search for: hommel

...lt;- order(p, decreasing = TRUE) ro <- order(o) pmin(1, cummin( n / i * p[o] ))[ro] How to explain the first and the fourth row. ====================p.adjust.R======================================= p.adjust.methods <- c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none") p.adjust <- function(p, method = p.adjust.methods, n = length(p)) { ## Methods 'Hommel', 'BH', 'BY' and speed improvements contributed by ## Gordon Smyth <smyth@we...

...GS> p.adjust() unfortunately gives incorrect results when GS> 'p' includes NAs. The results from topTable are GS> correct. topTable() takes care to remove NAs before GS> passing the values to p.adjust(). There's at least one bug in p.adjust(): The "hommel" method currently does not work at all with NAs (and I have an uncommitted fix ready for this bug). OTOH, the current version of p.adjust() ``works'' with NA's, apart from Hommel's method, but by using "n = length(p)" in the correction formulae, i.e. *including* the N...

...Upper case values for method "BH" or "YH" are also accepted. 4. p.adust() now preserves attributes like names for named vectors (as does cumsum and friends for example). 5. p.adjust() now works columnwise on numeric data.frames (as does cumsum and friends). 6. method="hommel" now works correctly even for n=2 7. The 'n' argument is removed. Setting this argument for any methods other than "none" or "bonferroni" make the p-values indeterminate, and the argument seems to be seldom used. (It isn't used in the R default distribution....

...tion: Bonferroni and Dunn-Sidak. Can anyone suggest why Partek implemented Dunn-Sidak and not the other methods that R has? Is there any particular advantage to the Dunn-Sidak method? R knows about these methods (in R 2.1.1): > p.adjust.methods [1] "holm" "hochberg" "hommel" "bonferroni" "BH" "BY" "fdr" [8] "none" BH is Benjamini & Hochberg (1995) and is also called "fdr" (I wish R's documentation said this clearly). BY is Benjamini & Yekutieli (2001). I found a few hits from Google on Dun...

Full_Name: Peter Ehlers Version: 1.6.0 OS: Windows 2000 Pro Submission from: (NULL) (136.159.61.178) In: p.adjust package:base R Documentation In the paragraph: Hochberg's and Hommel's methods are valid when the hypothesis tests are independent or when they are non-negatively associated (Sarkar, 1998; Sarker and Chang, 1997). Hommel's method is more powerful than Hochberg's, but the difference is usually small and the Hochberg p-values are faster to compute. C...

http://bugs.freedesktop.org/show_bug.cgi?id=25453 Summary: nouveau + multiple xorg servers + suspend2ram trashes root partition Product: xorg Version: unspecified Platform: x86-64 (AMD64) OS/Version: Linux (All) Status: NEW Severity: critical Priority: high Component: Driver/nouveau

Hi,?are the methods for multiple testing p value adjustment (Shaffer, Westfall, free) implemented in the function adjusted() in multcomp package so called closed testing procedure? what about those methods (holm, hochberg, hommel, BH, BY) implemented in the p.adjust() in the stats package? ? Thanks ? John

...ation bugs on gcc 3.1/2 on 32-bit Solaris. o The trace() function has been robustified and a new function tracingState() added to turn tracing temporarily on and off. o New cophenetic() in "mva" as utility for hierarchical clustering. o p.adjust() has two new methods, 'Hommel' and 'FDR', contributed by Gordon Smyth <smyth at wehi.edu.au>. o stars() now has add and plot arguments. DEPRECATED & DEFUNCT o The assignment operator `_' is deprecated: a warning is given once per R session. o machine() is deprecated in favour of .Pla...

...ation bugs on gcc 3.1/2 on 32-bit Solaris. o The trace() function has been robustified and a new function tracingState() added to turn tracing temporarily on and off. o New cophenetic() in "mva" as utility for hierarchical clustering. o p.adjust() has two new methods, 'Hommel' and 'FDR', contributed by Gordon Smyth <smyth at wehi.edu.au>. o stars() now has add and plot arguments. DEPRECATED & DEFUNCT o The assignment operator `_' is deprecated: a warning is given once per R session. o machine() is deprecated in favour of .Pla...

...6. o eval(expr, NULL, encl) now looks up variables in encl, as eval(expr, list(), encl) always did o Coercing as.data.frame(NULL) to a pairlist caused an error. o p.adjust(p, ..) now correctly works when `p' contains NAs (or when it is of length 0 or length 2 for method = "hommel"). o 'methods' initialization was calling a function intended for .Call() with .C(). o optim() needed a check that the objective function returns a value of length 1 (spotted by Ben Bolker). o X11() was only scaling its fonts to pointsize if the dpi was within 0.5 of...

...6. o eval(expr, NULL, encl) now looks up variables in encl, as eval(expr, list(), encl) always did o Coercing as.data.frame(NULL) to a pairlist caused an error. o p.adjust(p, ..) now correctly works when `p' contains NAs (or when it is of length 0 or length 2 for method = "hommel"). o 'methods' initialization was calling a function intended for .Call() with .C(). o optim() needed a check that the objective function returns a value of length 1 (spotted by Ben Bolker). o X11() was only scaling its fonts to pointsize if the dpi was within 0.5 of...

...Yost <johnyost@ptd.net> # AlleyTrotter John Drescher <drescherjm@gmail.com> John Dykstra <jdykstra@cray.com> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McCarron <john.mccarron@canonical.com> John...

...Yost <johnyost@ptd.net> # AlleyTrotter John Drescher <drescherjm@gmail.com> John Dykstra <jdykstra@cray.com> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McCarron <john.mccarron@canonical.com> John...

...Yost <johnyost@ptd.net> # AlleyTrotter John Drescher <drescherjm@gmail.com> John Dykstra <jdykstra@cray.com> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McCarron <john.mccarron@canonical.com> John...

...otter John Drescher <drescherjm@gmail.com> John Dykstra <jdykstra@cray.com> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Gong <john_gong@usish.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McCarron <john.mccarron@canonical.com> John...

...otter John Drescher <drescherjm@gmail.com> John Dykstra <jdykstra@cray.com> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Gong <john_gong@usish.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McCarron <john.mccarron@canonical.com> John...

...otter John Drescher <drescherjm@gmail.com> John Dykstra <jdykstra@cray.com> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Gong <john_gong@usish.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McCarron <john.mccarron@canonical.com> John...

...otter John Drescher <drescherjm@gmail.com> John Dykstra <jdykstra@cray.com> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Gong <john_gong@usish.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McCarron <john.mccarron@canonical.com> John...

...om> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Gong <john_gong@usish.com> John Greene <jogreene@redhat.com> John Haxby <john.haxby@oracle.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John L. Hammond <john.hammond@intel.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McC...

...om> on behalf of Cray Inc. John Eaglesham <linux@8192.net> John Ellson <john.ellson@comcast.net> John Fastabend <john.r.fastabend@intel.com> John Gong <john_gong@usish.com> John Greene <jogreene@redhat.com> John Haxby <john.haxby@oracle.com> John Hommel <john.hommel@hp.com> John Hughes <john@calva.com> John Johansen <john.johansen@canonical.com> John Kacur <jkacur@redhat.com> John L. Hammond <john.hammond@intel.com> John Li <chen-yang.li@mediatek.com> John Linn <john.linn@xilinx.com> John McC...