Comments (14)
It's done! I ran the CRAN checks again, and now there is only one warning:
WARNING 'qpdf' is needed for checks on size reduction of PDFs
I'm sending you the pull request.
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Hi @trotsiuk !
yes, no problem, but I am not totally sure if I understand this bit right:
please use (potentially modified) already existing internal data for var.default - i_parameters, sizeDist.default - d_sizeDist, param.default - d_parameters instead creating the new one in sysdata.rda
Do you mean that I should save d_param_lit in the visible data, instead of in the internal data? Do you want the code in 0_create_input_data.R or 0_create_internal_data.R?
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Yes, correct @Rasilgon . I would suggest to make the d_param_lit
(or whatever you name it) visible and document in the data.R
. And as mentioned, use (modify) existing d_..
tables for those purpose.
I hope this is ok from your side, and sorry that I didn't realise it during the merge request.
I guess it is easier to put everything into one file (e.g. 0_create_input_data.R
) but you can also keep it separately (0_create_internal_data.R
). Even those if you will be modifying d_..
tables it is easier to do everything in one file (e.g. 0_create_input_data.R
)
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No worries, I totally agree. I didn't think of it before. I was not that aware of the pkg structure.
If the d_param_lit
is the full version of the parameter database (parameter, source, and comments), there is no need of modifying any existing d_..
table, I'd say. The get_parameter
function would return subset or queries of d_param_lit
.
Or do you mean to append all parameter sets without source and comments to the d_parameters
?
If so, get_parameter
is perhaps not necessary. I mean, the d_param_lit
is already visible, and a run-ready version of it will be in d_parameters
.
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I have seen that you also created the var.default, sizeDist.default, param.default
tables which are similar/identical to i_parameters, d_sizeDist, d_parameters
and thus would suggest to remove the ...defaul
. If you are using them in any of the script you can replace them with d_...
tables.
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Hi @trotsiuk,
Yes, I can remove them, although I thought that they were meant to exist.
I ran the 0_create_internal_data.R
script, which creates the var.default, sizeDist.default, param.default
tables and saves them as internal data. Saving the defaults tables was part of the original code, so I assumed that it had to be run.
usethis::use_data(var.default, param.default, sizeDist.default, param.db, internal = TRUE, overwrite = TRUE)
I only added the param.db
. and committed it along with the internal data, to keep it updated.
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You are right. I totally confused myself :) I will then check whether we can potentially get rid of those system data. Sorry for confusion
from r3pg.
No worries! Let me know when you are done with it, and then I will go through my code and fix it accordingly. BTW, please feel free to modify it. My main contribution is to include the db, but you might better see how to fit it in the pkg.
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HI @Rasilgon, I have now made the changes.
Can you please:
- document
i_parameters_lit
(previouslyparam.df
) in thedata.R
(you might also consider splitting this list to separate data.frames, but not critical) - check the data preparation script whether correct in
0_create_input_data.R
- write your information in the
DESCRIPTION
Thanks in advance
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Hi @trotsiuk ,
sorry for the late reply, I did as you suggested 👍 The pull request is already sent.
from r3pg.
Hi @Rasilgon
There are two small issues with the modification
- I think this shall be renamed
Line 38 in 4448713
_lit
Data codoc mismatches from documentation object 'i_parameters_lit':
Variables in data frame 'i_parameters_lit'
- It is not directly taken the column names from other tables, either all need to be documented or a proper link made
Line 68 in 4448713
Code: BLcond CoeffCond D13CTissueDif Dlocation0 DlocationB DlocationC
Dlocationrh Dlocationt Dscale0 DscaleB DscaleC Dscalerh Dscalet
Dshape0 DshapeB DshapeC Dshaperh Dshapet LAIgcx LAImaxIntcptn
MaxAge MaxCond MaxIntcptn MinCond Qa Qb RGcGw SLA0 SLA1 SWconst
SWpower Tmax Tmin Topt Y aFracDiffu aH aHL aK aV aWS age
alphaCx bFracRubi cVPD country crownshape fCalpha700 fCg700 fN0
fNn fracBB0 fracBB1 fullCanAge gDM_mol gammaF0 gammaF1 gammaN0
gammaN1 gammaR k kF leaffall leafgrow link m0 mF mR mS
molPAR_MJ nAge nHB nHC nHLB nHLC nHLL nHLrh nKB nKC nKH nKrh
nVB nVBH nVH nWS ngammaN notes pFS2 pFS20 pRn pRx parset_id
rAge region rhoMax rhoMin source source_comments source_full
species tBB tRho tSLA tgammaF tgammaN thinPower type wSx1000
wslocation0 wslocationB wslocationC wslocationrh wslocationt
wsscale0 wsscaleB wsscaleC wsscalerh wsscalet wsshape0 wsshapeB
wsshapeC wsshaperh wsshapet year
Docs: age country link notes parset_id region remaining columns
source source_comments source_full species type year
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Hi @trotsiuk! Thanks for checking 👍, and sorry for the trouble.
- I think this shall be renamed
Sorry, I misspelled the i_parameters_lit. Already fixed.
- It is not directly taken the column names from other tables, either all need to be documented or a proper link made.
The remaining columns are the parameter names, which is the information in the column parameters from i_parameters
and i_sizeDist
. I think that listing all parameters in the data.R
does not make much sense. I did not mean the code to take the column names from other table or the value of one column, I just wanted to describe the structure of the table i_parameters_list
, and avoid listing all parameters.
From your comment, I figure, that this is not the way to do it and/or it is problematic. If so, I would remove this bit:
#' \item{remaining columns}{name of the parameters, consistent with naming in \code{\link{i_parameters}} or \code{\link{i_sizeDist}}}
and include this information in @details
. Would this be a valid solution? Or would you suggest another one?
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Hi @Rasilgon
This is unfortunately, but we indeed need to list all the items for the table. Otherwise the CRAN submission will complain.
You can simply use Check Package
during the build
to see whether there are complains.
Thanks for understanding.
from r3pg.
Hi @trotsiuk !
Yes, I ran the crank checks, but as it is only a warning, I thought we could get away with it ;) No problem, I will include the full description using the information in i_parameters and i_sizeDist.
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