1$species, "catches by Ocean")) + theme(legend.position="bottom")
aggData <-indicator1 plotRchartsNVD3 <- nPlot(value ~ year, group = 'ocean', data = indicator1$data, type = 'stackedAreaChart', id = 'chart') plotRchartsNVD3$xAxis(axisLabel = 'Year') plotRchartsNVD3$yAxis(axisLabel = 'Catches') # plotRchartsNVD3$chart(width = 500, height = 200, useInteractiveGuideline=TRUE) plotRchartsNVD3$print('chart_i1_d3js', include_assets = TRUE)
plotRchartsNVD3bis <- nPlot(value ~ year, group = 'ocean', data = indicator1$data, type = 'lineChart') plotRchartsNVD3bis$xAxis(axisLabel = 'Year') plotRchartsNVD3bis$yAxis(axisLabel = 'Catches') plotRchartsNVD3bis$print('chart_i1_d3js_bis', include_assets = TRUE)
plotRchartsRickshaw <- Rickshaw$new() plotRchartsRickshaw$layer(value ~ year, data = indicator1$data, group='ocean', type = 'area', title = "C'est de la balle") # plotRchartsRickshaw$yAxis(orientation = 'right') plotRchartsRickshaw$set(width = 400, height = 200, legend = TRUE, slider = TRUE) plotRchartsRickshaw$print('chart_i1_Rickshaw', include_assets = TRUE)
plotRchartsRickshaw$save(".",standalone=TRUE)
print(resultPlot)
ggplot_i1<-indicator1[2]
print(ggplot_i1)
See other rCharts examples here
## require(IndicatorsForFisheries) df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i1i2_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo></ogc:Filter>',withSparql=FALSE) indicator2 <- Atlas_i2_SpeciesByGear_julien(df=df, yearAttributeName="year", gearTypeAttributeName="gear_type", speciesAttributeName="species", valueAttributeName="value") resultPlot <- ggplot(indicator2$data, aes(x=year, y=value, fill=gear_type, order=gear_type)) + geom_bar(stat="identity", width=0.8) + geom_bar(stat="identity", width=0.8, colour="grey20", show_guide=FALSE) + scale_fill_manual(name="Gear type", values=indicator2$colors) + xlab("Year") + ylab("Catches in thousand tons") + ggtitle(paste(indicator2$species, "catches by gear type")) + theme(legend.position="bottom")
print(resultPlot)
## require(rCharts) aggData <-indicator2 plotRchartsHighcharts <- hPlot(value ~ year, data = indicator2$data, type = 'column', group = 'gear_type', radius = 6, title = "Catches per month per fishing gear",width = "100%") plotRchartsHighcharts$xAxis(labels = list(rotation = -45, align = 'right', style = list(fontSize = '13px', fontFamily = 'Verdana, sans-serif')), replace = F) plotRchartsHighcharts$plotOptions(column = list(stacking = "normal", dataLabels = list(enabled = T, rotation = -90, align = 'right', color = '#FFFFFF', x = 4, y = 10, style = list(fontSize = '13px', fontFamily = 'Verdana, sans-serif')))) plotRchartsHighcharts$legend(align = 'center', verticalAlign = 'top', y = 30, margin = 20) plotRchartsHighcharts$chart(width = 800,height = 400, zoomType = "xy") # plotRchartsHighcharts$chart(zoomType = "xy") plotRchartsHighcharts$exporting(enabled = T) plotRchartsHighcharts$print('chart_i2_Highcharts', include_assets = TRUE)
## require(IndicatorsForFisheries) df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo><ogc:PropertyIsEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2005</ogc:Literal></ogc:PropertyIsEqualTo></ogc:Filter>', layer="ns11:i3_mv") #build the I3 indicator indicator3 <- Atlas_i3_SpeciesYearByGearMonth_julien(df=df, yearAttributeName="year", monthAttributeName="month", gearTypeAttributeName="gear_type", speciesAttributeName="species", valueAttributeName="value", meanPrev5YearsAttributeName="mean_prev_5_years", stddevPrev5YearsAttributeName="stddev_prev_5_years")
External Web page rCharts result
print(indicator3)
#library(IndicatorsForFisheries) df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i4_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:And><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo><ogc:PropertyIsLessThanOrEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2005</ogc:Literal></ogc:PropertyIsLessThanOrEqualTo><ogc:PropertyIsGreaterThanOrEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2000</ogc:Literal></ogc:PropertyIsGreaterThanOrEqualTo></ogc:And></ogc:Filter>') #build the I4 indicator indicator4 <- Atlas_i4_SpeciesMonthByOcean_julien(df=df, oceanAttributeName="ocean", yearAttributeName="year", monthAttributeName="month", speciesAttributeName="species", valueAttributeName="value")
print(indicator4)
no rCharts version for now
## require(IndicatorsForFisheries) #fetch data from IRD WFS for indicator I6, with restriction on species="YFT" and year=2000 df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i6i7i8_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:And><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo><ogc:PropertyIsEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2000</ogc:Literal></ogc:PropertyIsEqualTo></ogc:And></ogc:Filter>',withSparql=FALSE) #build the I6 indicator indicator6 <- Atlas_i6_SpeciesMap_julien(df=df, geomIdAttributeName="geom_id", yearAttributeName="year", speciesAttributeName="species", valueAttributeName="value")
print(indicator6)
netCDF / Thredds & WMS & Openlayers result Exemple sur Thredds
#library(IndicatorsForFisheries) #fetch data from IRD WFS for indicator I7, with restriction on species="YFT" and year=2000 df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i6i7i8_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:And><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo><ogc:PropertyIsEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2000</ogc:Literal></ogc:PropertyIsEqualTo></ogc:And></ogc:Filter>') #build the I7 indicator indicator7 <- Atlas_i7_SpeciesMapRelativeCatches(df=df, geomIdAttributeName="geom_id", yearAttributeName="year", speciesAttributeName="species", valueAttributeName="value")
print(indicator7)
no rCharts version but Openlayers possible thourgh netCDF export and Thredds ncWMS
#library(IndicatorsForFisheries) #fetch data from IRD WFS for indicator I8, with restriction on species="YFT" and year=2000 df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i6i7i8_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:And><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo><ogc:PropertyIsEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2000</ogc:Literal></ogc:PropertyIsEqualTo></ogc:And></ogc:Filter>') #build the I8 indicator with targeted species = "YFT" indicator8 <- Atlas_i8_SpeciesMapRelativeCatchesOtherSpecies(df=df, targetedSpecies="YFT", geomIdAttributeName="geom_id", yearAttributeName="year", speciesAttributeName="species", valueAttributeName="value")
print(indicator8)
## require(IndicatorsForFisheries) df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i9i10_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:And><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo><ogc:PropertyIsEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2000</ogc:Literal></ogc:PropertyIsEqualTo></ogc:And></ogc:Filter>') #build the I9 indicator indicator9 <- Atlas_i9_RelativeSizeFrequenciesBySchoolType_julien(df=df, yearAttributeName="year", speciesAttributeName="species", schoolAttributeName="school", sizeClassLowerBoundAttributeName="class_low", sizeClassUpperBoundAttributeName="class_up", fishCountAttributeName="fish_count")
print(indicator9)
#library(IndicatorsForFisheries) #fetch data from IRD WFS for indicators I10, with restriction on species="YFT" and year >= 1980 and year <= 2005 df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i9i10_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:And><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo><ogc:PropertyIsLessThanOrEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2005</ogc:Literal></ogc:PropertyIsLessThanOrEqualTo><ogc:PropertyIsGreaterThanOrEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>1980</ogc:Literal></ogc:PropertyIsGreaterThanOrEqualTo></ogc:And></ogc:Filter>') #build the I10 indicator indicator10 <- Atlas_i10_RelativeSizeFrequenciesByDecade(df=df, temporalAgg=10, yearAttributeName="year", speciesAttributeName="species", sizeClassLowerBoundAttributeName="class_low", sizeClassUpperBoundAttributeName="class_up", fishCountAttributeName="fish_count")
print(indicator10)
#library(IndicatorsForFisheries) #fetch data from IRD WFS for indicators I11 with restriction on species="YFT" and year=2000 df <- readData(connectionType="remote", dataType="WFS", url="http://mdst-macroes.ird.fr:8080/constellation/WS/wfs/tuna_atlas", layer="ns11:i6i7i8_mv", ogcFilter='<ogc:Filter xmlns:ogc="http://www.opengis.net/ogc" xmlns:gml="http://www.opengis.net/gml"><ogc:And><ogc:PropertyIsEqualTo><ogc:PropertyName>species</ogc:PropertyName><ogc:Literal>YFT</ogc:Literal></ogc:PropertyIsEqualTo><ogc:PropertyIsEqualTo><ogc:PropertyName>year</ogc:PropertyName><ogc:Literal>2000</ogc:Literal></ogc:PropertyIsEqualTo></ogc:And></ogc:Filter>') #build the I11 indicator indicator11 <- Atlas_i11_CatchesByCountry(df=df, geomIdAttributeName="geom_id", countryAttributeName="country", speciesAttributeName="species", valueAttributeName="value")
print(indicator11)
This is a short tutorial on how to use NVD3 with rCharts. The source for this tutorial can be found here
#library(rCharts) options( rcharts.mode = 'iframesrc', rcharts.cdn = TRUE, RCHART_WIDTH = 700, RCHART_HEIGHT = 400 ) #library(knitr) opts_chunk$set(tidy = F, results = 'asis', comment = NA) #library(datasets)
library(plotly) p <- plot_ly(iris, x = Petal.Length, y = Petal.Width, color = Species, mode = "markers") # print(p) # p$print('plotly') p
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