search for: soil

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...d been getting the grips with this. I have been trying to use Adonis to find out if there are significant difference between groups on data that I have analyses with NMDS, and have been struggling with getting this to work and understanding what is going on. I am looking at diversity in different soils with either woodland or grassland habitats. I have run the scripts library(vegan) library(ecodist) library(MASS) mydata <- read.table("ash_data.csv", header=TRUE, sep=",", row.names="Site") envdata_fit <- read.table("ash_env.csv", header=TRUE, sep=&...

...0.439 0.943 2.5Y 0.8 4 0.82 0.64 0.943 2.5Y 1 2 0.4362 0.4177 1.21 I have converted xyY coordinates to XYZ coordinates, based on the equations presented here: http://www.brucelindbloom.com/index.html?ColorCalcHelp.html #read in the soil colors: munsell + xyY soil <- read.table("soil_colors", header=F, col.names=c("H","V","C","x","y","Y")) #convert to XYZ X <- (soil$x * soil$Y ) / soil$y Y <- soil$Y Z <- ( (1- soil$x - soil$y) * soil$Y ) / soil$y #...

...uot;:\n") means <- aggregate(data, list(label), FUN=mean) print(means) } } Here is a sample context-- a randomized block design with two crossed factors (Contour, Depth) and 9 responses (pH, N, ... Conduc). [An R-readable version of the data is appended at the bottom.] > soils <- read.delim("soils.dat") > str(soils) 'data.frame': 48 obs. of 14 variables: $ Group : int 1 1 1 1 2 2 2 2 3 3 ... $ Contour: Factor w/ 3 levels "Depression","Slope",..: 3 3 3 3 3 3 3 3 3 3 ... $ Depth : Factor w/ 4 levels "0-10&quo...

Hello. When one types "summary(fit)", where fit is an object from a call to aov(), one gets an ANOVA table. I want to save just one element of this summary. How does one extract this? As an example, here is my output from a split plot ANOVA: > summary(out)$"Error: soil.cores$block:soil.cores$treatment" Df Sum Sq Mean Sq F value Pr(>F) soil.cores$block 3 0.63626 0.21209 1.0557 0.4147 soil.cores$treatment 3 0.90276 0.30092 1.4978 0.2802 Residuals 9 1.80813 0.20090 I want to save only the F value of "soil.core...

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...rence vector between color space coordinates associated with a single analytical value and the entire lookup table. Then I found the smallest difference vector, and used that entry in the lookup table. Hoerver, This does not always produce logical results... here are the steps: # read in the data soil <- read.table("http://169.237.35.250/~dylan/temp/munsell-all.dat", header=T) x <- read.csv('http://169.237.35.250/~dylan/temp/data_dump_4-7-2007.csv', header=FALSE) # extract important variables X,Y,Z c <- data.frame(id=x$V1, X=x$V2, Y=x$V3, Z=x$V4) # convert munsell t...

Hi, every body! I am a new comer for R, so my question would unavoidablely sounds stupid. Sorry! In my experiment, there are two type of soil ( soil F and soil D), each half of them were subjected to steam sterilize (result in FS and DS soil). A equal volume of soil from two of the four soil types (F, D, FS, DS) were mixed as follows: F+F, F+D, F+FS, F+DS, D+F, D+FS, D+DS, FS+DS (eight treatment). Two type of plant (A, B) were planted i...

...this code on the web as part of an stats course (and it is not the only example I found). Because I'm not really into the details of the functions I would like to hear comments from people who have used these functions before. This is the code library(akima) library(fields) library(tripack) soil <- read.table("http://www.unc.edu/~zhuz/teaching/Stat890/Data/soil.txt",header=TRUE) attach(soil) soil.interp <- interp(u, v, moist) # linear interpolation works plot.surface(soil.interp) # spline interpolation soil.interp2 <- interp(u, v, moist, linear = F) # spline interpolati...

...rom an rgl call, but, I can't get a traceback or other information because my R session crashes. I've never seen this behavior before. The problem occurs *whenever* I try to supply linear hypotheses to be displayed along with the model terms. Here is a small example: library(heplots) # Soils data, from car package soils.mod <- lm(cbind(pH,N,Dens,P,Ca,Mg,K,Na,Conduc) ~ Block + Contour*Depth, data=Soils) Anova(soils.mod) heplot(soils.mod, variables=c("Ca", "Mg")) ## this works OK heplot3d(soils.mod, variables=c("Mg", "Ca", "Na")) #...

...n (different factors, so they are not nested), but R moves the two-way interaction to the front. I know it generally makes sense to fit the two-way interactions first, but in this case I think I know what I'm doing. + hv + hv:rep + hv:soil + hv:spdiv + hv:spdivnom + hv:fgdiv + hv:fgdivnom + hv:soil:spdiv + hv:soil:spdivnom + hv:soil:fgdiv + hv:soil:fgdivnom + hv:mx...

Hi, You didn't specify the satistical model you are intereted in, I will suppose it is something like: #Organims ~ Landscape + Soil + Depth + Species I suppose you have a table of with something like... Spec Lands Soil Depth #Organisms A 1 1 1 10 A 1 2 1 2 B 1 1 1 0 B 2 2 2 2 ... etc, Normally, the count of organisms in soil samples follows a posisson distribution, not a normal one. You should effectively check for normalit...

Hello Trying to develop variograms and kriged surfaces from a point file. Here is what I've done so far. library(gstat) # also loads library(sp) library(lattice) soilpts$x <- soilpts$UTM_X soilpts$y <- soilpts$UTM_Y soil.dat <- subset(soilpts, select=c(x, y, Area, BulkDensity, LOI, TP, TN, TC, Total_Mg)) dim(soil.dat) [1] 1292 7 coordinates(soil.dat) <- ~ x+y gridded(soil.dat) <- TRUE Warning messages: 1: In points2grid(points, toleranc...

Hi, every body! I am a new comer for R, so my question would unavoidablely sounds stupid. Sorry! in my experiment, there are two type of soil ( soil F and soil D), each half of them were subjected to steam sterilize (result in FS and DS soil). A equal volume of soil from two of the four soil types (F, D, FS, DS) were mixed as follows: F+F, F+D, F+FS, F+DS, D+F, D+FS, D+DS, FS+DS (eight treatment). Two type of plant (A, B) were planted in...

Hi, I am trying to create a triangular plot to show the 'composition' of a set of items with three variables (historically the percent sand, silt and clay in soil). So far I have tried the 'soil texture triangle plot' in the package plotrix and the 'ternary or triangular plots' in the package cwhtool (cwhmisc). Both have strengths and weaknesses, but neither has a 'standard' or 'generic' feel about it. To save myself tim...

Dear R community, I am using xYplot() from the Hmisc package. The package works great to plot means + CI. But I am having issues handling the scales. I am plotting "Soil Clay content" vs "Soil depth" by "land use". Usually in this type of graphs it is better to place the variable "soil depth" in the y-axis and it should be ordered downward by depth (0-5 cm, 5-10 cm, 10-20 cm). I can't figure out how to sort/order the scale...

Hello I am trying to fit a REML to some soil mineral data which has been collected over the time period 1999 - 2004. I want to know if the 19 different treatments imposed, differ in terms of their soil mineral content. A tree model of the data has shown differences between the treatments can be attributed to the Magnesium, Potassium and organ...

Dear all, I've used glm(family=binomial(link="logit")) several times, but now I think that a log link is more appropriate. I want to fit a model for probability of tree fall (TF)), with tree diameter (dbh) and soil moisure (soil) as predictors. A large number of trees have been checked every second year whether they stand up (0) or have fallen (1). I assume that the tree fall probability is predicted by TF = 1 - exp(-(dbh + soil)) log(1 - TF) = -(dbh + soil) I thought the following call would fit the model...

Hi I have a netCDF file of volumetric soil water content at four different soil layers and want to convert each soil layer in the netCDF file to a GeoTIFF layer. This code converts the netCDF file to one GeoTIFF layer, i.e. unclear which soil depth. file.nc <- "C:/Soil_Weather_data/Agro/VMC21/VMC21.nc" file.tiff <- "C...

Hi All, I am trying to lable the y-axis on my scatterplot with the following: "Soil moisture content (m3m-3)" I am using the following coding for plotting the graph: plot(soilmoisture~gradientlevel, xlab="Levels of droughting gradient", ylab="Soil moisture content (m3m-3)", bty="l", font.main="2", pch=16, las=1, cex.lab="1.13&quot...