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edits to work with new mdl_ingredients_ls
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@matthewphamilton
matthewphamilton committed Feb 21, 2022
1 parent 62b5606 commit edff6fe
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Showing 7 changed files with 44 additions and 30 deletions.
8 changes: 0 additions & 8 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -73,7 +73,6 @@ jobs:
do
eval sudo $cmd
done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
- name: Install system dependencies
if: runner.os == 'MacOS' && !matrix.config.autobrew
run: brew install harfbuzz fribidi
Expand All @@ -88,13 +87,6 @@ jobs:
remotes::install_cran("rcmdcheck")
shell: Rscript {0}

- name: Address conditional specific install fail
if: runner.os == 'Linux'
run: |
Rscript -e "remove.packages(c('igraph'))"
conda install -c r r-igraph
Rscript -e "install.packages('remotes')" -e "options(timeout=600)" -e "remotes::install_github('ready4-dev/specific')"
- name: Session info
run: |
options(width = 100)
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2 changes: 1 addition & 1 deletion .github/workflows/pkgdown.yaml
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Expand Up @@ -11,7 +11,7 @@ name: pkgdown

jobs:
pkgdown:
runs-on: macOS-latest
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
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15 changes: 10 additions & 5 deletions R/fn_get.R
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Expand Up @@ -232,7 +232,7 @@ get_mdl_smrys <- function (ingredients_ls, mdl_nms_chr = NULL)
#' @export
#' @importFrom purrr map2_dfr map_chr map_lgl
#' @importFrom ready4 get_from_lup_obj
#' @importFrom dplyr filter mutate
#' @importFrom dplyr filter mutate case_when
#' @keywords internal
get_mdls_lup <- function (ttu_dv_dss_tb = NULL, mdl_predrs_in_ds_chr = NULL,
utility_type_chr = NULL, ttu_dv_nms_chr = "TTU", server_1L_chr = "dataverse.harvard.edu",
Expand Down Expand Up @@ -263,6 +263,8 @@ get_mdls_lup <- function (ttu_dv_dss_tb = NULL, mdl_predrs_in_ds_chr = NULL,
character(0))
})) %>% dplyr::mutate(ds_url = urls_chr)
})
mdls_lup <- mdls_lup %>% dplyr::mutate(source_chr = dplyr::case_when(is.na(source_chr) ~
"Primary Analysis", T ~ source_chr))
}
else {
mdls_lup <- NULL
Expand All @@ -280,8 +282,8 @@ get_mdls_lup <- function (ttu_dv_dss_tb = NULL, mdl_predrs_in_ds_chr = NULL,
#' @return Model (a model)
#' @rdname get_model
#' @export
#' @importFrom specific get_table_predn_mdl
#' @importFrom ready4 get_from_lup_obj
#' @importFrom specific get_table_predn_mdl
#' @keywords internal
get_model <- function (mdls_lup, mdl_nm_1L_chr, make_from_tbl_1L_lgl = T,
mdl_meta_data_ls = NULL, server_1L_chr = "dataverse.harvard.edu",
Expand All @@ -292,10 +294,13 @@ get_model <- function (mdls_lup, mdl_nm_1L_chr, make_from_tbl_1L_lgl = T,
mdl_meta_data_ls <- get_mdl_metadata(mdls_lup, mdl_nm_1L_chr = mdl_nm_1L_chr,
server_1L_chr = server_1L_chr, key_1L_chr = key_1L_chr)
}
analysis_1L_chr <- ready4::get_from_lup_obj(mdls_lup,
match_value_xx = mdl_nm_1L_chr, match_var_nm_1L_chr = "mdl_nms_chr",
target_var_nm_1L_chr = "source_chr", evaluate_1L_lgl = F)
if (analysis_1L_chr == "Primary Analysis")
analysis_1L_chr <- NULL
model_mdl <- specific::get_table_predn_mdl(mdl_nm_1L_chr,
ingredients_ls = mdl_meta_data_ls, analysis_1L_chr = ready4::get_from_lup_obj(mdls_lup,
match_value_xx = mdl_nm_1L_chr, match_var_nm_1L_chr = "mdl_nms_chr",
target_var_nm_1L_chr = "source_chr", evaluate_1L_lgl = F))
ingredients_ls = mdl_meta_data_ls, analysis_1L_chr = analysis_1L_chr)
}
else {
model_mdl <- get_mdl_from_dv(mdl_nm_1L_chr, dv_ds_nm_1L_chr = get_mdl_ds_url(mdls_lup,
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4 changes: 4 additions & 0 deletions R/fn_make.R
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Expand Up @@ -356,6 +356,10 @@ make_predn_metadata_ls <- function (data_tb, cmprsn_groups_chr = NULL, cmprsn_va
data_tb <- specific::rename_from_nmd_vec(data_tb, nmd_vec_chr = predr_vars_nms_chr,
vec_nms_as_new_1L_lgl = T)
}
if (is.null(mdl_meta_data_ls)) {
mdl_meta_data_ls <- get_mdl_metadata(mdls_lup, mdl_nm_1L_chr = mdl_nm_1L_chr,
key_1L_chr = key_1L_chr, server_1L_chr = server_1L_chr)
}
predictors_lup <- get_predictors_lup(mdl_meta_data_ls = mdl_meta_data_ls,
mdls_lup = mdls_lup, mdl_nm_1L_chr = mdl_nm_1L_chr, outp_is_abbrs_tb = F,
server_1L_chr = server_1L_chr, key_1L_chr = key_1L_chr)
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29 changes: 18 additions & 11 deletions data-raw/fns/get.R
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Expand Up @@ -71,11 +71,12 @@ get_mdl_ctlg_url <- function(mdls_lup,
all_lbls_chr <- purrr::map_chr(ds_ls,~.x$label)
include_lgl <- all_lbls_chr %>% purrr::map_lgl(~startsWith(.x,"AAA_TTU_MDL_CTG"))
all_descs_chr <- purrr::map_chr(ds_ls,~.x$description)
include_lgl <- include_lgl & (all_descs_chr %>% purrr::map_lgl(~stringr::str_detect(.x,
ready4::get_from_lup_obj(mdls_lup,
match_value_xx = mdl_nm_1L_chr,
match_var_nm_1L_chr = "mdl_nms_chr",
target_var_nm_1L_chr = "source_chr",
include_lgl <- include_lgl & (all_descs_chr %>%
purrr::map_lgl(~stringr::str_detect(.x,
ready4::get_from_lup_obj(mdls_lup,
match_value_xx = mdl_nm_1L_chr,
match_var_nm_1L_chr = "mdl_nms_chr",
target_var_nm_1L_chr = "source_chr",
evaluate_1L_lgl = F))))
idx_1L_int <- which(include_lgl)
if(identical(idx_1L_int,integer(0))){
Expand Down Expand Up @@ -147,6 +148,9 @@ get_mdls_lup <- function(ttu_dv_dss_tb = NULL,
character(0))})) %>%
dplyr::mutate(ds_url = urls_chr)
})
mdls_lup <- mdls_lup %>%
dplyr::mutate(source_chr = dplyr::case_when(is.na(source_chr) ~ "Primary Analysis",
T ~ source_chr))
}else{
mdls_lup <- NULL
}
Expand Down Expand Up @@ -199,13 +203,16 @@ get_model <- function(mdls_lup,
server_1L_chr = server_1L_chr,
key_1L_chr = key_1L_chr)
}
analysis_1L_chr <- ready4::get_from_lup_obj(mdls_lup,
match_value_xx = mdl_nm_1L_chr,
match_var_nm_1L_chr = "mdl_nms_chr",
target_var_nm_1L_chr = "source_chr",
evaluate_1L_lgl = F)
if(analysis_1L_chr == "Primary Analysis")
analysis_1L_chr <- NULL
model_mdl <- specific::get_table_predn_mdl(mdl_nm_1L_chr,
ingredients_ls = mdl_meta_data_ls,
analysis_1L_chr = ready4::get_from_lup_obj(mdls_lup,
match_value_xx = mdl_nm_1L_chr,
match_var_nm_1L_chr = "mdl_nms_chr",
target_var_nm_1L_chr = "source_chr",
evaluate_1L_lgl = F))
ingredients_ls = mdl_meta_data_ls,
analysis_1L_chr = analysis_1L_chr)
}else{
model_mdl <- get_mdl_from_dv(mdl_nm_1L_chr,
dv_ds_nm_1L_chr = get_mdl_ds_url(mdls_lup,
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16 changes: 11 additions & 5 deletions data-raw/fns/make.R
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Original file line number Diff line number Diff line change
Expand Up @@ -274,11 +274,17 @@ make_predn_metadata_ls <- function(data_tb,
utl_var_nm_1L_chr = "AQoL6D_HU",
server_1L_chr = "dataverse.harvard.edu",
key_1L_chr = NULL){
if(!is.null(predr_vars_nms_chr)){
data_tb <- specific::rename_from_nmd_vec(data_tb,
nmd_vec_chr = predr_vars_nms_chr,
vec_nms_as_new_1L_lgl = T)
}
if(!is.null(predr_vars_nms_chr)){
data_tb <- specific::rename_from_nmd_vec(data_tb,
nmd_vec_chr = predr_vars_nms_chr,
vec_nms_as_new_1L_lgl = T)
}
if(is.null(mdl_meta_data_ls)){
mdl_meta_data_ls <- get_mdl_metadata(mdls_lup,
mdl_nm_1L_chr = mdl_nm_1L_chr,
key_1L_chr = key_1L_chr,
server_1L_chr = server_1L_chr)
}
predictors_lup <- get_predictors_lup(mdl_meta_data_ls = mdl_meta_data_ls,
mdls_lup = mdls_lup,
mdl_nm_1L_chr = mdl_nm_1L_chr,
Expand Down
Binary file modified data/mdls_lup.rda
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