[R] R related tools - GUI

For years I used Deducer (Package Deducer) developed by Ian Fellows.  This is still available and partially remains mostly functional.  He was working on a new GUI years ago but appears no longer to be in the pipeline I think replaced by R-Studio. Send R-help mailing list submissions to

[R] Package to generate moon phase - SR-SS

Hi all I have not found a package by Googling, but assume there must be at least one out there. I need to generate/write sun rise-sun set times (civil twilight) and moon phase/illumination. I would like to add a start date and end date along with location coordinates and have a table generat

[R] Need guidance on summarizing time data

Hi all, I need to summarize temporal activity. However date\times in R seem to be not easily handled. Seems I may need to convert date\time values to a recognizable format? My "raw data" is tab (text) includes a location ID, date and time(24 hr format). Format is like this: Location    Date 

[R] Indian Red

FWIW, There is also Naples Yellow and other colors related to "place names" on artist palettes.  "Indian Red" is not related to North American Native peoples. "/India Red/: Originally a natural, more purple iron oxide imported from /India/. First synthesized in the 18th century as a “Mars” colo

[R] did bot execute

Hi Abby, Tried this new version but did not execute... Clearly I am missing a step. Bruce > library (barsurf) > library (KernSmooth) > set.bs.theme ("heat") > > plot_ds <- function (dataset, main="", xlim, ylim, ..., + ncontours=3, labcex=0.8, ndec=3, + k1=1, k2=1, n=30) + {   names <- names

Re: [R] Query on contour plots

otrix) xylim<-par("usr") color.legend(xylim[1],xylim[3]-(xylim[4]-xylim[3])/7, xylim[1]+(xylim[2]-xylim[1])/4,xylim[3]-(xylim[4]-xylim[3])/10, legend=seq(0,10,length.out=5), rect.col=color.scale(0:4,extremes=c("#7be6bd","#bdb3df")),align="rb") text(xylim[1

Re: [R] Query on contour plots

ine on the plot. Most of my testing was with PDF output, I will need to do some more testing with PNG output. -- Bruce W. Miller, PhD. Neotropical bat risk assessments Conservation Fellow - Wildlife Conservation Society If we lose the bats, we may lose much of the tropical vegetation and the lungs

Re: [R] Query on contour plots

each new data set. I can not thank Jim and Abby enough.  Super helpful Cheers, Bruce -- Bruce W. Miller, PhD. Neotropical bat risk assessments Conservation Fellow - Wildlife Conservation Society If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet U

Re: [R] Query on contour plots

dwidth. >> (In this case, I've increased the smoothness). >> >> If you want to do it 200+ times: >> (1) Create another function, to iterate over each data set. >> (2) If you want to save the plots, you will need to add in a call to >> pdf/png/etc and close the dev

[R] Query on contour plots

Hi all, While exploring  packages for 3D plots that several folks suggested (Tnx all!) It seems what I really need is a contour plot.  This is not working int he Deducer GUI. This will be an aid to separating bats by their vocal signatures. What I need to do is plot *Fc *against *Sc* with the t

[R] Query on 3d plotting pacakges

Hi all, Fumbling around trying to find a plot package to do 3D plots. This will be an aid to separating bats by their vocal signatures. What I need to do is plot *Fc *against *Sc* with the third dimension being the *density* of the data points in the Fc-Sc plot. Data format is like this abbrevia

Re: [R] What is best way to calculate % of time?

Tnx all for the helpful suggestions. Life is good. Happy holidays Bruce -- Bruce W. Miller, PhD. Neotropical bat risk assessments Conservation Fellow - Wildlife Conservation Society If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet Using acoustic

Re: [R] What is best way to calculate % of time?

Hi Bert, Tnx for taking time to reply. For clarification... the data do EXPLICITLY indicate when each species is active and when a feeding buzz is recorded. That is ALL it provides based on acoustic data recorded in the field.  Only when a species is recorded  is it identified as active. How thi

Re: [R] What is best way to calculate % of time?

data dictionary? Can it > export a small subset of the relevant data to another Access DB, some > other DB or in .csv format? At the moment I just cannot visualize what > your data layout looks like. > Can you point us to any documentation that explains what information > i

[R] What is best way to calculate % of time?

s recorded and total bat activity to determine what percentage of time was spent with feeding attempts over the active period. This by all bats by survey night and by single species by survey night. Any suggestions welcomed. Happy holidays all -- Bruce W. Miller, PhD. Neotropical bat risk asse

[R] Need help with an iteration

les as it iterates one by one }) #also tried directing where to write the outputas I do when manually running this #write.csv(BatStats,name,file="C:\\Emballonurids\Results")) I would like to run this as an iteration as I have > 200 data files to process and would love to hav

[R] rewrite code from Deducer to run on R-Studio

Hi all, Apparently Deducer (a GUI for R) is no longer supported or being updated. What is the easiest way to re-write code to run using R-Studio? An example: BatStats<- Deducer::descriptive.table (vars = d (Dur,Fmin,Fmax,Fmean,Fk,Fc,Sc,Pmc),data= BatStats,func.names =c("Valid N","Minimum","M

[R] Syntax for capturing and writing file names

tic Parameters\\DataFile_Stats.csv")* -- Bruce W. Miller, PhD. Neotropical bat risk assessments Conservation Fellow - Wildlife Conservation Society If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet Using acoustic sampling to identify and map s

[R] Hacked

Hi all, Site has been hacked? Bad SPAM arriving __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide c

[R] iterative read - write

0.25), na.rm=TRUE),p75=function(x) quantile(x, c(0.75),na.rm=TRUE),p90=function(x) quantile(x, c(0.90),na.rm=TRUE)))* *## Write the results and change output name and directory for the calculated stats.* *write.csv(BatStats,file="C:\\=Bat data working\\Acoustic Parameters\\Corbre_Stats.c

[R] Need help with labeling a plot correctly

Hi all, Eons ago (~2007) Hadley Wickham extremely generously helped me developed a means for plotting temporal activity w/ ggplot. I need to revisit this and have it working again.  I failed to copy the entire legacy code over to my traveling laptop from my workstation, but found a partial bit

[R] New reshape2 question answered

Hi all, Thanks all who replied. Arun, Jim and Jeff. Seems like there are always multiple ways to achieve the same goals with R! Jim Holtman suggested using the base functions. Not PLYR or RESHAPE x <- read.table(text = "Species Location Date Time... Myochi Chena 5/26/09 18:38 remain

[R] New reshape2 question

100) so totals for each species should be the same (or 100%). What do folks suggest? Plyr, Reshape2 or try tables? Thanks, Bruce -- Bruce W. Miller, PhD. Neotropical bat risk assessments If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet Using a

[R] Replacing NA values solved

NAs is correct in this application as the NAs do not represent "missing data" but actually no occurrence of a critter in a given habitat location so the values need to be a 0. Tnx again, Bruce -- Bruce W. Miller, PhD. Neotropical bat risk assessments If we lose the bats, we may los

[R] How to replace NA values

d saving then reopening in R. There must be a simple way to do this in R. Any suggestions welcomed. -- Bruce W. Miller, PhD. Neotropical bat risk assessments If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet Using acoustic sampling to map species d

[R] reshape2 issue solved Tnx!

Hi again all, As the original code lines I had dated back to 2007 that may have predated reshape2? In any case the use of *dcast *rather than /*cast*/ solved the issue. Then with 3 steps: Stop read Think I saw I just needed to change the line input.cast <- cast(input.melt, Species ~ *Date*, fu

[R] reshape2 issue continued

Hi again all, Several replied ASAP that I also needed reshape loaded and not just reshape2. Hmmm tried that and I had some output but not the correct format. What I need is to run simulations of time overlap between species as per the simulation program data input constraints: The basis for the

[R] reshape2 issue

122:17 Any suggestions-help appreciated. Bruce -- Bruce W. Miller, PhD. Neotropical bat risk assessments If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet Using acoustic sampling to map species distributions for >15 years. Providing Intera

Re: [R] R-help Digest, Vol 123, Issue 30

Hi all are there any R packages that include "circular" stats similar to Oriana (http://www.kovcomp.co.uk/oriana/newver4.html)? I am interested in looking at annual patterns of bat activity where data will have date/times and relative abundance values for each Date. I would like to have a cir

[R] How does one set up logical functions?

asured value and also show the high & low "acceptable" values. Thanks for any who respond. Bruce -- Bruce W. Miller, PhD. Neotropical bat risk assessments If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet Using acoustic sampling to ma

[R] Merging data tables

Hi all, I am trying to merge several data sets and end up with a long data format by date & time so I can run correlations and plots. I am using Deducer as an R GUI but can just use the R console if easier. The data sets are weather with wind speed, relative humidity and temperatures by date

[R] Removing duplicated values

Hi all, I have been away from R for far too many months and have two questions. One is likely simple, but not found under help or in many of the available R ref., books. 1. How does one save the results of an analysis from the main console to a file without the need to copy and paste? 2. W

[R] Suggestions for RAM for new box

Hi all, My main Dell melted down a month ago and I need to buy a new workstation. It will be Win7 64 bit and fast graphics card with large RAM. For GIS (ArcGis) I am opting for 6 GB RAM. Is there any advantage for R to boost this to 8 GB or will 6 GB be sufficient for R applications? There hav

[R] How to open files that contain "0"

Conservation Ecologist Neotropical Bat Project office details Gallon Jug, Belize Mailing address P.O. Box 37, Belize City Belize, Central America Phone +501-220-9002 -- Bruce W. Miller, PhD. Neotropical bat risk assessments If we lose the bats, we may lose much of the tropical vegetation and t

[R] issue using package sos

Issue with sos package I am now using R 2.14 and the sos package did work with 2.13 > library(sos) Loading required package: brew Attaching package: 'sos' The following object(s) are masked from 'package:JGR': installPackages The following object(s) are masked from 'package:utils': > librar

[R] New PLYR issue

Issue with PLYR. Now using R 2.14 and this data and plyr command line worked with 2.13 I am also loading the same saved data that worked previously, but now some issue. > library(plyr) > UNESCO <- dget('C:/Carbon-GJ/BZE_ecosys.robj') > df2 <- ddply(df, "UNESCO", summarise, total_ha = sum(Ha))

[R] How to update an old unsupported package

Hi all, I have a package that is specific to a task I was repetitively using a few years ago. I now needed to run it again with new data. However I am told it was built with an older version or R and will not work. How can I tweak the package so it will run on 11.1? It was a one-off product

Re: [R] R-help Digest, Vol 77, Issue 13

Hi all, Where can I find detail of use of seewave? Seems no help included in the package using ??seewave does not provide anything. Tnx __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] Out of memory issue

Hi again all, I can read all of the data is in CSV format with a header row and with 1,200,240 rows. I can do all the plots and ggplot2 has no problems. Seems to be a problem with the MASS package??? It seems that the contour plots are the problem with the memory error. Error:

[R] Install packages not working in latest version?

Seems that the latest version R version 2.9.0 (2009-04-17) has a glitch and will not install packages. Issue with unzipping? Works fine with R version 2.8.1 (2008-12-22) > install.packages("ff") --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.fhcrc.org/bin/w

[R] Memory issues in R

How do people deal with R and memory issues? I have tried using gc() to see how much memory is used at each step. Scanned Crawley R-Book and all other R books I have available and the FAQ on-line but no help really found. Running WinXP Pro (32 bit) with 4 GB RAM. One SATA drive p

[R] Out of memory issue

Hi all, Julian just reminded me I need to include the lines of code so here it is below. I am trying to run some plots on data, but when loading the CSV data file it doss that but in ggplot R is stopping and I am getting an out of memory error. > > d <- read.csv batcalls.rd

[R] Out of memory issue

Hi all, I am trying to run some plots on data, but when loading he CSV data file R is stopping and I am getting an out of memory error. Anyway to tweak this somehow to get it to run? Using WinXP with 4 GB RAM Tnx Bruce __ R-help@r-project.org mai

[R] Converting time from HH:MM:SS to only HH:MM

Hi all, I need to compare between times and put all similar times in specific 1 minute bins. Unfortunately the original data include seconds as well. My data is in HH:MM:SS format but I need it rounded to only HH:MM and trying in Excel to display "unique" records only does not work since the

[R] Time Zone query

I am working with time-date data to plot temporal activity. I would like to create a "template" to repeat the date and time for all potential data sets that may have differing time zone origins. Reading the > ?strptime help section I note that time zone is a variable to add. Looking at the

[R] User manual or tutorial for GAM package

Hi all, Tnx for the number of suggestion to buy one of the books. Unfortunately being a non profit conservation project now w/o funding since all Central American projects were shut down 2 years ago due to lack of donor funding I have nothing now at all for books or even my support, to cover e

[R] User manual or tutorial for GAM package

Hi all, I would like to run the gam package, but can not quite seem to get the syntax correct for my data format as simple as it is. The gamlss package has a user manual but other than the help with gam package I can not find a user manual per se. I did install the gamair that has loads of

[R] Problems with labeling a set X axis in chron plots

I am having difficulties getting the X-axis labels (dates) to be as needed when plotting from chron The help syntax from chron lists this example: x <- chron(dates = c("02/27/92", "02/27/92", "01/14/92", "02/28/92"), I have activity plots by time on the y-axis and the dates on the x-axis. Wh

[R] meaning of warning messages

Hi all, Read a string of data and had this message during a plot run. Warning message: closing unused connection 3 (Lines) Not sure what this means or if it should be of concern. Tnx. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman

[R] Suggestions on which package to use

Hi all, I have been working with the chron package thanks to some guidance from Gabor Grothendieck so I could plot activity by times. What it the best or "recommended" package to compare such activity between sites? I want to compare the acetify time (multiple bat species) between sites and

[R] plotting time and dates revisited

__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

[R] Zoo for plotting time and dates

Hi all, For some reason the messages keep getting rejected. trying again... As I understand the zoo package will aggregate dates and times, but unclear how to tackle this problem. I need to accomplish the following: 1. Generate a scatter plot of bat activity with dates on the X-axis and ti

[R] Plotting activity by time and dates

Hi all, As I understand the zoo package will aggregate dates and times, but unclear how to tackle this problem. I need to accomplish the following: 1. Generate a scatter plot of bat activity with dates on the X-axis and time on the Y-axis. include sunset and sunrise curves as an added part