[R-sig-eco] R-sig-ecology Digest, Vol 60, Issue 15

Wed Mar 20 17:09:25 CET 2013

Can anyone recommend a good weeklong (or less) workshop to learn some basic programming in R with an ecological focus? I've taken some online courses and know a little, but wouldn't mind more emersion to help with my learning curve.

Thank you!
Travis

Travis Belote, Ph.D.
Research Ecologist
The Wilderness Society | Northern Rockies Regional Office
503 W. Mendenhall, Bozeman, MT 59715
office: 406.586.1600 x110 | cell: 406.581.3808

-----Original Message-----
From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of r-sig-ecology-request at r-project.org
Sent: Wednesday, March 20, 2013 5:00 AM
To: r-sig-ecology at r-project.org
Subject: R-sig-ecology Digest, Vol 60, Issue 15

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Today's Topics:

   1. Re: Adaptive landscape graphic (AdrianR)
   2. Spatstat: Residual analysis for Thomas cluster processes
      (Emily Mitchell)
   3.  RE:  Feather plots for oceanic currents (Levy, Yair)
   4. Issue with Boosted Regression Trees (Waite, Ian)
   5. Repeated measures: interaction plot problem (multcomp)
      (Marcelo Laia)
   6. Conversion of lat/long coordinates to ETRS89 (Daniel Fl?)
   7. Re: Conversion of lat/long coordinates to ETRS89
      (Mauricio Zambrano-Bigiarini)
   8. Re: Conversion of lat/long coordinates to ETRS89 (Levy, Yair)
   9. Re: Conversion of lat/long coordinates to ETRS89 (Jari Oksanen)

----------------------------------------------------------------------

Message: 1
Date: Tue, 19 Mar 2013 04:25:39 -0700 (PDT)
From: AdrianR <adrasmu at gmail.com>
To: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] Adaptive landscape graphic
Message-ID: <1363692339081-7578005.post at n2.nabble.com>
Content-Type: text/plain; charset=UTF-8

Hi, Daniel.

I believe the packages misc3d or scatterplot3d will do the job.

Regards,
Adrian Rasmussen

Daniel Torres wrote
> Dear list members, I?m trying to help a friend to make a 3-dimensions
> adaptive landscape graphic with 3 variables, however I don?t know which
> function or package makes this kind of graphic. I would appreciate a lot
> your help.
>
> Daniel
>
>       [[alternative HTML version deleted]]
>
>
> _______________________________________________
> R-sig-ecology mailing list

> R-sig-ecology@

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View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Adaptive-landscape-graphic-tp7577979p7578005.html
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------------------------------

Message: 2
Date: 19 Mar 2013 14:09:51 +0000
From: Emily Mitchell <ek338 at cam.ac.uk>
To: r-sig-ecology at r-project.org
Cc: emilyghmitchell at gmail.com
Subject: [R-sig-eco] Spatstat: Residual analysis for Thomas cluster
        processes
Message-ID: <Prayer.1.3.5.1303191409510.29258 at hermes-1.csi.cam.ac.uk>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1

Hi,
I wish to test the fit of a homogeneous Thomas cluster process,
ideally using residual plots like diagnose.ppm and qqplot.ppm.
Since the most straightforward way to fit a Thomas cluster process is
using kppm, I can't use the above functions. Can anyone suggest ways
to do this?
e.g. transforming kppm to ppm or using ppm to fit a Thomas cluster process,
Many thanks
Emily

------------------------------

Message: 3
Date: Tue, 19 Mar 2013 15:11:46 +0100
From: "Levy, Yair" <yair.levy at mow.vlaanderen.be>
To: "r-sig-ecology at r-project.org" <r-sig-ecology at r-project.org>
Subject: [R-sig-eco]  RE:  Feather plots for oceanic currents
Message-ID:
        <FFB4E658B7DD2F46BD4E6E9555AE1492DB97FAA477 at WCV010001V.alfa.top.vlaanderen.be>

Content-Type: text/plain

_____________________________________________
Van: Levy, Yair
Verzonden: mardi 19 mars 2013 15:08
Aan: 'Diaz Justine'
Onderwerp: RE: [R-sig-eco] FW: Feather plots for oceanic currents

Hi Justine,

Inside the original function, see below, I changed the “axes” parameter of the basic plot function setting it to produce axes and I added the “xaxt” parameter defining it to “n” so that the X axis shall not be plotted.

Upon calling the function, I applied the ensembles values to the X axis using the feather.plot(2) function’s “xlabels” parameter to represent the “ensemble” object instead of the default axis labels above.

The Y axis does represent r * sin(theta) which is the equation calculating the vertical component of the speed vectors. Hence, the Y axis does not strictly represent the absolute speeds of the vectors but only their vertical component.

It wouldn’t make sense anyway to try and represent the vectors’ speeds along the Y axis. Because for any one height, you can always have different vectors ending which do have respective different lengths (= current speed magnitudes).

Perhaps you could consider adding labels at the vectors’ ends.

I hope this helps further. Meanwhile, I remain interested in any further ADCP/hydrology developments which you may have gathered or will do in the future. Certainly my algorithms could benefit from any such updates.

Friendly regards,

[X]

        Yaïr Levy
Researcher
Flemish Government
Mobility and Public Works Department
Flanders’ Hydraulics
Berchemlei 115 - 2140 Antwerpen
T. 03 224 61 89 - G. 0476 75 47 25 - F. 03 224 60 36
www.watlab.be <http://www.watlab.be/>

                 • Before printing, think about the environment!

-----Oorspronkelijk bericht-----
Van: Diaz Justine [mailto:justine.diaz at imr.no]
Verzonden: mardi 19 mars 2013 12:01
Aan: Levy, Yair
Onderwerp: RE: [R-sig-eco] FW: Feather plots for oceanic currents

Hello Yair,

Thanks for this! It works great, but can you explain to me how it works so that I can explain it to my supervisors?

The y axis labels are the magnitude, correct? When I plot my data, I am getting the arrows pointing down at -50 and up at 100. My data is provided in mm/s, but afterwards, I correct it to be m/s.

Thanks again, this has been helpful!
Justine

-----Original Message-----
From: Levy, Yair [mailto:yair.levy at mow.vlaanderen.be]
Sent: 18. mars 2013 18:02
To: r-sig-ecology at r-project.org<mailto:r-sig-ecology at r-project.org>
Cc: Diaz Justine
Subject: RE: [R-sig-eco] FW: Feather plots for oceanic currents

Hi Justine,

I modified the feather.plot function creating a feather.plot2 function as coded here under. Using that one instead would produce a feather plot with x and y axis.

  feather.plot2 <- function (r, theta, xpos, yref = 0, use.arrows = TRUE, col.refline = "lightgray",
      fp.type = "s", main = "", xlab = "", ylab = "", xlabels = NULL,
      ...)
  {
      if (missing(xpos))
          xpos <- 1:length(theta)
      if (fp.type == "m")
          theta <- 5 * pi/2 - theta
      x <- r * cos(theta)
      y <- r * sin(theta)
      xmult <- diff(range(xpos))/(diff(range(y)) * 2)
      x <- x * xmult
      xlim <- range(c(xpos, x + xpos))
      ylim <- range(c(y, yref))
      oldpin <- par("pin")
      xdiff <- xlim[2] - xlim[1]
      ydiff <- ylim[2] - ylim[1]
      plot(0, xlim = xlim, ylim = ylim, type = "n", main = main,
          xlab = xlab, ylab = ylab, axes = TRUE, xaxt = "n")
      box()
      if (is.null(xlabels))
          axis(1)
      else axis(1, at = xpos, labels = xlabels)
      abline(h = yref, col = col.refline)
      if (use.arrows)
          arrows(xpos, yref, xpos + x, y, length = 0.1, ...)
      else segments(xpos, yref, xpos + x, y, ...)
      par(pin = oldpin)
  }

#Then You could apply the function as such:

  feather.plot2(r,theta,xlabels=ensembles, main="ADCP feather plot",
  xlab = "Ensembles", ylab = "Current speed", col.reflin = "white", fp.type = "m")

The result figure is visible in attachement.

Best regards,

Yaïr Levy
Onderzoeker
Vlaamse overheid
Departement Mobiliteit en Openbare Werken Waterbouwkundig Laboratorium Berchemlei 115 - 2140 Antwerpen T. 03 224 61 89 - G. 0476 75 47 25 - F. 03 224 60 36 www.watlab.be<http://www.watlab.be>

                 P Before printing, think about the environment!

-----Oorspronkelijk bericht-----
Van: Diaz Justine [mailto:justine.diaz at imr.no]
Verzonden: lundi 18 mars 2013 14:39
Aan: Levy, Yair
Onderwerp: RE: [R-sig-eco] FW: Feather plots for oceanic currents

Hi Yair,
Preferably tomorrow, but at the very latest probably by the 25th.
Thanks for your help again!
Cheers,
Justine

-----Original Message-----
From: Levy, Yair [mailto:yair.levy at mow.vlaanderen.be]
Sent: 18. mars 2013 14:33
To: r-sig-ecology-bounces at r-project.org<mailto:r-sig-ecology-bounces at r-project.org>
Cc: Diaz Justine
Subject: RE: [R-sig-eco] FW: Feather plots for oceanic currents

Hi Justine,

I can probably answer you shortly, how soon do you need an answer?

Yaïr Levy
Onderzoeker
Vlaamse overheid
Departement Mobiliteit en Openbare Werken Waterbouwkundig Laboratorium Berchemlei 115 - 2140 Antwerpen T. 03 224 61 89 - G. 0476 75 47 25 - F. 03 224 60 36 www.watlab.be<http://www.watlab.be>

                 P Before printing, think about the environment!

Yaïr Levy

-----Oorspronkelijk bericht-----
Van: r-sig-ecology-bounces at r-project.org<mailto:r-sig-ecology-bounces at r-project.org> [mailto:r-sig-ecology-bounces at r-project.org] Namens Diaz Justine
Verzonden: lundi 18 mars 2013 13:45
Aan: r-sig-ecology at r-project.org<mailto:r-sig-ecology at r-project.org>
Onderwerp: [R-sig-eco] FW: Feather plots for oceanic currents

From: Diaz Justine
Sent: 18. mars 2013 13:42
To: 'r-sig-ecology at r-project.org'
Subject: [R-sig-eco] Feather plots for oceanic currents

Hello all listers,

Previously I had some help with creating a feather plot for ADCP data. I was able to make the plot but the y axis is missing integers for the magnitude values. Huge thank you in advance!!!

R-syntax:
library(plotrix)
ADCP <- read.table("C:/Users/justine/Dropbox/Stats/ADCP Data/SE_USE2.txt", header=T,quote ="",row.names=NULL,
colClasses="numeric",skip=0,fill=TRUE,blank.lines.skip=TRUE,comment.char="")

r <- ADCP[, 7]
theta <- ADCP[, 7] * pi / 180

ensembles <- ADCP[, 1]

feather.plot(r,theta,xlabels=ensembles, main="ADCP feather plot", xlab = "Ensembles (10 min averages)", ylab = "Magnitude (m/s)", col.reflin = "white", fp.type = "m")

Sample data set:
Ens

HH

MM

SS

HH

Mag

Dir

550

12

56

40

48

234

61.4

551

13

6

38

69

278

54.1

552

13

16

38

52

259

58.4

553

13

26

41

80

221

324.9

554

13

36

37

56

395

71.6

555

13

46

40

64

198

68.4

556

13

56

38

64

226

334.3

557

14

6

36

64

235

51.6

558

14

16

42

16

194

55.7

559

14

26

39

55

140

78

560

14

36

37

14

150

60.9

561

14

46

38

59

86

48.3

562

14

56

37

61

33

327.3

563

15

6

39

88

54

212.8

564

15

16

40

11

49

144.1

565

15

26

38

11

80

85

566

15

36

39

16

73

195.9

567

15

46

38

98

78

192.6

568

15

56

39

63

149

191.2

569

16

6

38

84

270

186.4

570

16

16

39

69

327

191.7

571

16

26

40

53

365

191.2

572

16

36

40

56

342

201.8

573

16

46

37

75

341

209.1

574

16

56

41

23

308

216.7

575

17

6

38

22

299

228.8

576

17

16

39

88

259

245.8

577

17

26

37

27

247

264.9

578

17

36

36

89

200

275.2

579

17

46

40

38

197

298.1

580

17

56

36

95

170

298.8

581

18

6

41

5

170

297.8

582

18

16

41

28

208

306.2

583

18

26

37

25

106

310.4

584

18

36

39

11

63

224.4

585

18

46

37

72

86

269.3

586

18

56

38

16

149

273.5

587

19

6

38

19

89

244.6

588

19

16

37

81

18

247.6

589

19

26

40

28

122

200.1

590

19

36

36

86

206

191.7

591

19

46

38

11

246

211.4

592

19

56

38

34

516

258.5

593

20

6

41

63

110

179

594

20

16

37

39

179

188.4

595

20

26

37

63

263

211.3

596

20

36

41

72

152

200

597

20

46

40

33

157

188.4

598

20

56

38

13

214

185.6

599

21

6

36

94

230

169.7

600

21

16

37

78

179

164.1

601

21

26

40

5

150

154.3

602

21

36

37

23

154

206.2

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------------------------------

Message: 4
Date: Tue, 19 Mar 2013 10:51:24 -0700
From: "Waite, Ian" <iwaite at usgs.gov>
To: <r-sig-ecology at r-project.org>
Subject: [R-sig-eco] Issue with Boosted Regression Trees
Message-ID:
        <CAO6jzHyWfQiwbkXmveYpcp7WckZfX0bjTdxevOBKszoz=WFtdw at mail.gmail.com>
Content-Type: text/plain

Hi everyone in R land,

   I'm trying to help a colleague who ran the follow script to develop
boosted regression tree models on fish traits.
He's run models on eight fish traits as the response variable with a sample
size of 1048, models for six of the fish traits seem to run properly but
with 2 variables the models stop after only 50 trees and gives this
statement (warning or error ?) "folds are unstratified". Initially these
two variables show up as integers while the others are numeric but that
shouldn't be the problem. However, the results show that the "total mean
deviance" 66 billion + for Ave_FECUNDITYr is way out there.The traits that
he's trying to model that don't work are Ave Fecundity (number of eggs per
fish species, very large numbers) and Ave Maximum Total Length which are
not particularly large numbers. I tried googling this issue of "fold are
unstratified" and couldn't find anything.
Has anyone run into this problem before. We are using Elith's code which is
modified from De'ath's original gbm code.
   Any suggestions would be appreciated. Original script and output copied
below.

Cheers and Thanks,
    Ian

#~~~~~~~~~~~~~~~~ original script ~~~~~~~~~~~
library (gbm)

set.seed(7)
gbm_n <- gbm.step(data=RTrait,
                  gbm.x = c(3:5, 7, 9, 22,35:43, 52:66,69:72,79:84), ##
explanatory variables
                  gbm.y = 89,           # (Ave_FECUNDITYr)
                  family = "gaussian",
                  tree.complexity = 8,
                  learning.rate = 0.001,
                  bag.fraction=0.50)
par(mfrow=c(3,4))
gbm.plot(gbm_n,n.plots=12)
gbm_n$contributions

#~~~~~~~ Output from gbm Boosted Regression Tree models ~~~~~~~~~~
Hey Ian,

I got those traits to show up as numbers but it's still doing the same
thing- 10 of 50 trees thing: below is the output from the run I just
did...it plots but doesn't seem like their any power associated with these
relationships.
        ~~~~~~~~~~~~
OUTPUT --

 "Performing cross-validation optimisation of a boosted regression tree
model
     for Ave_FECUNDITYr with dataframe RTrait and using a family of
gaussian

Using 1048 observations and 40 predictors

creating 10 initial models of 50 trees

* folds are unstratified *

total mean deviance =  66375444926

tolerance is fixed at  66375445

ntrees resid. dev.
50    64643104316

now adding trees...
fitting final gbm model with a fixed number of  50  trees for
 Ave_FECUNDITYr

mean total deviance = 66375444926
mean residual deviance = 63992100339

estimated cv deviance = 64643104316 ; se = 5286718478

training data correlation = 0.704
cv correlation =  0.568 ; se = 0.027

elapsed time -  0.09 minutes

--

~~~~~~~```````````~~~~~~~~~`````````~~~~~~~~~```````````~~~~~~~~~~
Ian R. Waite, Ph.D
Aquatic Ecologist
U.S. Geological Survey
Portland, OR 97201
503-251-3463
                       "Nature is a giver, helper, true friend and
sustainer.
                           It is constant harmony."

        [[alternative HTML version deleted]]

------------------------------

Message: 5
Date: Tue, 19 Mar 2013 19:30:55 -0300
From: Marcelo Laia <marcelolaia at gmail.com>
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] Repeated measures: interaction plot problem
        (multcomp)
Message-ID: <20130319223055.GB6917 at localhost>
Content-Type: text/plain; charset=utf-8

After reading some works, I began to analyze our data set. We are
interested in see how Trat (treatment), Clone (genotype), and Dia (day
in which each variable was measured), could be interfering in the
Planta (plant) growth, and others characteristics.

Everything was fine until I trying to make a graph of interactions
using the function cld () from multcomp package.

For the data analyzed without interaction, it works perfectly. The
problem is when I make the interaction graphic. Please could you run
the code below to view the problem?

datafilename="http://dl.dropbox.com/u/34009642/Dados_Omissao.csv"

data.min <- read.table(datafilename, header=T, sep="\t", dec=",")

head(data.min)

data.min <- within(data.min, {
  Clone <- factor(Clone)
  Dia <- factor(Dia)
  Trat <- factor(Trat)
  Planta <- factor(Planta)
})

summary(data.min)

library(nlme)

anova.lme.repetida <- lme(d ~ Clone * Trat * Dia, random = \
~1|Planta/Dia, method = "ML", data = data.min)

anova(anova.lme.repetida)

library(multcomp)

Trat.h.Tukey <- glht(anova.lme.repetida, linfct=mcp(Trat="Tukey"))

letras <- cld(Trat.h.Tukey)

plot(letras)

# # # # # # # # # # # # # # # # # # # # #
# UNTIL HERE THE GRAPH IS OK
# # # # # # # # # # # # # # # # # # # # #

data.min$CloneTrat <- interaction(data.min$Clone, data.min$Trat)

head(data.min)

anova.lme.repetida.CloneTrat <- lme(h ~ CloneTrat, random = \
~1|Planta/Dia, method = "ML", data = data.min)

anova(anova.lme.repetida.CloneTrat)

CloneTrat.Tukey <- glht(anova.lme.repetida.CloneTrat, \
linfct=mcp(CloneTrat="Tukey"))

summary(CloneTrat.Tukey)

letras <- cld(CloneTrat.Tukey)

#par(cex=0.6)

opar <- par(mai=c(1,1,2.5,1))

plot(letras)

par(opar)

Here it generates a different graph. Note that in the y axis it didn't
show the linear predictor as label, but writes ??clone 144 and
224. The boxplots are weird. How can I fix this chart to show the
interaction more human-readable?

Thank you!

--
  O___   - Marcelo Luiz de Laia
 c/  /'_ - Diamantina
(*)  \(*)- Minas Gerais
~~~~~~~~~- Brazil
^^^^^^^^^- Linux user number 487797

------------------------------

Message: 6
Date: Wed, 20 Mar 2013 07:33:24 +0000
From: Daniel Fl? <daniel.flo at skogoglandskap.no>
To: "r-sig-ecology at r-project.org" <r-sig-ecology at r-project.org>
Subject: [R-sig-eco] Conversion of lat/long coordinates to ETRS89
Message-ID:
        <C5353251F5B2EB419DBD9D1341E24F3B48BFF5A1 at exdb1.ad.skogoglandskap.no>
Content-Type: text/plain

Hi,

We have several lat/long coordinates for Finland that we would like to convert into a selected projection (such as ETRS89/ETRS-TM35FIN or other).
Could someone inform us about what package and function we should use to batch converte, and details in the procedure we should be aware of?
We do not have additional information to the lat/long coordinates, but this is may be not necessary?

Daniel Fl
PhD Fellow, Forest Health
The Norwegian Forest and Landscape Institute
Pb 115, NO-1431  s
Office:   (+47) 64 94 90 28
Mobile: (+47) 91 14 52 74
Skype:    floe.daniel
-----------------------------------------------------------------
www.skogoglandskap.no<http://www.skogoglandskap.no/>
-----------------------------------------------------------------

        [[alternative HTML version deleted]]

------------------------------

Message: 7
Date: Wed, 20 Mar 2013 09:29:15 +0100
From: Mauricio Zambrano-Bigiarini <mauricio.zambrano at jrc.ec.europa.eu>
To: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] Conversion of lat/long coordinates to ETRS89
Message-ID: <5149735B.1080702 at jrc.ec.europa.eu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 20/03/13 08:33, Daniel Fl? wrote:
> Hi,
>
> We have several lat/long coordinates for Finland that we would like to convert into a selected projection (such as ETRS89/ETRS-TM35FIN or other).
> Could someone inform us about what package and function we should use to batch converte, and details in the procedure we should be aware of?

?rgdal::spTransform

r-sig-geo is a better place for more specific questions.

Kind regards,

Mauricio Zambrano-Bigiarini

--
=================================================
Water Resources Unit
Institute for Environment and Sustainability (IES)
Joint Research Centre (JRC), European Commission
TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
webinfo    : http://floods.jrc.ec.europa.eu/
=================================================
DISCLAIMER:
"The views expressed are purely those of the writer
and may not in any circumstances be regarded as sta-
ting an official position of the European Commission"
=================================================
Linux user #454569 -- Ubuntu user #17469
=================================================
"It is not enough to have knowledge;
one must also apply it" (Goethe)

> We do not have additional information to the lat/long coordinates, but this is may be not necessary?

>
>
>
> Daniel Fl?
> PhD Fellow, Forest Health
> The Norwegian Forest and Landscape Institute
> Pb 115, NO-1431 ?s
> Office:   (+47) 64 94 90 28
> Mobile: (+47) 91 14 52 74
> Skype:    floe.daniel
> -----------------------------------------------------------------
> www.skogoglandskap.no<http://www.skogoglandskap.no/>
> -----------------------------------------------------------------
>
>
>       [[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>

------------------------------

Message: 8
Date: Wed, 20 Mar 2013 09:45:19 +0100
From: "Levy, Yair" <yair.levy at mow.vlaanderen.be>
To: "mauricio.zambrano at jrc.ec.europa.eu"
        <mauricio.zambrano at jrc.ec.europa.eu>,   "r-sig-ecology at r-project.org"
        <r-sig-ecology at r-project.org>
Subject: Re: [R-sig-eco] Conversion of lat/long coordinates to ETRS89
Message-ID:
        <FFB4E658B7DD2F46BD4E6E9555AE1492DB97FAA51E at WCV010001V.alfa.top.vlaanderen.be>

Content-Type: text/plain; charset="utf-8"

Dear Mauricio,

I would confirm the use of rgdal::spTransform as appropriate. Also, one could add creating a CRS database as follows:

#European Petroleum Survey Group list creation
EPSG <- make_EPSG()

The geographical ETRS89 CRS is then the following I believe:

#ETRS89 (= EUREF89 = GRS80)
CRS("+init=epsg:4258")

Applying spTransform following this function's instructions shouldn't be a challenge I believe. I would strongly recommend comparing your new geographical/cartographical projections the first time you use this function in order to validate their accuracies.

Please let me know if it worked.

Best regards,

Ya?r Levy
Researcher
Flemish Government
Mobility and Public Works Department
Flanders? Hydraulics
Berchemlei 115 - 2140 Antwerpen
T. 03 224 61?89 - G.?0476 75 47 25?- F. 03 224 60 36
www.watlab.be

?????????????????? Before printing, think about the environment!

-----Oorspronkelijk bericht-----
Van: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] Namens Mauricio Zambrano-Bigiarini
Verzonden: mercredi 20 mars 2013 09:29
Aan: r-sig-ecology at r-project.org
Onderwerp: Re: [R-sig-eco] Conversion of lat/long coordinates to ETRS89

On 20/03/13 08:33, Daniel Fl? wrote:
> Hi,
>
> We have several lat/long coordinates for Finland that we would like to convert into a selected projection (such as ETRS89/ETRS-TM35FIN or other).
> Could someone inform us about what package and function we should use to batch converte, and details in the procedure we should be aware of?

?rgdal::spTransform

r-sig-geo is a better place for more specific questions.

Kind regards,

Mauricio Zambrano-Bigiarini

--
=================================================
Water Resources Unit
Institute for Environment and Sustainability (IES) Joint Research Centre (JRC), European Commission TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
webinfo    : http://floods.jrc.ec.europa.eu/
=================================================
DISCLAIMER:
"The views expressed are purely those of the writer and may not in any circumstances be regarded as sta- ting an official position of the European Commission"
=================================================
Linux user #454569 -- Ubuntu user #17469 =================================================
"It is not enough to have knowledge;
one must also apply it" (Goethe)

> We do not have additional information to the lat/long coordinates, but this is may be not necessary?

>
>
>
> Daniel Fl?
> PhD Fellow, Forest Health
> The Norwegian Forest and Landscape Institute Pb 115, NO-1431 ?s
> Office:   (+47) 64 94 90 28
> Mobile: (+47) 91 14 52 74
> Skype:    floe.daniel
> -----------------------------------------------------------------
> www.skogoglandskap.no<http://www.skogoglandskap.no/>
> -----------------------------------------------------------------
>
>
>       [[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
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------------------------------

Message: 9
Date: Wed, 20 Mar 2013 09:32:43 +0000
From: Jari Oksanen <jari.oksanen at oulu.fi>
To: "Levy, Yair" <yair.levy at mow.vlaanderen.be>
Cc: "r-sig-ecology at r-project.org" <r-sig-ecology at r-project.org>
Subject: Re: [R-sig-eco] Conversion of lat/long coordinates to ETRS89
Message-ID: <F08FB5B0-3F6C-41BE-8294-12ACF86533AF at oulu.fi>
Content-Type: text/plain; charset="iso-8859-1"

Daniel,
On 20/03/2013, at 10:45 AM, Levy, Yair wrote:

> Dear Mauricio,
>
>
> I would confirm the use of rgdal::spTransform as appropriate. Also, one could add creating a CRS database as follows:
>
> #European Petroleum Survey Group list creation
> EPSG <- make_EPSG()
>
> The geographical ETRS89 CRS is then the following I believe:
>
> #ETRS89 (= EUREF89 = GRS80)
> CRS("+init=epsg:4258")
>
>

Actually ETRS89 / ETRS-TM35FIN for Finland is epsg code 3067.

> Applying spTransform following this function's instructions shouldn't be a challenge I believe. I would strongly recommend comparing your new geographical/cartographical projections the first time you use this function in order to validate their accuracies.
>

The following should work:

library(rgdal)
xy <- data.frame(N = 60, E = 27)
coordinates(xy) <- ~ E + N
proj4string(xy) <- CRS("+proj=longlat")
spTransform(xy, CRS("+init=epsg:3067"))

and it is really useful to validate the results...

Cheers, Jari Oksanen (Finland)

> -----Oorspronkelijk bericht-----
> Van: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] Namens Mauricio Zambrano-Bigiarini
> Verzonden: mercredi 20 mars 2013 09:29
> Aan: r-sig-ecology at r-project.org
> Onderwerp: Re: [R-sig-eco] Conversion of lat/long coordinates to ETRS89
>
> On 20/03/13 08:33, Daniel Fl? wrote:
>> Hi,
>>
>> We have several lat/long coordinates for Finland that we would like to convert into a selected projection (such as ETRS89/ETRS-TM35FIN or other).
>> Could someone inform us about what package and function we should use to batch converte, and details in the procedure we should be aware of?
>
> ?rgdal::spTransform
>
> r-sig-geo is a better place for more specific questions.
>
> Kind regards,
>
> Mauricio Zambrano-Bigiarini
>
> --
> =================================================
> Water Resources Unit
> Institute for Environment and Sustainability (IES) Joint Research Centre (JRC), European Commission TP 261, Via Enrico Fermi 2749, 21027 Ispra (VA), IT
> webinfo    : http://floods.jrc.ec.europa.eu/
> =================================================
> DISCLAIMER:
> "The views expressed are purely those of the writer and may not in any circumstances be regarded as sta- ting an official position of the European Commission"
> =================================================
> Linux user #454569 -- Ubuntu user #17469 =================================================
> "It is not enough to have knowledge;
> one must also apply it" (Goethe)
>
>> We do not have additional information to the lat/long coordinates, but this is may be not necessary?
>
>
>>
>>
>>
>> Daniel Fl?
>> PhD Fellow, Forest Health
>> The Norwegian Forest and Landscape Institute Pb 115, NO-1431 ?s
>> Office:   (+47) 64 94 90 28
>> Mobile: (+47) 91 14 52 74
>> Skype:    floe.daniel
>> -----------------------------------------------------------------
>> www.skogoglandskap.no<http://www.skogoglandskap.no/>
>> -----------------------------------------------------------------
>>
>>
>>      [[alternative HTML version deleted]]
>>
>>
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland

------------------------------

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