Opened 12 years ago

Closed 6 years ago

#998 closed enhancement (fixed)

R demo portion fails, add more geo packages

Reported by: darkblueb Owned by: barryrowlingson
Priority: normal Milestone: OSGeoLive12.0
Component: OSGeoLive Keywords: R
Cc: live-demo@…


due to a missing dependency maps

> library(gstat)
> demo(wind)

	---- ~~~~

Type  <Return>	 to start : 

> #pdf("wind.pdf")
> library(gstat)

> library(rgdal)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.9.1, released 2012/05/15
Path to GDAL shared files: /usr/share/gdal/1.9
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
Path to PROJ.4 shared files: (autodetected)

> library(maptools)
Loading required package: foreign
Checking rgeos availability: FALSE
 	Note: when rgeos is not available, polygon geometry 	computations in maptools depend on gpclib,
 	which has a restricted licence. It is disabled by default;
 	to enable gpclib, type gpclibPermit()

> # load wind data, run test:
> example(wind)

wind> data(wind)

wind> summary(wind)
      year          month             day             RPT       
 Min.   :61.0   Min.   : 1.000   Min.   : 1.00   Min.   : 0.67  
 1st Qu.:65.0   1st Qu.: 4.000   1st Qu.: 8.00   1st Qu.: 8.12  
 Median :69.5   Median : 7.000   Median :16.00   Median :11.71  
 Mean   :69.5   Mean   : 6.523   Mean   :15.73   Mean   :12.36  
 3rd Qu.:74.0   3rd Qu.:10.000   3rd Qu.:23.00   3rd Qu.:15.92  
 Max.   :78.0   Max.   :12.000   Max.   :31.00   Max.   :35.80  
      VAL             ROS             KIL              SHA       
 Min.   : 0.21   Min.   : 1.50   Min.   : 0.000   Min.   : 0.13  
 1st Qu.: 6.67   1st Qu.: 8.00   1st Qu.: 3.580   1st Qu.: 6.75  
 Median :10.17   Median :10.92   Median : 5.750   Median : 9.96  
 Mean   :10.65   Mean   :11.66   Mean   : 6.306   Mean   :10.46  
 3rd Qu.:14.04   3rd Qu.:14.67   3rd Qu.: 8.420   3rd Qu.:13.54  
 Max.   :33.37   Max.   :33.84   Max.   :28.460   Max.   :37.54  
      BIR              DUB              CLA              MUL        
 Min.   : 0.000   Min.   : 0.000   Min.   : 0.000   Min.   : 0.000  
 1st Qu.: 4.000   1st Qu.: 6.000   1st Qu.: 5.090   1st Qu.: 5.370  
 Median : 6.830   Median : 9.210   Median : 8.080   Median : 8.170  
 Mean   : 7.092   Mean   : 9.797   Mean   : 8.494   Mean   : 8.496  
 3rd Qu.: 9.670   3rd Qu.:12.960   3rd Qu.:11.420   3rd Qu.:11.210  
 Max.   :26.160   Max.   :30.370   Max.   :31.080   Max.   :25.880  
      CLO              BEL             MAL       
 Min.   : 0.040   Min.   : 0.13   Min.   : 0.67  
 1st Qu.: 5.330   1st Qu.: 8.71   1st Qu.:10.71  
 Median : 8.290   Median :12.50   Median :15.00  
 Mean   : 8.707   Mean   :13.12   Mean   :15.60  
 3rd Qu.:11.630   3rd Qu.:16.88   3rd Qu.:19.83  
 Max.   :28.210   Max.   :42.38   Max.   :42.54  

wind> wind.loc
         Station Code       Latitude     Longitude MeanWind
1       Valentia  VAL        51d56'N       10d15'W     5.48
2      Belmullet  BEL        54d14'N       10d00'W     6.75
3    Claremorris  CLA        53d43'N        8d59'W     4.32
4        Shannon  SHA        52d42'N        8d55'W     5.38
5  Roche's Point  RPT        51d48'N        8d15'W     6.36
6           Birr  BIR        53d05'N        7d53'W     3.65
7      Mullingar  MUL        53d32'N        7d22'W     4.38
8     Malin Head  MAL        55d22'N        7d20'W     8.03
9       Kilkenny  KIL        52d40'N        7d16'W     3.25
10        Clones  CLO        54d11'N        7d14'W     4.48
11        Dublin  DUB        53d26'N        6d15'W     5.05
12       Roslare  ROS 52d16'56.791"N 6d21'25.056"W     6.00

wind> wind.loc$y = as.numeric(char2dms(as.character(wind.loc[["Latitude"]])))

wind> wind.loc$x = as.numeric(char2dms(as.character(wind.loc[["Longitude"]])))

wind> coordinates(wind.loc) = ~x+y

wind> # fig 1:
wind> ## No test: 
wind>  if (require(mapdata)) {
wind+    map("worldHires", xlim = c(-11,-5.4), ylim = c(51,55.5))
wind+    plot(wind.loc, add=TRUE, pch=16)
wind+    text(coordinates(wind.loc), pos=1, label=wind.loc$Station)
wind+  }
Loading required package: mapdata

wind> ## End(No test)
wind> wind$time = ISOdate(wind$year+1900, wind$month, wind$day)

wind> # time series of e.g. Dublin data:
wind> plot(DUB~time, wind, type= 'l', ylab = "windspeed (knots)", main = "Dublin")
Hit <Return> to see next plot: 

wind> # fig 2:
wind> #wind = wind[!(wind$month == 2 & wind$day == 29),]
wind> wind$jday = as.numeric(format(wind$time, '%j'))

wind> windsqrt = sqrt(0.5148 * as.matrix(wind[4:15]))

wind> Jday = 1:366

wind> windsqrt = windsqrt - mean(windsqrt)

wind> daymeans = sapply(split(windsqrt, wind$jday), mean)

wind> plot(daymeans ~ Jday)
Hit <Return> to see next plot: 

wind> lines(lowess(daymeans ~ Jday, f = 0.1))

wind> # subtract the trend:
wind> meanwind = lowess(daymeans ~ Jday, f = 0.1)$y[wind$jday]

wind> velocity = apply(windsqrt, 2, function(x) { x - meanwind })

wind> # match order of columns in wind to Code in wind.loc:
wind> pts = coordinates(wind.loc[match(names(wind[4:15]), wind.loc$Code),])

wind> # fig 3, but not really yet...
wind> dists = spDists(pts, longlat=TRUE)

wind> corv = cor(velocity)

wind> sel = !(as.vector(dists) == 0)

wind> plot(as.vector(corv[sel]) ~ as.vector(dists[sel]),
wind+ 	xlim = c(0,500), ylim = c(.4, 1), xlab = "distance (km.)", 
wind+ 	ylab = "correlation") 
Hit <Return> to see next plot: 

wind> # plots all points twice, ignores zero distance 
wind> # now really get fig 3:
wind> ros = rownames(corv) == "ROS"

wind> = dists[!ros,!ros]

wind> = corv[!ros,!ros]

wind> sel = !(as.vector( == 0)

wind> plot(as.vector([sel]) ~ as.vector([sel]), pch = 3,
wind+ 	xlim = c(0,500), ylim = c(.4, 1), xlab = "distance (km.)", 
wind+ 	ylab = "correlation") 
Hit <Return> to see next plot: 

wind> # add outlier:
wind> points(corv[ros,!ros] ~ dists[ros,!ros], pch=16, cex=.5)

wind> xdiscr = 1:500

wind> # add correlation model:
wind> lines(xdiscr, .968 * exp(- .00134 * xdiscr))

> m = map2SpatialLines(
+ 	map("worldHires", xlim = c(-11,-5.4), ylim = c(51,55.5), plot=F))
Loading required package: maps
Error in cbind(map$x, map$y) : could not find function "map"
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mapdata’
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘maps’

Change history (23)

comment:1 by barryrowlingson, 12 years ago

Actually the demo(wind) doesn't fail, it correctly checks for the presence of the mapdata package and skips the section if its not there. mapdata is only a 'suggested' dependency for gstat, and the 'maps' package is a dependency of that.

The R packaging system allows packages to say another package is not criticial, its just used for demos or documentation. I don't see this as a defect.

However... some of us have been scheming about improving the R component of the live-DVD by including more of the spatial packages so we can do groovy things like drawing cute maps on OSM tiles and so on. The maps package would probably be nice to have too. But it can pull in a large dataset in its own special format in the mapdata package...

Perhaps I should open a new ticket for that enhancement process? I think this one is a 'wontfix'?

comment:2 by barryrowlingson, 12 years ago

Owner: changed from live-demo@… to barryrowlingson
Status: newassigned
Type: defectenhancement

comment:3 by barryrowlingson, 12 years ago

Summary: R demo portion failsR demo portion fails, add more geo packages

comment:4 by kalxas, 11 years ago

Milestone: OSGeoLive6.5OSGeoLive7.0

Barry, +1, this is a wontfix for 6.5.

comment:5 by hamish, 11 years ago

Cc: live-demo@… added

please move the ML email addr from the owner field if you take ownership of a ticket so it doesn't get lost

comment:6 by kalxas, 11 years ago

Milestone: OSGeoLive7.0OSGeoLive7.5

still a wontfix for 7.0

comment:7 by kalxas, 10 years ago

Milestone: OSGeoLive7.9OSGeoLive8.0

comment:8 by darkblueb, 10 years ago

Milestone: OSGeoLive8.0OSGeoLive8.5

comment:9 by kalxas, 9 years ago

Milestone: OSGeoLive8.5OSGeoLive9.0

comment:10 by nuest, 9 years ago

This ticket is inactive for a while, but the generic title "add more geo packages" somewhat covers my following question. If I should start a new ticket for this I'll do it!

I would like to add a package to the list of installed R packages , namely sos4R ( It would very nicely connect R with the 52°North SOS that is also on the live DVD. Afaics I would only need to extend the list of installed packages ( Then I would extend the quickstart of the 52°North SOS with a few lines of R to demonstrate the package and add a new demo to the package that more extensively uses the locally available SOS and its data.

Any comments are highly appreciated!

comment:11 by kalxas, 9 years ago

Thank you for the proposed improvement. Can you please make a pull request so we can test this?

Thanks, Angelos

comment:12 by kalxas, 9 years ago

Milestone: OSGeoLive9.0OSGeoLive9.5

Ticket retargeted after milestone closed

comment:13 by kalxas, 8 years ago

Milestone: OSGeoLive9.5OSGeoLive10.0

Ticket retargeted after milestone closed

comment:14 by kalxas, 7 years ago

Milestone: OSGeoLive10.0OSGeoLive10.5

Ticket retargeted after milestone closed

comment:15 by kalxas, 7 years ago

Milestone: OSGeoLive10.5OSGeoLive11.0

Ticket retargeted after milestone closed

comment:16 by darkblueb, 7 years ago

rOpenSci Community involvement; great progress, however sf does not build cleanly yet.

comment:17 by darkblueb, 7 years ago

Milestone: OSGeoLive11.0OSGeoLive12.0

comment:18 by bakaniko, 7 years ago

@kalxas: I think we can close it if we improve the R quickstart with Tina and Etienne

comment:19 by darkblueb, 6 years ago

bump 12dev alpha1; this PR adds module sp

sf next

comment:20 by darkblueb, 6 years ago

R sf added in branch notebooktest

comment:21 by darkblueb, 6 years ago

12dev beta2

R sf included; no tidyverse

comment:22 by darkblueb, 6 years ago

12dev beta3

R Quickstart updated to use sf and ggplot2

minimal R Notebook installed; R sf project info page added

comment:23 by bakaniko, 6 years ago

Resolution: fixed
Status: assignedclosed

OSGeoLive PR 238 [1] and OSGeoLive 12.0 release add more spatial capabilities to R. OSGeolive PR 240 [2] add a notebook with mapping with R

OSGeoLive-doc PR 424 [3] fix R quickstart.

Closing this long overdue ticket.




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