CRAN Package Check Results for Package aods3

Last updated on 2018-04-22 00:46:22 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4-1 5.30 58.90 64.20 ERROR
r-devel-linux-x86_64-debian-gcc 0.4-1 5.20 47.55 52.75 ERROR
r-devel-linux-x86_64-fedora-clang 0.4-1 87.18 NOTE
r-devel-linux-x86_64-fedora-gcc 0.4-1 80.92 NOTE
r-devel-windows-ix86+x86_64 0.4-1 13.00 101.00 114.00 NOTE
r-devel-osx-x86_64 0.4-1 NOTE
r-patched-linux-x86_64 0.4-1 5.82 58.79 64.61 ERROR
r-patched-solaris-x86 0.4-1 124.70 NOTE
r-release-linux-x86_64 0.4-1 5.20 65.01 70.21 NOTE
r-release-windows-ix86+x86_64 0.4-1 7.00 104.00 111.00 NOTE
r-release-osx-x86_64 0.4-1 NOTE
r-oldrel-windows-ix86+x86_64 0.4-1 12.00 69.00 81.00 NOTE

Check Details

Version: 0.4-1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘boot’ which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘boot’ ‘lme4’ ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-osx-x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.4-1
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     AIC.aodml anova.aodml anova.aodql coef.aodml coef.aodql
     deviance.aodml deviance.aodql df.residual.aodml df.residual.aodql
     fitted.aodml fitted.aodql logLik.aodml logLik.aodql predict.aodml
     predict.aodql print.anova.aodml print.aodml print.aodql print.drs
     print.gof print.iccbin print.summary.aodml print.varbin
     print.wald.test residuals.aodml residuals.aodql summary.aodml
     summary.aodql vcov.aodml vcov.aodql
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.4-1
Check: R code for possible problems
Result: NOTE
    AIC.aodml: no visible binding for global variable ‘logLik’
    anova.aodml: no visible global function definition for ‘AIC’
    anova.aodml: no visible global function definition for ‘df.residual’
    anova.aodml: no visible global function definition for ‘pchisq’
    anova.aodql: no visible global function definition for ‘anova’
    aodml: no visible global function definition for ‘update.formula’
    aodml: no visible global function definition for ‘model.frame’
    aodml: no visible global function definition for ‘model.response’
    aodml: no visible global function definition for ‘model.offset’
    aodml: no visible global function definition for ‘model.matrix’
    aodml: no visible global function definition for ‘glm’
    aodml: no visible global function definition for ‘coef’
    aodml : m.logL: no visible global function definition for ‘dnbinom’
    aodml: no visible global function definition for ‘optim’
    aodml: no visible global function definition for ‘dnbinom’
    aodql: no visible global function definition for ‘model.frame’
    aodql: no visible global function definition for ‘model.response’
    aodql: no visible global function definition for ‘glm’
    aodql: no visible global function definition for ‘residuals’
    aodql: no visible global function definition for ‘deviance’
    aodql: no visible global function definition for ‘df.residual’
    aodql: no visible global function definition for ‘logLik’
    coef.aodql: no visible global function definition for ‘coef’
    deviance.aodql: no visible global function definition for ‘deviance’
    df.residual.aodql: no visible global function definition for
     ‘df.residual’
    drs: no visible global function definition for ‘model.frame’
    drs: no visible global function definition for ‘model.response’
    drs: no visible global function definition for ‘terms’
    fitted.aodql: no visible global function definition for ‘fitted’
    gof: no visible global function definition for ‘deviance’
    gof: no visible global function definition for ‘residuals’
    gof: no visible global function definition for ‘df.residual’
    iccbin: no visible binding for global variable ‘binomial’
    iccbin: no visible global function definition for ‘rnorm’
    iccbin: no visible global function definition for ‘var’
    iccbin: no visible global function definition for ‘lm’
    iccbin: no visible global function definition for ‘anova’
    invlink: no visible global function definition for ‘plogis’
    invlink: no visible global function definition for ‘pnorm’
    link: no visible global function definition for ‘qlogis’
    link: no visible global function definition for ‘qnorm’
    logLik.aodql: no visible global function definition for ‘logLik’
    predict.aodml: no visible global function definition for ‘model.matrix’
    predict.aodml: no visible global function definition for ‘model.frame’
    predict.aodml: no visible global function definition for ‘model.offset’
    predict.aodml: no visible global function definition for ‘vcov’
    predict.aodml: no visible global function definition for ‘dnorm’
    predict.aodql: no visible global function definition for ‘predict’
    print.drs: no visible global function definition for ‘pchisq’
    print.gof: no visible global function definition for ‘pchisq’
    print.summary.aodml: no visible global function definition for ‘AIC’
    print.summary.aodml: no visible global function definition for
     ‘df.residual’
    print.summary.aodml: no visible global function definition for
     ‘deviance’
    residuals.aodml: no visible global function definition for ‘fitted’
    residuals.aodql: no visible global function definition for ‘residuals’
    splitbin : splitbin.w: no visible global function definition for
     ‘model.frame’
    splitbin : splitbin.w: no visible global function definition for
     ‘model.response’
    summary.aodml: no visible global function definition for ‘coef’
    summary.aodml: no visible global function definition for ‘pnorm’
    varbin: no visible global function definition for ‘var’
    varbin: no visible global function definition for ‘boot’
    varbin: no visible global function definition for ‘qnorm’
    vcov.aodml: no visible global function definition for ‘coef’
    vcov.aodql: no visible global function definition for ‘vcov’
    wald.test: no visible global function definition for ‘pchisq’
    wald.test: no visible global function definition for ‘pf’
    Undefined global functions or variables:
     AIC anova binomial boot coef deviance df.residual dnbinom dnorm
     fitted glm lm logLik model.frame model.matrix model.offset
     model.response optim pchisq pf plogis pnorm predict qlogis qnorm
     residuals rnorm terms update.formula var vcov
    Consider adding
     importFrom("stats", "AIC", "anova", "binomial", "coef", "deviance",
     "df.residual", "dnbinom", "dnorm", "fitted", "glm", "lm",
     "logLik", "model.frame", "model.matrix", "model.offset",
     "model.response", "optim", "pchisq", "pf", "plogis",
     "pnorm", "predict", "qlogis", "qnorm", "residuals", "rnorm",
     "terms", "update.formula", "var", "vcov")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-osx-x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.4-1
Check: examples
Result: ERROR
    Running examples in ‘aods3-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: aodml
    > ### Title: ML Estimation of Generalized Linear Models for Overdispersed
    > ### Count Data
    > ### Aliases: aodml print.aodml summary.aodml print.summary.aodml
    > ### anova.aodml print.anova.aodml fitted.aodml residuals.aodml coef.aodml
    > ### logLik.aodml deviance.aodml df.residual.aodml AIC.aodml vcov.aodml
    > ### predict.aodml
    > ### Keywords: regression
    >
    > ### ** Examples
    >
    >
    > #------ Beta-binomial model
    >
    > data(orob2)
    > fm1 <- aodml(cbind(m, n - m) ~ seed, data = orob2, family = "bb")
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    >
    > # summaries
    > fm1
    $call
    aodml(formula = cbind(m, n - m) ~ seed, data = orob2, family = "bb")
    
    $family
    [1] "bb"
    
    $link
    [1] "logit"
    
    $dat
     seed root n m
    1 O75 BEAN 39 10
    2 O75 BEAN 62 23
    3 O75 BEAN 81 23
    4 O75 BEAN 51 26
    5 O75 BEAN 39 17
    6 O75 CUCUMBER 6 5
    7 O75 CUCUMBER 74 53
    8 O75 CUCUMBER 72 55
    9 O75 CUCUMBER 51 32
    10 O75 CUCUMBER 79 46
    11 O75 CUCUMBER 13 10
    12 O73 BEAN 16 8
    13 O73 BEAN 30 10
    14 O73 BEAN 28 8
    15 O73 BEAN 45 23
    16 O73 BEAN 4 0
    17 O73 CUCUMBER 12 3
    18 O73 CUCUMBER 41 22
    19 O73 CUCUMBER 30 15
    20 O73 CUCUMBER 51 32
    21 O73 CUCUMBER 7 3
    
    $formula
    cbind(m, n - m) ~ seed
    
    $phi.formula
    ~1
    <environment: 0xc796500>
    
    $phi.scale
    [1] "identity"
    
    $X.b
     (Intercept) seedO75
    1 1 1
    2 1 1
    3 1 1
    4 1 1
    5 1 1
    6 1 1
    7 1 1
    8 1 1
    9 1 1
    10 1 1
    11 1 1
    12 1 0
    13 1 0
    14 1 0
    15 1 0
    16 1 0
    17 1 0
    18 1 0
    19 1 0
    20 1 0
    21 1 0
    attr(,"assign")
    [1] 0 1
    attr(,"contrasts")
    attr(,"contrasts")$seed
    [1] "contr.treatment"
    
    
    $X.phi
     (Intercept)
    1 1
    2 1
    3 1
    4 1
    5 1
    6 1
    7 1
    8 1
    9 1
    10 1
    11 1
    12 1
    13 1
    14 1
    15 1
    16 1
    17 1
    18 1
    19 1
    20 1
    21 1
    attr(,"assign")
    [1] 0
    
    $resp
     m
    1 10 29
    2 23 39
    3 23 58
    4 26 25
    5 17 22
    6 5 1
    7 53 21
    8 55 17
    9 32 19
    10 46 33
    11 10 3
    12 8 8
    13 10 20
    14 8 20
    15 23 22
    16 0 4
    17 3 9
    18 22 19
    19 15 15
    20 32 19
    21 3 4
    
    $offset
    NULL
    
    $param
     (Intercept) seedO75 phi.(Intercept)
     -0.26012090 0.41281583 0.07804472
    
    $b
    (Intercept) seedO75
     -0.2601209 0.4128158
    
    $phi
    phi.(Intercept)
     0.07804472
    
    $varparam
     (Intercept) seedO75 phi.(Intercept)
    (Intercept) 0.0511613215 -0.051370647 -0.0006190502
    seedO75 -0.0513706469 0.089589078 0.0009264330
    phi.(Intercept) -0.0006190502 0.000926433 0.0009090414
    
    $nbpar
    [1] 3
    
    $df.model
    [1] 3
    
    $df.residual
    [1] 18
    
    $logL
    [1] -63.5527
    
    $l
     1 2 3 4 5 6 7 8
    -4.181229 -3.741692 -4.740453 -3.067050 -2.991442 -1.893377 -3.926968 -4.290464
     9 10 11 12 13 14 15 16
    -3.152602 -3.470219 -2.439709 -2.132455 -2.681300 -2.781843 -3.053052 -1.976747
     17 18 19 20 21
    -2.128583 -3.048137 -2.661269 -3.728689 -1.465422
    
    $lmax
     1 2 3 4 5 6 7 8
    -2.683520 -3.194906 -3.378448 -3.049058 -2.801886 -1.131462 -3.293978 -3.213239
     9 10 11 12 13 14 15 16
    -3.017682 -3.438929 -1.754747 -2.067999 -2.526883 -2.428793 -2.936460 0.000000
     17 18 19 20 21
    -1.720217 -2.851328 -2.581879 -3.017682 -1.465751
    
    $iterations
    function gradient
     35 7
    
    $code
    [1] 0
    
    $msg
    character(0)
    
    $singular.hessian
    [1] FALSE
    
    attr(,"class")
    [1] "aodml"
    > summary(fm1)
     Length Class Mode
    call 4 -none- call
    family 1 -none- character
    link 1 -none- character
    dat 4 data.frame list
    formula 3 formula call
    phi.formula 2 formula call
    phi.scale 1 -none- character
    X.b 42 -none- numeric
    X.phi 21 -none- numeric
    resp 42 -none- numeric
    offset 0 -none- NULL
    param 3 -none- numeric
    b 2 -none- numeric
    phi 1 -none- numeric
    varparam 9 -none- numeric
    nbpar 1 -none- numeric
    df.model 1 -none- numeric
    df.residual 1 -none- numeric
    logL 1 -none- numeric
    l 21 -none- numeric
    lmax 21 -none- numeric
    iterations 2 -none- numeric
    code 1 -none- numeric
    msg 0 -none- character
    singular.hessian 1 -none- logical
    > coef(fm1)
    NULL
    > vcov(fm1)
    Error in UseMethod("vcov") :
     no applicable method for 'vcov' applied to an object of class "aodml"
    Calls: vcov
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.4-1
Check: examples
Result: ERROR
    Running examples in ‘aods3-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: aodml
    > ### Title: ML Estimation of Generalized Linear Models for Overdispersed
    > ### Count Data
    > ### Aliases: aodml print.aodml summary.aodml print.summary.aodml
    > ### anova.aodml print.anova.aodml fitted.aodml residuals.aodml coef.aodml
    > ### logLik.aodml deviance.aodml df.residual.aodml AIC.aodml vcov.aodml
    > ### predict.aodml
    > ### Keywords: regression
    >
    > ### ** Examples
    >
    >
    > #------ Beta-binomial model
    >
    > data(orob2)
    > fm1 <- aodml(cbind(m, n - m) ~ seed, data = orob2, family = "bb")
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    >
    > # summaries
    > fm1
    $call
    aodml(formula = cbind(m, n - m) ~ seed, data = orob2, family = "bb")
    
    $family
    [1] "bb"
    
    $link
    [1] "logit"
    
    $dat
     seed root n m
    1 O75 BEAN 39 10
    2 O75 BEAN 62 23
    3 O75 BEAN 81 23
    4 O75 BEAN 51 26
    5 O75 BEAN 39 17
    6 O75 CUCUMBER 6 5
    7 O75 CUCUMBER 74 53
    8 O75 CUCUMBER 72 55
    9 O75 CUCUMBER 51 32
    10 O75 CUCUMBER 79 46
    11 O75 CUCUMBER 13 10
    12 O73 BEAN 16 8
    13 O73 BEAN 30 10
    14 O73 BEAN 28 8
    15 O73 BEAN 45 23
    16 O73 BEAN 4 0
    17 O73 CUCUMBER 12 3
    18 O73 CUCUMBER 41 22
    19 O73 CUCUMBER 30 15
    20 O73 CUCUMBER 51 32
    21 O73 CUCUMBER 7 3
    
    $formula
    cbind(m, n - m) ~ seed
    
    $phi.formula
    ~1
    <environment: 0x55a6dca36068>
    
    $phi.scale
    [1] "identity"
    
    $X.b
     (Intercept) seedO75
    1 1 1
    2 1 1
    3 1 1
    4 1 1
    5 1 1
    6 1 1
    7 1 1
    8 1 1
    9 1 1
    10 1 1
    11 1 1
    12 1 0
    13 1 0
    14 1 0
    15 1 0
    16 1 0
    17 1 0
    18 1 0
    19 1 0
    20 1 0
    21 1 0
    attr(,"assign")
    [1] 0 1
    attr(,"contrasts")
    attr(,"contrasts")$seed
    [1] "contr.treatment"
    
    
    $X.phi
     (Intercept)
    1 1
    2 1
    3 1
    4 1
    5 1
    6 1
    7 1
    8 1
    9 1
    10 1
    11 1
    12 1
    13 1
    14 1
    15 1
    16 1
    17 1
    18 1
    19 1
    20 1
    21 1
    attr(,"assign")
    [1] 0
    
    $resp
     m
    1 10 29
    2 23 39
    3 23 58
    4 26 25
    5 17 22
    6 5 1
    7 53 21
    8 55 17
    9 32 19
    10 46 33
    11 10 3
    12 8 8
    13 10 20
    14 8 20
    15 23 22
    16 0 4
    17 3 9
    18 22 19
    19 15 15
    20 32 19
    21 3 4
    
    $offset
    NULL
    
    $param
     (Intercept) seedO75 phi.(Intercept)
     -0.26012090 0.41281583 0.07804472
    
    $b
    (Intercept) seedO75
     -0.2601209 0.4128158
    
    $phi
    phi.(Intercept)
     0.07804472
    
    $varparam
     (Intercept) seedO75 phi.(Intercept)
    (Intercept) 0.0511613215 -0.051370647 -0.0006190502
    seedO75 -0.0513706469 0.089589078 0.0009264330
    phi.(Intercept) -0.0006190502 0.000926433 0.0009090414
    
    $nbpar
    [1] 3
    
    $df.model
    [1] 3
    
    $df.residual
    [1] 18
    
    $logL
    [1] -63.5527
    
    $l
     1 2 3 4 5 6 7 8
    -4.181229 -3.741692 -4.740453 -3.067050 -2.991442 -1.893377 -3.926968 -4.290464
     9 10 11 12 13 14 15 16
    -3.152602 -3.470219 -2.439709 -2.132455 -2.681300 -2.781843 -3.053052 -1.976747
     17 18 19 20 21
    -2.128583 -3.048137 -2.661269 -3.728689 -1.465422
    
    $lmax
     1 2 3 4 5 6 7 8
    -2.683520 -3.194906 -3.378448 -3.049058 -2.801886 -1.131462 -3.293978 -3.213239
     9 10 11 12 13 14 15 16
    -3.017682 -3.438929 -1.754747 -2.067999 -2.526883 -2.428793 -2.936460 0.000000
     17 18 19 20 21
    -1.720217 -2.851328 -2.581879 -3.017682 -1.465751
    
    $iterations
    function gradient
     35 7
    
    $code
    [1] 0
    
    $msg
    character(0)
    
    $singular.hessian
    [1] FALSE
    
    attr(,"class")
    [1] "aodml"
    > summary(fm1)
     Length Class Mode
    call 4 -none- call
    family 1 -none- character
    link 1 -none- character
    dat 4 data.frame list
    formula 3 formula call
    phi.formula 2 formula call
    phi.scale 1 -none- character
    X.b 42 -none- numeric
    X.phi 21 -none- numeric
    resp 42 -none- numeric
    offset 0 -none- NULL
    param 3 -none- numeric
    b 2 -none- numeric
    phi 1 -none- numeric
    varparam 9 -none- numeric
    nbpar 1 -none- numeric
    df.model 1 -none- numeric
    df.residual 1 -none- numeric
    logL 1 -none- numeric
    l 21 -none- numeric
    lmax 21 -none- numeric
    iterations 2 -none- numeric
    code 1 -none- numeric
    msg 0 -none- character
    singular.hessian 1 -none- logical
    > coef(fm1)
    NULL
    > vcov(fm1)
    Error in UseMethod("vcov") :
     no applicable method for 'vcov' applied to an object of class "aodml"
    Calls: vcov
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.4-1
Check: examples
Result: ERROR
    Running examples in ‘aods3-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: aodml
    > ### Title: ML Estimation of Generalized Linear Models for Overdispersed
    > ### Count Data
    > ### Aliases: aodml print.aodml summary.aodml print.summary.aodml
    > ### anova.aodml print.anova.aodml fitted.aodml residuals.aodml coef.aodml
    > ### logLik.aodml deviance.aodml df.residual.aodml AIC.aodml vcov.aodml
    > ### predict.aodml
    > ### Keywords: regression
    >
    > ### ** Examples
    >
    >
    > #------ Beta-binomial model
    >
    > data(orob2)
    > fm1 <- aodml(cbind(m, n - m) ~ seed, data = orob2, family = "bb")
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    Warning in lbeta(a + m, b + n - m) : NaNs produced
    Warning in lbeta(a, b) : NaNs produced
    >
    > # summaries
    > fm1
    $call
    aodml(formula = cbind(m, n - m) ~ seed, data = orob2, family = "bb")
    
    $family
    [1] "bb"
    
    $link
    [1] "logit"
    
    $dat
     seed root n m
    1 O75 BEAN 39 10
    2 O75 BEAN 62 23
    3 O75 BEAN 81 23
    4 O75 BEAN 51 26
    5 O75 BEAN 39 17
    6 O75 CUCUMBER 6 5
    7 O75 CUCUMBER 74 53
    8 O75 CUCUMBER 72 55
    9 O75 CUCUMBER 51 32
    10 O75 CUCUMBER 79 46
    11 O75 CUCUMBER 13 10
    12 O73 BEAN 16 8
    13 O73 BEAN 30 10
    14 O73 BEAN 28 8
    15 O73 BEAN 45 23
    16 O73 BEAN 4 0
    17 O73 CUCUMBER 12 3
    18 O73 CUCUMBER 41 22
    19 O73 CUCUMBER 30 15
    20 O73 CUCUMBER 51 32
    21 O73 CUCUMBER 7 3
    
    $formula
    cbind(m, n - m) ~ seed
    
    $phi.formula
    ~1
    <environment: 0x5583cf97b5c0>
    
    $phi.scale
    [1] "identity"
    
    $X.b
     (Intercept) seedO75
    1 1 1
    2 1 1
    3 1 1
    4 1 1
    5 1 1
    6 1 1
    7 1 1
    8 1 1
    9 1 1
    10 1 1
    11 1 1
    12 1 0
    13 1 0
    14 1 0
    15 1 0
    16 1 0
    17 1 0
    18 1 0
    19 1 0
    20 1 0
    21 1 0
    attr(,"assign")
    [1] 0 1
    attr(,"contrasts")
    attr(,"contrasts")$seed
    [1] "contr.treatment"
    
    
    $X.phi
     (Intercept)
    1 1
    2 1
    3 1
    4 1
    5 1
    6 1
    7 1
    8 1
    9 1
    10 1
    11 1
    12 1
    13 1
    14 1
    15 1
    16 1
    17 1
    18 1
    19 1
    20 1
    21 1
    attr(,"assign")
    [1] 0
    
    $resp
     m
    1 10 29
    2 23 39
    3 23 58
    4 26 25
    5 17 22
    6 5 1
    7 53 21
    8 55 17
    9 32 19
    10 46 33
    11 10 3
    12 8 8
    13 10 20
    14 8 20
    15 23 22
    16 0 4
    17 3 9
    18 22 19
    19 15 15
    20 32 19
    21 3 4
    
    $offset
    NULL
    
    $param
     (Intercept) seedO75 phi.(Intercept)
     -0.26012090 0.41281583 0.07804472
    
    $b
    (Intercept) seedO75
     -0.2601209 0.4128158
    
    $phi
    phi.(Intercept)
     0.07804472
    
    $varparam
     (Intercept) seedO75 phi.(Intercept)
    (Intercept) 0.0511613215 -0.051370647 -0.0006190502
    seedO75 -0.0513706469 0.089589078 0.0009264330
    phi.(Intercept) -0.0006190502 0.000926433 0.0009090414
    
    $nbpar
    [1] 3
    
    $df.model
    [1] 3
    
    $df.residual
    [1] 18
    
    $logL
    [1] -63.5527
    
    $l
     1 2 3 4 5 6 7 8
    -4.181229 -3.741692 -4.740453 -3.067050 -2.991442 -1.893377 -3.926968 -4.290464
     9 10 11 12 13 14 15 16
    -3.152602 -3.470219 -2.439709 -2.132455 -2.681300 -2.781843 -3.053052 -1.976747
     17 18 19 20 21
    -2.128583 -3.048137 -2.661269 -3.728689 -1.465422
    
    $lmax
     1 2 3 4 5 6 7 8
    -2.683520 -3.194906 -3.378448 -3.049058 -2.801886 -1.131462 -3.293978 -3.213239
     9 10 11 12 13 14 15 16
    -3.017682 -3.438929 -1.754747 -2.067999 -2.526883 -2.428793 -2.936460 0.000000
     17 18 19 20 21
    -1.720217 -2.851328 -2.581879 -3.017682 -1.465751
    
    $iterations
    function gradient
     35 7
    
    $code
    [1] 0
    
    $msg
    character(0)
    
    $singular.hessian
    [1] FALSE
    
    attr(,"class")
    [1] "aodml"
    > summary(fm1)
     Length Class Mode
    call 4 -none- call
    family 1 -none- character
    link 1 -none- character
    dat 4 data.frame list
    formula 3 formula call
    phi.formula 2 formula call
    phi.scale 1 -none- character
    X.b 42 -none- numeric
    X.phi 21 -none- numeric
    resp 42 -none- numeric
    offset 0 -none- NULL
    param 3 -none- numeric
    b 2 -none- numeric
    phi 1 -none- numeric
    varparam 9 -none- numeric
    nbpar 1 -none- numeric
    df.model 1 -none- numeric
    df.residual 1 -none- numeric
    logL 1 -none- numeric
    l 21 -none- numeric
    lmax 21 -none- numeric
    iterations 2 -none- numeric
    code 1 -none- numeric
    msg 0 -none- character
    singular.hessian 1 -none- logical
    > coef(fm1)
    NULL
    > vcov(fm1)
    Error in UseMethod("vcov") :
     no applicable method for 'vcov' applied to an object of class "aodml"
    Calls: vcov
    Execution halted
Flavor: r-patched-linux-x86_64