search for: transect

Dear All, I would like to make partial sums (or means or any other function) of the values in intervals along a sequence (spatial transect) where groups are defined. For instance: habitats<-rep(c("meadow","forest","meadow","pasture"),c(10,5,12,6)) observations<-rpois(length(habitats),2) transect<-data.frame(observations=observations,habitats=habitats) aggregate() is not suitable for...

Dear R friends, I have a matrix with 2060 rows and 41 columns. One column is Date, another is Transect, and another is Segment. I want to ensure that there are 9 Transects (1 to 9) for each Date, and 8 Segments (1 to 8) for each Transect in the matrix, by inserting rows where these are missing. I am new to coding, but am trying to write a loop which checks if each of the transects already exists,...

I'm trying out a basic plot, but something about the way I subset my data leads to problems with the plot. Here is the first bit of my data set year,date,location,quadrat_juvenile,photo_location,photo_exists,genus,count,divers 2005,2005-04-30, 1 Fringing Reef,1, 1 Fringing Reef Coral Transect Pole 1-2 Quadrat 1,t,Acanthastrea,0,HP+MEM 2005,2005-04-30, 1 Fringing Reef,1, 1 Fringing Reef Coral Transect Pole 1-2 Quadrat 1,t,Acropora,0,HP+MEM 2005,2005-04-30, 1 Fringing Reef,1, 1 Fringing Reef Coral Transect Pole 1-2 Quadrat 1,t,Astreopora,0,HP+MEM 2005,2005-04-30, 1 Fringing Reef,1, 1 Frin...

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...script (see below), which regularly generates the error message, Error in start:(start + (sample.length - 1)) : NA/NaN argument , for which I am unsure of the cause. In essence, the script (below) generates the start and end points for random subsamples from along a vector (in reality a transect (of a given length, sample.length), that may be used to subsample from another vector of data. The important point is that once a section of the transect has been sampled, it cannot be resampled by an overlapping sub-transect. WHile there are obvious limits on the number of non-overlapping subvec...

Hi all, I'm trying to fit models for data with three levels of nested random effects: site/transect/plot. For example, modelincrBS<-glmer(l.ru.ba.incr~shigo.av+pre.f.crwn.length+bark.thick.bh+Date+slope.pos.num+dens.T+dbh+leaf.area+can.pos.num+(1|site/transect/plot), data=rws30.UL, family=gaussian, na.action=na.omit) but I get the following error: Error: length(f1) == length(f2) is not TRUE...

...ollowing glmm question (using glmmPQL from the MASS library): "We have two different forest habitats (first rotation thicket, and high forest) which we want to survey for the presence of our study animal. We survey both habitats on each of 10 days, and within each habitat we have five transects. The sampling unit is the number of animals counted per transect. We therefore have two sources of random variation: ? counts will vary between days due, say, to variation in weather ? counts will vary between transects, within sites, for any number of (known and unknown) reasons There...

# I need to create an xyplot() where I control the specific order of # both my conditioning variables. The default code below plots the # data correctly (dispersed across all 14 columns), but fails in two # ways. Both the primary conditioning variable (Transect), and the # secondary conditioning variable (Offset) are in alphanumeric order, # rather than the specific order I need. # Here is a call to the input datafile, which should be attached. df <- read.csv(file = "T_5-04b_LTC-SE-SO-Compared.csv") # Basic default plot (correct data,...

Dear R gurus, I have XY data giving the locations of tree seedlings that were surveyed during a 210 meter belt transect. This belt transect was taken by stretching a line across the field, then measuring all seedlings within 1 meter on either side of the line. The end result was XY coordinates and height for ~1,300 seedlings. I would like to use that data to calculate density of seedlings per 10 meters pe...

...t al. 2000. Analysis of count data from before-after control-impact studies. J. Agric. Biol. Envir Stat., 5:262-279) Data were collected from 1984, 1989, 1990, 1991, 1993, and 1996. Samples from 1984 are considered as before an impact and the remaining years as after the impact. Each year, 96 transects were sampled (36 in the oiled area and 60 in the non-oiled area; "0" is for oiled and "1" for non-oiled). The authors compare 3 different ways of analysing the data including glmm. The data can be reproduced with the following commands (density is fake numbers but I can pro...

...e data. The dataset is small (n=6) and was arranged so that the data from the two different years was arranged in two columns ("2010", "2011). I've pasted the rest of the code below for reference. I'd appreciate any suggestions as to what the issue here is! Thanks, Varina transect=read.csv("Transect data.csv") attach(transect) replicates=c(1,2) yearfactor=as.factor(replicates) yearframe=data.frame(yearfactor) yearbind=cbind(transect$TP10, transect$TP11) yearmodel=lm(yearbind~1) rmanova=anova(yearmodel, idata=yearframe, idesign=~yearfactor) summary(rmanova...

Hello, I'm a final-year student in statistics and I deal with as subject of thesis "rare and elusive populations". I want make a simulation, in which I want generate a population and estimate its density with "line transect method" using R language. Is there someone that can send me the program that generate a population and estimate its density with "line transect method" in R language, please? I'm sure of your courtesy I'd like immediately to thank for whoever wants to answer me and send the...

...ble in Specific, Non-Alphanumeric Order. # I need to create an xyplot() where I control the specific order of # both my conditioning variables. The default code below plots the # data correctly (dispersed across all 14 columns), but fails in two # ways. Both the primary conditioning variable (Transect), and the # secondary conditioning variable (Offset) are in alphanumeric order, # rather than the specific order I need. # Here is a call to the input datafile, which should be attached. You may rename that .txt file to .csv for processing in the following line. df <- read.csv(file = &qu...

Sub: using glmer to fit a mixed-effects model with gamma-distributed response variable Hello, I'm currently trying to fit a mixed effects model , i.e.: > burnedmodel1.2<-glmer(gpost.f.crwn.length~lg.shigo.av+dbh+leaf.area+ bark.thick.bh+ht.any+ht.alive+(1|site/transect/plot), family=gaussian, na.action=na.omit, data=rws30.BL) If I run this code, I get the error below: Error: length(f1) == length(f2) is not TRUE In addition: Warning messages: 1: In plot:(transect:site) : numerical expression has 175 elements: only the first used 2: In plot:(transect:site) :...

Dear R Community! We analyse the impact of climbing activity on cliff vegetation. During our fieldwork, we recorded 90 Transects in 3 climbing sites. The aim is to see, if the plant cover (response: Cover) is influenced only by crevice availability (predictor: Cracs), or, additional, by the distance to the climbing route (predictor: Distance). Six plots are nested within one Transect (ID.Transekt), the Transects are nested...

Hi again. Perhaps a simple question this time.... I am analysing data with a dependent variable of insect counts, a fixed effect of site and two random effects, day, which is the same set of 10 days for each site, and then transect, which is nested within site (5 each). I am trying to fit the cross classified model using GLMM in lme4. I have, for potential use, created a second coding of transect with levels 1-5 for site 1 and 6-10 for site2. Likewise, if a groupedData object is necessary, there are als ts1 and ts2...

...g presences then the rows containing absences and combining them. e.g. presence_records<-sample(1:117,size=75,replace=FALSE) absence_records<-sample(118:936,size=549,replace=FALSE) ss<-c(presence_records,absence_records) but... b) My samples are within video transects and due to the risk of autocorrelation within each transect, ideally it is by transect cluster that they will be randomly selected. (a point within a transect cannot be allocated to the training dataset when another point from that same transect is already allocated to the test dataset) Is there...

Hi, I have a question about computing shortest Euclidean distances between two data frames of spatial points... I have 2 dataframes (not yet converted to spatial class) >Sewers<-data.frame(x=c(10,20,35,50),y=c(100,150,200,300)) >transect <- data.frame(x=seq(from=0, to=50, by=1),y=seq(from=100, to=150, by=1)) I would like to be able to compute the shortest distance from the transect points the nearest sewer (Euclidean distance) I've tried a number of different loops, but so far ave had no luck. Any help would be apprecia...

...some data I have imported into R from a .csv file but when I carry out the aov command the results show only one degree of freedom when there should be 14. Does anyone know why? I'd really appreciate some help, the data is pasted below. /The imported table looks ike this this:/ Order Transect Sample Abundance 1 Coleoptera 1 1 13 2 Coleoptera 1 2 12 3 Coleoptera 1 3 11 4 Coleoptera 1 4 13 5 Coleoptera 1 5 6 6 Coleoptera 2 1 18 7 Coleoptera 2 2 18 8...

Hi, We are analizing the relationship between the abundance of groupers in line transects and some variables. We are using the quasipoisson distribution. Do we need to include the length of the transects as an offset if they all have the same length?? Also, can we include in the gam models variables that are measured at different spatial scales? We have done an analysis to see what v...