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Proposal of some updates to read_habitatmap_xxx() #140

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merged 13 commits into from
May 12, 2021
Merged

Proposal of some updates to read_habitatmap_xxx() #140

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7d230bf
read_hm_stdized/terr(): minor code style update
florisvdh May 11, 2021
3fb9b2a
read_habitatmap(): do filter_hab version check earlier (errors much f…
florisvdh May 11, 2021
314ec66
read_hm_stdized() docu: add note specific for version 2020_v1
florisvdh May 11, 2021
8c542bb
read_habitatmap() docu: minor update for filter_hab arg
florisvdh May 11, 2021
f95a1ea
read_hm_stdized/terr(): reorder columns of aspatial table in 2018 *
florisvdh May 11, 2021
9eff6ec
read_hm_stdized/terr(): mention the key of the types tibble since 2020
florisvdh May 11, 2021
ec2ad0b
read_hm_stdized() docu: update xxxx_rbbmr note for version 2020_v1
florisvdh May 12, 2021
1784b70
read_hm_stdized() docu: explain phab interpretation
florisvdh May 12, 2021
ebae03c
read_habitatmap_stdized(): according Rd file updates
florisvdh May 12, 2021
1359996
read_hm_stdized() docu: minor update (drop 'e.g.') *
florisvdh May 12, 2021
03ce6e5
read_hm_stdized() docu: remove indentation
florisvdh May 12, 2021
ba4a72e
read_hm_stdized() docu: expand on totalling phab values
florisvdh May 12, 2021
2549261
read_hm_stdized() docu: minor updates, mostly dropping term 'vegetation'
florisvdh May 12, 2021
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22 changes: 10 additions & 12 deletions R/read_habitatdata.R
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Original file line number Diff line number Diff line change
Expand Up @@ -40,17 +40,16 @@
#' each of them. The variable \code{certain} will be \code{FALSE} if
#' the original code consists of 2 or 3 possible vegetation types, and \code{TRUE}
#' if only one vegetation type is provided.
#' \itemize{
#' \item Note that this does not hold for the following codes:
#' \code{3130,rbbmr},
#' \code{3140,rbbmr},
#' \code{3150,rbbmr} and
#' \code{3160,rbbmr}.
#' These are standing water bodies that contain both \code{rbbmr} and the
#' habitat type.
#' Since \code{habitatmap_stdized_2020_v1} this has been taken into
#' account (setting \code{certain} as \code{TRUE} for both types).
#' }
#' \item Some polygons contain both a standing water habitat type
#' and \code{rbbmr}, e.g.:
#' \code{3130_rbbmr},
#' \code{3140_rbbmr},
#' \code{3150_rbbmr} and
#' \code{3160_rbbmr}.
#' Since \code{habitatmap_stdized_2020_v1}, the two vegetation
#' types \code{31xx} and \code{rbbmr} are split up and one row is
#' created for each of them.
#' The variable \code{certain} in this case will be \code{TRUE} for both types.
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About issue #117:

you may want to add a note on the interpretation of phab for code combinations from one column of the original habitatmap

Should also be mentioned in the geospatial hab vignette, but I think this can be useful here too, so:

Suggested change
#' created for each of them.
#' The variable \code{certain} in this case will be \code{TRUE} for both types.
#' created for each of them, with \code{phab} for each new row simply
#' set to the original value of \code{phab}.
#' The variable \code{certain} in this case will be \code{TRUE} for both types.
#' \itemize{
#' \item Note that this implies that the a given polygon could contain the same
#' type with variable \code{certain} as \code{TRUE} several times, e.g. when:
#' \code{31xx_rbbmr} is present with \code{phab} = yy% and
#' \code{31xx} is present with \code{phab} = zz%.
#' In that case the rows with the same \code{polygon_id}, \code{type}
#' and \code{certain} were gathered into one row and the respective
#' \code{phab} were summed up

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Perfect, thanks! I'll re-add your suggestion as a new commit, as the lines it depends on are flagged as outdated (so cannot apply suggestion).

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I'm supposing this bullet is at a lower level. The {} of \itemize needed to be closed 😉

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Yes, of course :-)

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@cecileherr Are you sure this is restricted to 31xx_rbbmr and it does not occur in general?

Anyway, the code executes this as a general rule. So I think it will be better to state it in general and add this bullet as a subnote under the first bullet (where you added 'with phab for each new row simply set to the original value of phab').

I leave consideration to you; I'll postpone the initial plan of adding the above suggestion.

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Sidenote: it appears that '%' needs to be escaped as \%

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@cecileherr Are you sure this is restricted to 31xx_rbbmr and it does not occur in general?

Anyway, the code executes this as a general rule. So I think it will be better to state it in general and add this bullet as a subnote under the first bullet (where you added 'with phab for each new row simply set to the original value of phab').

I thought it was a general rule in the code, but that it only happened for the 31xx_rbbmr case, but I was wrong (e.g. 605723_v2014 is an example for the uncertain case). I would be tempted to add this is as 3rd item (after the uncertain case and the 31xx_rbbmr case), instead of making a subitem out of it.

Something like (other items abbreviated):

#'     \itemize{

#'     \item For some polygons the vegetation type is uncertain (...)
#'     if only one vegetation type is provided.

#'     \item Some polygons contain both a standing water habitat type (...)
#'     created for each of them, with \code{phab} for each new row simply 
#'     set to the original value of \code{phab}. 
#'     The variable \code{certain} in this case will be \code{TRUE} for both types.

#'     \item After those first two steps, a given polygon could contain the same 
#'     type with the same value for \code{certain} several times, e.g. when:
#'     \code{31xx_rbbmr} is present with \code{phab} = yy\% and
#'     \code{31xx} is present with \code{phab} = zz\%.
#'     In that case the rows with the same \code{polygon_id}, \code{type} 
#'     and \code{certain} were gathered into one row and the respective 
#'     \code{phab} were summed up.

#'     \item For some polygons the original vegetation code in the (...)
#'     code was adjusted.
#'   }

@florisvdh : your thought on this?

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Good idea @cecileherr. It better fits the idea of 'steps'.

Minor comments:

  • when: drop colon
  • summed up: means 'enumerated'; should become something like 'added up'.
  • with the same value for \code{certain} several times: I think '[...] repeated several times' is better

I suggest you add another suggestion in this PR, or else do it as commit in your branch update_habitat2020_ch (including the Rd file update) after merging this PR. Merging this branch is up to you anyway, since its target branch is yours.

#' \item For some polygons the original vegetation code in the
#' \code{habitatmap} was not consistent with general coding syntax or
#' with the type codes from the \code{\link{types}}. In that case the
Expand Down Expand Up @@ -1647,4 +1646,3 @@ if (references) {
return(habitatquarries)

}