CRAN Package Check Results for Package mvabund

Last updated on 2016-07-30 14:49:48.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.11.9 16.91 73.07 89.98 ERROR
r-devel-linux-x86_64-debian-gcc 3.11.9 19.00 71.82 90.82 ERROR
r-devel-linux-x86_64-fedora-clang 3.11.9 155.15 ERROR
r-devel-linux-x86_64-fedora-gcc 3.11.9 147.87 ERROR
r-devel-osx-x86_64-clang 3.11.9 120.68 ERROR
r-devel-windows-ix86+x86_64 3.11.9 54.00 140.00 194.00 ERROR
r-patched-linux-x86_64 3.11.9 15.67 84.52 100.19 OK
r-patched-solaris-sparc 3.11.9 1337.80 OK
r-patched-solaris-x86 3.11.9 242.70 OK
r-release-linux-x86_64 3.11.9 20.21 100.75 120.96 OK
r-release-osx-x86_64-mavericks 3.11.9 OK
r-release-windows-ix86+x86_64 3.11.9 76.00 216.00 292.00 OK
r-oldrel-windows-ix86+x86_64 3.11.9 59.00 235.00 294.00 OK

Check Details

Version: 3.11.9
Check: examples
Result: ERROR
    Running examples in ‘mvabund-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: plot.mvabund
    > ### Title: Plot Multivariate Abundance Data and Formulae
    > ### Aliases: plot.mvabund plot.mvformula
    > ### Keywords: hplot
    >
    > ### ** Examples
    >
    >
    > require(graphics)
    >
    > ############################
    > ## Some "type (1)" plots ##
    > ############################
    >
    > data(solberg)
    > solbdat <- solberg$abund
    > treatment<- solberg$x
    >
    > ## Plot a multivariate dataset (Species vs Abundance)
    > plot.mvabund(solbdat)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Alternatively, the plot command could be used directly if spiddat is
    > ## defined as an mvabund object:
    > solbmvabund <- mvabund(solbdat)
    > plot(solbmvabund)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Draw an mvabund object in a boxplot, but using the 20 most abundant
    > ## variables in the plot, using the square root transform, and adding
    > ## coloured axes and title:
    > plot.mvabund(solbdat, n.vars=20, type="bx", transformation="sqrt",
    + fg="lightblue", main="Solberg abundances", col.main="red")
    Kicking off BoxPlot sequence
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata, Dichromadora_sp., Neochromadora_sp., Richtersia_inaequalis, Pandolaimus_latilaimus, Leptolaimus_elegans, Halalaimus_sp., Desmolaimus_sp., Linhomieidae_un.A were included in the plot
    (the variables with highest total abundance).
    >
    > ## Plot Species (split by treatment) vs Abundance
    > plot(solbmvabund,treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 1st MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## This can also be produced using
    > plot(solbmvabund~treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## To use plot.mvabund to plot only the variables with P-values less than 0.1:
    > lm.solberg <- manylm(log(solbmvabund+1)~treatment)
    > anova.solb <- anova(lm.solberg, p.uni="unadjusted")
    > pj = anova.solb$uni.p
    >
    > plot(solbmvabund~treatment, var.subset=pj<0.1)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Paramesacanthion_sp., Viscosia_sp., Dichromadora_sp., Prochromadorella_sp., Neotonchus_sp., Sabatieria_sp., Daptonema_sp.1, Theristus_aff_acer, Sphaerolaimus_macrocirculus, Odontophora_sp., Unidentified were included in the plot (user selected).
    >
    > ## Or to plot only the 12 most significant variables, according to their
    > ## univariate ANOVA P-values:
    > pj.sort = sort(pj, index.return=TRUE)
    > plot(solbmvabund~treatment, var.subset=pj.sort$ix[1:12])
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Error in default.plotMvaFactor(x = c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, :
     You have passed an invalid 'var.subset'
    Calls: plot ... default.plot.mvabund -> do.call -> default.plotMvaFactor
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 3.11.9
Check: examples
Result: ERROR
    Running examples in ‘mvabund-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: plot.mvabund
    > ### Title: Plot Multivariate Abundance Data and Formulae
    > ### Aliases: plot.mvabund plot.mvformula
    > ### Keywords: hplot
    >
    > ### ** Examples
    >
    >
    > require(graphics)
    >
    > ############################
    > ## Some "type (1)" plots ##
    > ############################
    >
    > data(solberg)
    > solbdat <- solberg$abund
    > treatment<- solberg$x
    >
    > ## Plot a multivariate dataset (Species vs Abundance)
    > plot.mvabund(solbdat)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Alternatively, the plot command could be used directly if spiddat is
    > ## defined as an mvabund object:
    > solbmvabund <- mvabund(solbdat)
    > plot(solbmvabund)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Draw an mvabund object in a boxplot, but using the 20 most abundant
    > ## variables in the plot, using the square root transform, and adding
    > ## coloured axes and title:
    > plot.mvabund(solbdat, n.vars=20, type="bx", transformation="sqrt",
    + fg="lightblue", main="Solberg abundances", col.main="red")
    Kicking off BoxPlot sequence
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata, Dichromadora_sp., Neochromadora_sp., Richtersia_inaequalis, Pandolaimus_latilaimus, Leptolaimus_elegans, Halalaimus_sp., Desmolaimus_sp., Linhomieidae_un.A were included in the plot
    (the variables with highest total abundance).
    >
    > ## Plot Species (split by treatment) vs Abundance
    > plot(solbmvabund,treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 1st MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## This can also be produced using
    > plot(solbmvabund~treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## To use plot.mvabund to plot only the variables with P-values less than 0.1:
    > lm.solberg <- manylm(log(solbmvabund+1)~treatment)
    > anova.solb <- anova(lm.solberg, p.uni="unadjusted")
    > pj = anova.solb$uni.p
    >
    > plot(solbmvabund~treatment, var.subset=pj<0.1)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Paramesacanthion_sp., Viscosia_sp., Prochromadorella_sp., Neotonchus_sp., Sabatieria_sp., Daptonema_sp.1, Theristus_aff_acer, Sphaerolaimus_macrocirculus, Odontophora_sp., Unidentified were included in the plot (user selected).
    >
    > ## Or to plot only the 12 most significant variables, according to their
    > ## univariate ANOVA P-values:
    > pj.sort = sort(pj, index.return=TRUE)
    > plot(solbmvabund~treatment, var.subset=pj.sort$ix[1:12])
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Error in default.plotMvaFactor(x = c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, :
     You have passed an invalid 'var.subset'
    Calls: plot ... default.plot.mvabund -> do.call -> default.plotMvaFactor
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 3.11.9
Check: examples
Result: ERROR
    Running examples in ‘mvabund-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: plot.mvabund
    > ### Title: Plot Multivariate Abundance Data and Formulae
    > ### Aliases: plot.mvabund plot.mvformula
    > ### Keywords: hplot
    >
    > ### ** Examples
    >
    >
    > require(graphics)
    >
    > ############################
    > ## Some "type (1)" plots ##
    > ############################
    >
    > data(solberg)
    > solbdat <- solberg$abund
    > treatment<- solberg$x
    >
    > ## Plot a multivariate dataset (Species vs Abundance)
    > plot.mvabund(solbdat)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Alternatively, the plot command could be used directly if spiddat is
    > ## defined as an mvabund object:
    > solbmvabund <- mvabund(solbdat)
    > plot(solbmvabund)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Draw an mvabund object in a boxplot, but using the 20 most abundant
    > ## variables in the plot, using the square root transform, and adding
    > ## coloured axes and title:
    > plot.mvabund(solbdat, n.vars=20, type="bx", transformation="sqrt",
    + fg="lightblue", main="Solberg abundances", col.main="red")
    Kicking off BoxPlot sequence
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata, Dichromadora_sp., Neochromadora_sp., Richtersia_inaequalis, Pandolaimus_latilaimus, Leptolaimus_elegans, Halalaimus_sp., Desmolaimus_sp., Linhomieidae_un.A were included in the plot
    (the variables with highest total abundance).
    >
    > ## Plot Species (split by treatment) vs Abundance
    > plot(solbmvabund,treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 1st MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## This can also be produced using
    > plot(solbmvabund~treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## To use plot.mvabund to plot only the variables with P-values less than 0.1:
    > lm.solberg <- manylm(log(solbmvabund+1)~treatment)
    > anova.solb <- anova(lm.solberg, p.uni="unadjusted")
    > pj = anova.solb$uni.p
    >
    > plot(solbmvabund~treatment, var.subset=pj<0.1)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Paramesacanthion_sp., Viscosia_sp., Dichromadora_sp., Prochromadorella_sp., Neotonchus_sp., Sabatieria_sp., Daptonema_sp.1, Theristus_aff_acer, Odontophora_sp., Unidentified were included in the plot (user selected).
    >
    > ## Or to plot only the 12 most significant variables, according to their
    > ## univariate ANOVA P-values:
    > pj.sort = sort(pj, index.return=TRUE)
    > plot(solbmvabund~treatment, var.subset=pj.sort$ix[1:12])
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Error in default.plotMvaFactor(x = c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, :
     You have passed an invalid 'var.subset'
    Calls: plot ... default.plot.mvabund -> do.call -> default.plotMvaFactor
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 3.11.9
Check: examples
Result: ERROR
    Running examples in ‘mvabund-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: plot.mvabund
    > ### Title: Plot Multivariate Abundance Data and Formulae
    > ### Aliases: plot.mvabund plot.mvformula
    > ### Keywords: hplot
    >
    > ### ** Examples
    >
    >
    > require(graphics)
    >
    > ############################
    > ## Some "type (1)" plots ##
    > ############################
    >
    > data(solberg)
    > solbdat <- solberg$abund
    > treatment<- solberg$x
    >
    > ## Plot a multivariate dataset (Species vs Abundance)
    > plot.mvabund(solbdat)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Alternatively, the plot command could be used directly if spiddat is
    > ## defined as an mvabund object:
    > solbmvabund <- mvabund(solbdat)
    > plot(solbmvabund)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Draw an mvabund object in a boxplot, but using the 20 most abundant
    > ## variables in the plot, using the square root transform, and adding
    > ## coloured axes and title:
    > plot.mvabund(solbdat, n.vars=20, type="bx", transformation="sqrt",
    + fg="lightblue", main="Solberg abundances", col.main="red")
    Kicking off BoxPlot sequence
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata, Dichromadora_sp., Neochromadora_sp., Richtersia_inaequalis, Pandolaimus_latilaimus, Leptolaimus_elegans, Halalaimus_sp., Desmolaimus_sp., Linhomieidae_un.A were included in the plot
    (the variables with highest total abundance).
    >
    > ## Plot Species (split by treatment) vs Abundance
    > plot(solbmvabund,treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 1st MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## This can also be produced using
    > plot(solbmvabund~treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## To use plot.mvabund to plot only the variables with P-values less than 0.1:
    > lm.solberg <- manylm(log(solbmvabund+1)~treatment)
    > anova.solb <- anova(lm.solberg, p.uni="unadjusted")
    > pj = anova.solb$uni.p
    >
    > plot(solbmvabund~treatment, var.subset=pj<0.1)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Paramesacanthion_sp., Viscosia_sp., Prochromadorella_sp., Neotonchus_sp., Sabatieria_sp., Daptonema_sp.1, Theristus_aff_acer, Sphaerolaimus_macrocirculus, Unidentified were included in the plot (user selected).
    >
    > ## Or to plot only the 12 most significant variables, according to their
    > ## univariate ANOVA P-values:
    > pj.sort = sort(pj, index.return=TRUE)
    > plot(solbmvabund~treatment, var.subset=pj.sort$ix[1:12])
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Error in default.plotMvaFactor(x = c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, :
     You have passed an invalid 'var.subset'
    Calls: plot ... default.plot.mvabund -> do.call -> default.plotMvaFactor
    Execution halted
Flavor: r-devel-osx-x86_64-clang

Version: 3.11.9
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'mvabund-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: plot.mvabund
    > ### Title: Plot Multivariate Abundance Data and Formulae
    > ### Aliases: plot.mvabund plot.mvformula
    > ### Keywords: hplot
    >
    > ### ** Examples
    >
    >
    > require(graphics)
    >
    > ############################
    > ## Some "type (1)" plots ##
    > ############################
    >
    > data(solberg)
    > solbdat <- solberg$abund
    > treatment<- solberg$x
    >
    > ## Plot a multivariate dataset (Species vs Abundance)
    > plot.mvabund(solbdat)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Alternatively, the plot command could be used directly if spiddat is
    > ## defined as an mvabund object:
    > solbmvabund <- mvabund(solbdat)
    > plot(solbmvabund)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Draw an mvabund object in a boxplot, but using the 20 most abundant
    > ## variables in the plot, using the square root transform, and adding
    > ## coloured axes and title:
    > plot.mvabund(solbdat, n.vars=20, type="bx", transformation="sqrt",
    + fg="lightblue", main="Solberg abundances", col.main="red")
    Kicking off BoxPlot sequence
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata, Dichromadora_sp., Neochromadora_sp., Richtersia_inaequalis, Pandolaimus_latilaimus, Leptolaimus_elegans, Halalaimus_sp., Desmolaimus_sp., Linhomieidae_un.A were included in the plot
    (the variables with highest total abundance).
    >
    > ## Plot Species (split by treatment) vs Abundance
    > plot(solbmvabund,treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 1st MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## This can also be produced using
    > plot(solbmvabund~treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## To use plot.mvabund to plot only the variables with P-values less than 0.1:
    > lm.solberg <- manylm(log(solbmvabund+1)~treatment)
    > anova.solb <- anova(lm.solberg, p.uni="unadjusted")
    > pj = anova.solb$uni.p
    >
    > plot(solbmvabund~treatment, var.subset=pj<0.1)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Paramesacanthion_sp., Viscosia_sp., Dichromadora_sp., Prochromadorella_sp., Neotonchus_sp., Daptonema_sp.1, Theristus_aff_acer, Unidentified were included in the plot (user selected).
    >
    > ## Or to plot only the 12 most significant variables, according to their
    > ## univariate ANOVA P-values:
    > pj.sort = sort(pj, index.return=TRUE)
    > plot(solbmvabund~treatment, var.subset=pj.sort$ix[1:12])
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Error in default.plotMvaFactor(x = c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, :
     You have passed an invalid 'var.subset'
    Calls: plot ... default.plot.mvabund -> do.call -> default.plotMvaFactor
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 3.11.9
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'mvabund-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: plot.mvabund
    > ### Title: Plot Multivariate Abundance Data and Formulae
    > ### Aliases: plot.mvabund plot.mvformula
    > ### Keywords: hplot
    >
    > ### ** Examples
    >
    >
    > require(graphics)
    >
    > ############################
    > ## Some "type (1)" plots ##
    > ############################
    >
    > data(solberg)
    > solbdat <- solberg$abund
    > treatment<- solberg$x
    >
    > ## Plot a multivariate dataset (Species vs Abundance)
    > plot.mvabund(solbdat)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Alternatively, the plot command could be used directly if spiddat is
    > ## defined as an mvabund object:
    > solbmvabund <- mvabund(solbdat)
    > plot(solbmvabund)
    Kicking off BoxPlot sequence
    Overlapping points were shifted along the y-axis to make them visible.
    
    
    ABOUT TO PLOT THE FUNCTION
    
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## Draw an mvabund object in a boxplot, but using the 20 most abundant
    > ## variables in the plot, using the square root transform, and adding
    > ## coloured axes and title:
    > plot.mvabund(solbdat, n.vars=20, type="bx", transformation="sqrt",
    + fg="lightblue", main="Solberg abundances", col.main="red")
    Kicking off BoxPlot sequence
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata, Dichromadora_sp., Neochromadora_sp., Richtersia_inaequalis, Pandolaimus_latilaimus, Leptolaimus_elegans, Halalaimus_sp., Desmolaimus_sp., Linhomieidae_un.A were included in the plot
    (the variables with highest total abundance).
    >
    > ## Plot Species (split by treatment) vs Abundance
    > plot(solbmvabund,treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 1st MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## This can also be produced using
    > plot(solbmvabund~treatment)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Halanonchus_sp., Terschellingia_longicaudata, Dorylaimopsis_punctatus, Marylynnia_complexa, Molgolaimus_sp., Aponema_torosa, Spirinia_parasitifera, Odontophora_sp., Daptonema_sp.1, Prochromadorella_sp., Halichoanolaimus_dolichurus, Sabatieria_longicaudata were included in the plot
    (the variables with highest total abundance).
    >
    > ## To use plot.mvabund to plot only the variables with P-values less than 0.1:
    > lm.solberg <- manylm(log(solbmvabund+1)~treatment)
    > anova.solb <- anova(lm.solberg, p.uni="unadjusted")
    > pj = anova.solb$uni.p
    >
    > plot(solbmvabund~treatment, var.subset=pj<0.1)
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Only the variables Paramesacanthion_sp., Viscosia_sp., Prochromadorella_sp., Neotonchus_sp., Sabatieria_sp., Daptonema_sp.1, Theristus_aff_acer, Sphaerolaimus_macrocirculus, Unidentified were included in the plot (user selected).
    >
    > ## Or to plot only the 12 most significant variables, according to their
    > ## univariate ANOVA P-values:
    > pj.sort = sort(pj, index.return=TRUE)
    > plot(solbmvabund~treatment, var.subset=pj.sort$ix[1:12])
    Overlapping points were shifted along the y-axis to make them visible.
    
     PIPING TO 2nd MVFACTOR
    Error in default.plotMvaFactor(x = c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, :
     You have passed an invalid 'var.subset'
    Calls: plot ... default.plot.mvabund -> do.call -> default.plotMvaFactor
    Execution halted
Flavor: r-devel-windows-ix86+x86_64