Re: [R] NADA Package install disappearance

On 22/05/2013 21:06, Rich Shepard wrote: On Wed, 22 May 2013, rwillims wrote: I have been using the NADA package to do some statistical analysis, however I have just found that the package is no longer available for install. I've downloaded an older version ( NADA_1.5-4.tar.gz ) and tried to u

Re: [R] NADA Package install disappearance

On Wed, 22 May 2013, rwillims wrote: I have been using the NADA package to do some statistical analysis, however I have just found that the package is no longer available for install. I've downloaded an older version ( NADA_1.5-4.tar.gz ) and tried to use install.packages to install it in two v

[R] NADA Package install disappearance

I have been using the NADA package to do some statistical analysis, however I have just found that the package is no longer available for install. I've downloaded an older version ( NADA_1.5-4.tar.gz ) and tried to use install.packages to install it in two versions of R ( 3.0.0 and 2.15.1

Re: [R] NADA

Hello Don, Jeff, Thanks a lot for the comments and suggestions. Best Janh On Thu, Mar 21, 2013 at 10:57 AM, MacQueen, Don wrote: > According to ?ros, one of the arguments is: > > reverseT: A name of a function to use for reversing the transformation > after performing the ROS fit.

Re: [R] NADA

According to ?ros, one of the arguments is: reverseT: A name of a function to use for reversing the transformation after performing the ROS fit. Defaults to 'exp'. And in the Details section: By default, 'ros' performs a log transformation prior to, and after operations over the data

Re: [R] NADA

Somebody just might be able to help if you read the Posting Guide mentioned in the email footer, post using plain text, and make a reproducible example [1]. [1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example -

[R] NADA

Dear Users Regarding the NADA package, would anyone be able to help me understand what values are actually plotted on the Y axis of the plot obtained by using the *ros* function on the data and plotting the result with the plot() function? The Y axis is labeled "Values". According to the NADA user

Re: [R] NADA and cenmle

Ah ok, thanks. I understand now. The data are chemical concentrations but are reported back as negative values. I have a Lower limit of detection (LLD) of 1 for one element but a value of -2.9 gets reported back to me. One last question, for a different element the LLD is reported as 10, anything

Re: [R] NADA and cenmle

On Thu, 14 Mar 2013, Shane Carey wrote: Ah ok, thanks. I understand now. The data are chemical concentrations but are reported back as negative values. I have a Lower limit of detection (LLD) of 1 for one element but a value of -2.9 gets reported back to me. One last question, for a different e

Re: [R] NADA and cenmle

Shane: Just to add some practical advice on top of Rich's interpretation of the censoring process (which is correct), my recent experiences with analyzing below-detection limit chemical concentrations in water using left-censoring estimators indicates that historically people have not always indic

Re: [R] NADA and cenmle

On Thu, 14 Mar 2013, Shane Carey wrote: Thanks for your reply. My data frame contains the value and a true/false to indicate whether they are censored or not. So I have something like: Data Censored -1.2 TRUE -5.5 TRUE 5 FALSE These negative

Re: [R] NADA and cenmle

On Thu, 14 Mar 2013, Shane Carey wrote: I am using the cenmle function from the NADA package and some of my data are negative values. As a result the cenmle function will not work and NaN's are produced. I try to change the distribution to Gaussian, but it still will not run. Could somebody ple

[R] NADA and cenmle

Hi, I am using the cenmle function from the NADA package and some of my data are negative values. As a result the cenmle function will not work and NaN's are produced. I try to change the distribution to Gaussian, but it still will not run. Could somebody please help me with this? Thanks -- Sh

Re: [R] NADA package/cenboxplot() method: maximum censored percentage [RESOLVED] (fwd)

On Mon, 20 Aug 2012, William Dunlap wrote: This is where summary(as.d) can give information that str(as.d) does not. Bill, Ah, ha! That finds the error: all observations are in one era. I did not notice that before. A valuable lesson for me. Thank you very much, Rich

Re: [R] NADA package/cenboxplot() method: maximum censored percentage

On Mon, 20 Aug 2012, David Winsemius wrote: I see no evidence from what you have posted that the function "obtains a censored ratio > 0.8". The error messages says there were missing values. You might consider looking at : David, Missing values were removed from the data before reading into

Re: [R] NADA package/cenboxplot() method: maximum censored percentage

On Mon, 20 Aug 2012, William Dunlap wrote: You get this error if the factor given as the group argument has any unused factor levels. E.g., with(Golden, cenboxplot(Blood, BloodCen, factor(DosageGroup,levels=c("Low","High","" Error in if ((length(obs[censored])/length(obs)) > 0.8) { : m

Re: [R] NADA package/cenboxplot() method: maximum censored percentage

onday, August 20, 2012 10:15 AM > To: Rich Shepard > Cc: r-help@r-project.org > Subject: Re: [R] NADA package/cenboxplot() method: maximum censored percentage > > > On Aug 20, 2012, at 9:22 AM, Rich Shepard wrote: > > > On Thu, 16 Aug 2012, David L Lorenz wrote: > &g

Re: [R] NADA package/cenboxplot() method: maximum censored percentage

On Aug 20, 2012, at 9:22 AM, Rich Shepard wrote: On Thu, 16 Aug 2012, David L Lorenz wrote: The cenboxplot function uses cenros to estimate the censored values. The cenros function requires at least 2 uncensored observations to be able to do the regression. The cenros function does issue a

Re: [R] NADA package/cenboxplot() method: maximum censored percentage

On Thu, 16 Aug 2012, David L Lorenz wrote: The cenboxplot function uses cenros to estimate the censored values. The cenros function requires at least 2 uncensored observations to be able to do the regression. The cenros function does issue a warning when there are more than 80% censored data, b

Re: [R] NADA package/cenboxplot() method: maximum censored percentage

On Thu, 16 Aug 2012, David L Lorenz wrote: The cenboxplot function uses cenros to estimate the censored values. The cenros function requires at least 2 uncensored observations to be able to do the regression. The cenros function does issue a warning when there are more than 80% censored data, bu

Re: [R] NADA package/cenboxplot() method: maximum censored percentage

. Hope this helps. Dave Date: Wed, 15 Aug 2012 14:28:54 -0700 (PDT) From: Rich Shepard To: r-help@r-project.org Subject: [R] NADA package/cenboxplot() method: maximum censored percentage Message-ID: Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII One set of data

[R] NADA package/cenboxplot() method: maximum censored percentage

One set of data has censored (less-than detection limits) water chemistry concentrations for 80-100% of all observations. My initial trial-and-error attempts to apply the cenboxplot() method suggests that it has an upper limit to the percentage of censored observations. I do not see this limit i

Re: [R] NADA Package: Referencing Data Frame Columns

Hi > > > Specifically, since it has only a single detection indicator column > > (ceneq1), it implies that within any single sample either all the analytes > > were detected, or all were not. Not what I would expect. > > Don, > >I have been thinking about this and wondered whether the cast

Re: [R] NADA Package: Referencing Data Frame Columns

On Wed, 8 Aug 2012, MacQueen, Don wrote: Specifically, since it has only a single detection indicator column (ceneq1), it implies that within any single sample either all the analytes were detected, or all were not. Not what I would expect. Don, I have been thinking about this and wondered

Re: [R] NADA Package: Referencing Data Frame Columns

Hi Rich, I may not have the complete picture here, but I do see what looks to me like a problem with your chem.cast. Specifically, since it has only a single detection indicator column (ceneq1), it implies that within any single sample either all the analytes were detected, or all were not. Not w

Re: [R] NADA Package: Referencing Data Frame Columns

On Aug 7, 2012, at 11:31 AM, R. Michael Weylandt wrote: On Tue, Aug 7, 2012 at 11:26 AM, Rich Shepard > wrote: The sample data sets that come with the NADA package are limited to one or two variables and a censored measurement indicator column. I try to mimic examples using my data but kee

Re: [R] NADA Package: Referencing Data Frame Columns

On Tue, 7 Aug 2012, R. Michael Weylandt wrote: Take a look at with() Michael, Works like a charm! Thanks again for the pointer. Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting gui

Re: [R] NADA Package: Referencing Data Frame Columns

On Tue, 7 Aug 2012, David Winsemius wrote: cenboxplot(chem&Vdis, chem$ceneq1, chem$era) ___^ Incorrect use of '&' when '$' was intended. Mea culpa, David! Thanks for catching my typo. Rich __ R-help@r-project.org mailing list https://

Re: [R] NADA Package: Referencing Data Frame Columns

On Tue, 7 Aug 2012, R. Michael Weylandt wrote: Take a look at with() Michael, Thank you. I will. Rich -- Richard B. Shepard, Ph.D. | Integrity - Credibility - Innovation Applied Ecosystem Services, Inc. |Helping Ensure Our Clients' Futures

Re: [R] NADA Package: Referencing Data Frame Columns

On Tue, Aug 7, 2012 at 11:26 AM, Rich Shepard wrote: > The sample data sets that come with the NADA package are limited to one or > two variables and a censored measurement indicator column. I try to mimic > examples using my data but keep missing the target. > > My water chemistry data is ava

[R] NADA Package: Referencing Data Frame Columns

The sample data sets that come with the NADA package are limited to one or two variables and a censored measurement indicator column. I try to mimic examples using my data but keep missing the target. My water chemistry data is available in two formats: long (as seen in a database table) and

Re: [R] NADA Data Frame Format: Wide or Long?

On Fri, 6 Jul 2012, MacQueen, Don wrote: So what you're faced with is that the cenros() function has no built-in methods for grouping or subsetting -- unlike some other R methods, especially those that work with the lattice package, or the many modeling functions like lm() that have a subset arg

Re: [R] NADA Data Frame Format: Wide or Long?

Hi Rich, So what you're faced with is that the cenros() function has no built-in methods for grouping or subsetting -- unlike some other R methods, especially those that work with the lattice package, or the many modeling functions like lm() that have a subset argument or employ a conditioning syn

Re: [R] NADA Data Frame Format: Wide or Long?

On Thu, 5 Jul 2012, MacQueen, Don wrote: This example follows exactly the example in ?cenros. with( subset(yourdataframe, param=='Ag'), cenros(quant,ceneq1) ) This should do a simple censored summary statistica calculation for silver (assuming quant contains your reporting level for ce

Re: [R] NADA Data Frame Format: Wide or Long?

I haven't used NADA functions in quite a while, but from what I recall, you will likely be using the "narrow" format, and sub-setting as needed for the different analytes. As Jean suggested, the examples in the help pages for the NADA function(s) of interest should make it clear. This example fol

Re: [R] NADA Data Frame Format: Wide or Long?

Rich, I am not familiar with the NADA package, but the reference manual ( http://cran.r-project.org/web/packages/NADA/NADA.pdf) has many examples using several data sets included in the package. Look up one of the functions that you plan to use, run the example in R, and look at the data that

[R] NADA Data Frame Format: Wide or Long?

I have water chemistry data with censored values (i.e., those less than reporting levels) in a data frame with a narrow (i.e., database table) format. The structure is: $ site: Factor w/ 64 levels "D-1","D-2","D-3",..: 1 1 1 1 1 1 1 1 ... $ sampdate: Date, format: "2007-12-12" "2007-12-12

[R] NADA Applied to my Data

I need a nudge in the right direction to get started using NADA. I bought Helsel's second addition and am currently reading it; NADA is installed in R. My data has been restructured with a couple of awk scripts. The data frame structure now has a flag if the quantity is censored (ceneq1 colum