Re: [R] nlmixr2 installation problems

[Troels Ring]

Thanks a lot - I was not offered the opportunity to recompile - the 
system just stopped. Also, today trying

> install.packages("sass") Installing package into 
‘C:/Users/Admin/AppData/Local/R/win-library/4.3’ (as ‘lib’ is 
unspecified) also installing the dependencies ‘digest’, ‘base64enc’, 
‘fastmap’, ‘ellipsis’, ‘fs’, ‘htmltools’, ‘rappdirs’ There is a binary 
version available but the source version is later: binary source 
needs_compilation sass 0.4.6 0.4.7 TRUE - and nothing further - so 
definitely not a nlmixr2 issue, right? Best wishes Troels

Den 16-07-2023 kl. 17:21 skrev Rui Barradas:
> Às 12:55 de 16/07/2023, Troels Ring escreveu:
>> Hi friends - Trying to install nlmixr2 caused problems. I'm on windows
>> with R4.3.1 so made sure to have rtools 4.3 and also reinstalled R 
>> and then
>>
>> ran
>>
>> install.packages("nlmixr2",dependencies = TRUE)and got the
>> responseInstalling package into
>> ‘C:/Users/Admin/AppData/Local/R/win-library/4.3’ (as ‘lib’ is
>> unspecified) also installing the dependencies ‘fs’, ‘rappdirs’, ‘bit’,
>> ‘prettyunits’, ‘rematch’, ‘askpass’, ‘sass’, ‘commonmark’, ‘proxy’,
>> ‘bit64’, ‘progress’, ‘rootSolve’, ‘lmom’, ‘cellranger’, ‘jsonlite’,
>> ‘mime’, ‘openssl’, ‘htmlwidgets’, ‘ellipsis’, ‘bslib’, ‘fontawesome’,
>> ‘jquerylib’, ‘tinytex’, ‘curl’, ‘markdown’, ‘jpeg’, ‘xml2’, ‘fastmap’,
>> ‘e1071’, ‘generics’, ‘tidyselect’, ‘clipr’, ‘hms’, ‘vroom’, ‘cpp11’,
>> ‘tzdb’, ‘stringi’, ‘purrr’, ‘mvtnorm’, ‘expm’, ‘rstudioapi’, ‘Exact’,
>> ‘gld’, ‘readxl’, ‘httr’, ‘gridExtra’, ‘htmlTable’, ‘viridis’,
>> ‘htmltools’, ‘base64enc’, ‘rmarkdown’, ‘Formula’, ‘bitops’, ‘evaluate’,
>> ‘highr’, ‘xfun’, ‘yaml’, ‘numDeriv’, ‘lazyeval’, ‘optextras’, ‘dparser’,
>> ‘RcppEigen’, ‘StanHeaders’, ‘sitmo’, ‘gridtext’, ‘cachem’,
>> ‘RcppParallel’, ‘RApiSerialize’, ‘stringfish’, ‘classInt’, ‘dplyr’,
>> ‘readr’, ‘stringr’, ‘tidyr’, ‘assertthat’, ‘binom’, ‘Deriv’,
>> ‘DescTools’, ‘Hmisc’, ‘minpack.lm’, ‘pander’, ‘png’, ‘RCurl’,
>> ‘backports’, ‘checkmate’, ‘knitr’, ‘lbfgsb3c’, ‘minqa’, ‘n1qn1’, ‘Rcpp’,
>> ‘rex’, ‘Rvmmin’, ‘symengine’, ‘BH’, ‘RcppArmadillo’, ‘rxode2parse’,
>> ‘rxode2random’, ‘data.table’, ‘digest’, ‘ggtext’, ‘PreciseSums’,
>> ‘inline’, ‘memoise’, ‘sys’, ‘rxode2ll’, ‘rxode2et’, ‘qs’, ‘vpc’, ‘xgxr’,
>> ‘nlmixr2data’, ‘nlmixr2est’, ‘nlmixr2extra’, ‘rxode2’, ‘lotri’,
>> ‘nlmixr2plot’, ‘crayon’ There are binary versions available but the
>> source versions are later: binary source needs_compilation sass 0.4.6
>> 0.4.7 TRUE openssl 2.0.6 2.1.0 TRUE
>> - and nothing more happened But when trying to install sass and openssl
>> individually the same announcement of later source versions appeared
>> without making it possible to ask for recompilation. All best wishes 
>> Troels
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> Hello,
>
> Maybe this [1] is relevant.
>
>
> [1] 
> https://community.rstudio.com/t/meaning-of-common-message-when-install-a-package-there-are-binary-versions-available-but-the-source-versions-are-later/2431
>
> Hope this helps,
>
> Rui Barradas
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]

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Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

[Ivan Krylov]

On Sun, 16 Jul 2023 21:51:10 + (UTC)
Maria Lathouri via R-help  wrote:

> As you can see, the values range from 0 to 400. I want it to plot it
> in bars; when I am plotting it as you can imagine the values near
> zero don't show at all.

A logarithmic scale won't work when the range of numbers to display
includes 0. It would have worked if it was some small non-zero
quantity, but an actual zero is infinitely far down; it won't fit.

There is a number of transformations described in
help(scale_y_continuous). You may find trans="pseudo_log" or
trans="sqrt" useful.

help(geom_bar) recommends geom_col() instead of geom_bar() to represent
values (not counts of occurrences).

We could help you more efficiently if you clarified the relationship
between your data (with columns `ID`, `values`, `databases`) and your
code (which mentions `Temp`, `mean`, `Glass`).

-- 
Best regards,
Ivan

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Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

[Bert Gunter]

Maria,

ggplot is part of the Posit -- formerly RStudio -- assortment of
contributed packages. They have their own support site here
 , which you *may* find useful for such
questions, also. Though ggplot queries *are* frequently posted and answered
on R-Help.

Cheers,
Bert

On Sun, Jul 16, 2023 at 3:58 PM Maria Lathouri via R-help <
r-help@r-project.org> wrote:

> I will find the ggplot help.
>
> But I have tried everything, including what you have suggested and nothing
> works.
>
> Kind regards,
> Maria
>
>
>
>
>
>
> Στις Κυριακή 16 Ιουλίου 2023 στις 11:22:36 μ.μ. GMT+1, ο χρήστης CALUM
> POLWART  έγραψε:
>
>
>
>
>
> Try adding
>
> scale_y_log10()
>
> This is a general R help list. It's not a ggplot list and you are likely
> to be chased off to ggplot's package maintainers nominated support pages.
>
> But really a Google search should surely have found this?
>
>
>
> On Sun, 16 Jul 2023, 22:51 Maria Lathouri via R-help, <
> r-help@r-project.org> wrote:
> > Dear all,
> >
> > ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) +
> > geom_bar(stat = "identity", position = "dodge", aes(y=log(mean)))
> > + theme_bw() + theme(panel.grid.major = element_blank(),
> panel.grid.minor = element_blank()) + theme(legend.position = c(0.45,
> 0.85), legend.title = element_blank())
> > + scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette =
> "Dark2") +
> >
> scale_y_log10()
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

[CALUM POLWART]

The data snippet doesn't make sense for the code you provided

Using the snippet I'd be doing

ggplot2(fc,  aes(x = ID, y= value)) +
geom_col() +
scale_y_log10()

And adjusting...

Not sure if that's what you are trying to do?


On Sun, 16 Jul 2023, 23:57 Maria Lathouri,  wrote:

> I will find the ggplot help.
>
> But I have tried everything, including what you have suggested and nothing
> works.
>
> Kind regards,
> Maria
>
>
>
>
>
>
> Στις Κυριακή 16 Ιουλίου 2023 στις 11:22:36 μ.μ. GMT+1, ο χρήστης CALUM
> POLWART  έγραψε:
>
>
>
>
>
> Try adding
>
> scale_y_log10()
>
> This is a general R help list. It's not a ggplot list and you are likely
> to be chased off to ggplot's package maintainers nominated support pages.
>
> But really a Google search should surely have found this?
>
>
>
> On Sun, 16 Jul 2023, 22:51 Maria Lathouri via R-help, <
> r-help@r-project.org> wrote:
> > Dear all,
> >
> > ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) +
> > geom_bar(stat = "identity", position = "dodge", aes(y=log(mean)))
> > + theme_bw() + theme(panel.grid.major = element_blank(),
> panel.grid.minor = element_blank()) + theme(legend.position = c(0.45,
> 0.85), legend.title = element_blank())
> > + scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette =
> "Dark2") +
> >
> scale_y_log10()
>
>

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

[Maria Lathouri via R-help]

I will find the ggplot help. 

But I have tried everything, including what you have suggested and nothing 
works.

Kind regards,
Maria






Στις Κυριακή 16 Ιουλίου 2023 στις 11:22:36 μ.μ. GMT+1, ο χρήστης CALUM POLWART 
 έγραψε: 





Try adding

scale_y_log10()

This is a general R help list. It's not a ggplot list and you are likely to be 
chased off to ggplot's package maintainers nominated support pages.

But really a Google search should surely have found this?



On Sun, 16 Jul 2023, 22:51 Maria Lathouri via R-help,  
wrote:
> Dear all, 
> 
> ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) + 
> geom_bar(stat = "identity", position = "dodge", aes(y=log(mean))) 
> + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = 
> element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title = 
> element_blank()) 
> + scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette = 
> "Dark2") +
> 
scale_y_log10()

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

[CALUM POLWART]

Try adding

scale_y_log10()

This is a general R help list. It's not a ggplot list and you are likely to
be chased off to ggplot's package maintainers nominated support pages.

But really a Google search should surely have found this?



On Sun, 16 Jul 2023, 22:51 Maria Lathouri via R-help, 
wrote:

> Dear all,
>
> ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) +
> geom_bar(stat = "identity", position = "dodge", aes(y=log(mean)))
> + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor
> = element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title =
> element_blank())
> + scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette =
> "Dark2") +
>
scale_y_log10()

[[alternative HTML version deleted]]

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Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

[David Winsemius]

On 7/16/23 14:51, Maria Lathouri via R-help wrote:

Dear all,


I am having the following dataset
fc<-
ID    values    databases
Al    0.15    phreeqc
Al    0.6    carbfix
Al    0.47    actual
Ca    7.2    phreeqc
Ca    7.2    carbfix
Ca    0.3    actual
Na    14.4    phreeqc
Na    84    carbfix
Na    106    actual
Cl    22    phreeqc
Cl    21.9    carbfix
Cl    72.1    actual
Fe    0.05    phreeqc
Fe    0.43    carbfix
Fe    1.25    actual
Mg    0.35    phreeqc
Mg    0.17    carbfix
Mg    0.08    actual
SO4    0    phreeqc
SO4    0    carbfix
SO4    416    actual


As you can see, the values range from 0 to 400. I want it to plot it in bars; 
when I am plotting it as you can imagine the values near zero don't show at 
all. So I am trying to make the y axis logarithmic. I have created the 
following code but it doesn't work. I get the bars with zero above and the 
others on top.


ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) +



None of those aes() names are in your data object. They should be one of

ID    values    databases



geom_bar(stat = "identity", position = "dodge", aes(y=log(mean)))


What are you intending with `

aes(y=log(mean)

`

+ theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = 
element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title = 
element_blank())
+ scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette = "Dark2")


--

David.



I would very much appreciate your help. I am stuck.


Kind regards,
Maria

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[R] how to change the y-axis to logarithmic in a barplot ggplot

[Maria Lathouri via R-help]

Dear all, 


I am having the following dataset
fc<-
ID    values    databases
Al    0.15    phreeqc
Al    0.6    carbfix
Al    0.47    actual
Ca    7.2    phreeqc
Ca    7.2    carbfix
Ca    0.3    actual
Na    14.4    phreeqc
Na    84    carbfix
Na    106    actual
Cl    22    phreeqc
Cl    21.9    carbfix
Cl    72.1    actual
Fe    0.05    phreeqc
Fe    0.43    carbfix
Fe    1.25    actual
Mg    0.35    phreeqc
Mg    0.17    carbfix
Mg    0.08    actual
SO4    0    phreeqc
SO4    0    carbfix
SO4    416    actual


As you can see, the values range from 0 to 400. I want it to plot it in bars; 
when I am plotting it as you can imagine the values near zero don't show at 
all. So I am trying to make the y axis logarithmic. I have created the 
following code but it doesn't work. I get the bars with zero above and the 
others on top. 


ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) + 
geom_bar(stat = "identity", position = "dodge", aes(y=log(mean))) 
+ theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = 
element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title = 
element_blank()) 
+ scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette = "Dark2")


I would very much appreciate your help. I am stuck. 


Kind regards,
Maria

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Re: [R] nlmixr2 installation problems

[Rui Barradas]

Às 12:55 de 16/07/2023, Troels Ring escreveu:

Hi friends - Trying to install nlmixr2 caused problems. I'm on windows
with R4.3.1 so made sure to have rtools 4.3 and also reinstalled R and then

ran

install.packages("nlmixr2",dependencies = TRUE)and got the
responseInstalling package into
‘C:/Users/Admin/AppData/Local/R/win-library/4.3’ (as ‘lib’ is
unspecified) also installing the dependencies ‘fs’, ‘rappdirs’, ‘bit’,
‘prettyunits’, ‘rematch’, ‘askpass’, ‘sass’, ‘commonmark’, ‘proxy’,
‘bit64’, ‘progress’, ‘rootSolve’, ‘lmom’, ‘cellranger’, ‘jsonlite’,
‘mime’, ‘openssl’, ‘htmlwidgets’, ‘ellipsis’, ‘bslib’, ‘fontawesome’,
‘jquerylib’, ‘tinytex’, ‘curl’, ‘markdown’, ‘jpeg’, ‘xml2’, ‘fastmap’,
‘e1071’, ‘generics’, ‘tidyselect’, ‘clipr’, ‘hms’, ‘vroom’, ‘cpp11’,
‘tzdb’, ‘stringi’, ‘purrr’, ‘mvtnorm’, ‘expm’, ‘rstudioapi’, ‘Exact’,
‘gld’, ‘readxl’, ‘httr’, ‘gridExtra’, ‘htmlTable’, ‘viridis’,
‘htmltools’, ‘base64enc’, ‘rmarkdown’, ‘Formula’, ‘bitops’, ‘evaluate’,
‘highr’, ‘xfun’, ‘yaml’, ‘numDeriv’, ‘lazyeval’, ‘optextras’, ‘dparser’,
‘RcppEigen’, ‘StanHeaders’, ‘sitmo’, ‘gridtext’, ‘cachem’,
‘RcppParallel’, ‘RApiSerialize’, ‘stringfish’, ‘classInt’, ‘dplyr’,
‘readr’, ‘stringr’, ‘tidyr’, ‘assertthat’, ‘binom’, ‘Deriv’,
‘DescTools’, ‘Hmisc’, ‘minpack.lm’, ‘pander’, ‘png’, ‘RCurl’,
‘backports’, ‘checkmate’, ‘knitr’, ‘lbfgsb3c’, ‘minqa’, ‘n1qn1’, ‘Rcpp’,
‘rex’, ‘Rvmmin’, ‘symengine’, ‘BH’, ‘RcppArmadillo’, ‘rxode2parse’,
‘rxode2random’, ‘data.table’, ‘digest’, ‘ggtext’, ‘PreciseSums’,
‘inline’, ‘memoise’, ‘sys’, ‘rxode2ll’, ‘rxode2et’, ‘qs’, ‘vpc’, ‘xgxr’,
‘nlmixr2data’, ‘nlmixr2est’, ‘nlmixr2extra’, ‘rxode2’, ‘lotri’,
‘nlmixr2plot’, ‘crayon’ There are binary versions available but the
source versions are later: binary source needs_compilation sass 0.4.6
0.4.7 TRUE openssl 2.0.6 2.1.0 TRUE
- and nothing more happened But when trying to install sass and openssl
individually the same announcement of later source versions appeared
without making it possible to ask for recompilation. All best wishes Troels

[[alternative HTML version deleted]]

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Hello,

Maybe this [1] is relevant.


[1] 
https://community.rstudio.com/t/meaning-of-common-message-when-install-a-package-there-are-binary-versions-available-but-the-source-versions-are-later/2431


Hope this helps,

Rui Barradas

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[R] nlmixr2 installation problems

[Troels Ring]

Hi friends - Trying to install nlmixr2 caused problems. I'm on windows 
with R4.3.1 so made sure to have rtools 4.3 and also reinstalled R and then

ran

install.packages("nlmixr2",dependencies = TRUE)and got the 
responseInstalling package into 
‘C:/Users/Admin/AppData/Local/R/win-library/4.3’ (as ‘lib’ is 
unspecified) also installing the dependencies ‘fs’, ‘rappdirs’, ‘bit’, 
‘prettyunits’, ‘rematch’, ‘askpass’, ‘sass’, ‘commonmark’, ‘proxy’, 
‘bit64’, ‘progress’, ‘rootSolve’, ‘lmom’, ‘cellranger’, ‘jsonlite’, 
‘mime’, ‘openssl’, ‘htmlwidgets’, ‘ellipsis’, ‘bslib’, ‘fontawesome’, 
‘jquerylib’, ‘tinytex’, ‘curl’, ‘markdown’, ‘jpeg’, ‘xml2’, ‘fastmap’, 
‘e1071’, ‘generics’, ‘tidyselect’, ‘clipr’, ‘hms’, ‘vroom’, ‘cpp11’, 
‘tzdb’, ‘stringi’, ‘purrr’, ‘mvtnorm’, ‘expm’, ‘rstudioapi’, ‘Exact’, 
‘gld’, ‘readxl’, ‘httr’, ‘gridExtra’, ‘htmlTable’, ‘viridis’, 
‘htmltools’, ‘base64enc’, ‘rmarkdown’, ‘Formula’, ‘bitops’, ‘evaluate’, 
‘highr’, ‘xfun’, ‘yaml’, ‘numDeriv’, ‘lazyeval’, ‘optextras’, ‘dparser’, 
‘RcppEigen’, ‘StanHeaders’, ‘sitmo’, ‘gridtext’, ‘cachem’, 
‘RcppParallel’, ‘RApiSerialize’, ‘stringfish’, ‘classInt’, ‘dplyr’, 
‘readr’, ‘stringr’, ‘tidyr’, ‘assertthat’, ‘binom’, ‘Deriv’, 
‘DescTools’, ‘Hmisc’, ‘minpack.lm’, ‘pander’, ‘png’, ‘RCurl’, 
‘backports’, ‘checkmate’, ‘knitr’, ‘lbfgsb3c’, ‘minqa’, ‘n1qn1’, ‘Rcpp’, 
‘rex’, ‘Rvmmin’, ‘symengine’, ‘BH’, ‘RcppArmadillo’, ‘rxode2parse’, 
‘rxode2random’, ‘data.table’, ‘digest’, ‘ggtext’, ‘PreciseSums’, 
‘inline’, ‘memoise’, ‘sys’, ‘rxode2ll’, ‘rxode2et’, ‘qs’, ‘vpc’, ‘xgxr’, 
‘nlmixr2data’, ‘nlmixr2est’, ‘nlmixr2extra’, ‘rxode2’, ‘lotri’, 
‘nlmixr2plot’, ‘crayon’ There are binary versions available but the 
source versions are later: binary source needs_compilation sass 0.4.6 
0.4.7 TRUE openssl 2.0.6 2.1.0 TRUE
- and nothing more happened But when trying to install sass and openssl 
individually the same announcement of later source versions appeared 
without making it possible to ask for recompilation. All best wishes Troels

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.