Skip to content

Commit edff6fe

Browse files
matthewphamiltonmatthewphamilton
committed
edits to work with new mdl_ingredients_ls
1 parent 62b5606 commit edff6fe

File tree

7 files changed

+44
-30
lines changed

7 files changed

+44
-30
lines changed

‎.github/workflows/R-CMD-check.yaml‎

Lines changed: 0 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -73,7 +73,6 @@ jobs:
7373
do
7474
eval sudo $cmd
7575
done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
76-
7776
- name: Install system dependencies
7877
if: runner.os == 'MacOS' && !matrix.config.autobrew
7978
run: brew install harfbuzz fribidi
@@ -88,13 +87,6 @@ jobs:
8887
remotes::install_cran("rcmdcheck")
8988
shell: Rscript {0}
9089

91-
- name: Address conditional specific install fail
92-
if: runner.os == 'Linux'
93-
run: |
94-
Rscript -e "remove.packages(c('igraph'))"
95-
conda install -c r r-igraph
96-
Rscript -e "install.packages('remotes')" -e "options(timeout=600)" -e "remotes::install_github('ready4-dev/specific')"
97-
9890
- name: Session info
9991
run: |
10092
options(width = 100)

‎.github/workflows/pkgdown.yaml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ name: pkgdown
1111

1212
jobs:
1313
pkgdown:
14-
runs-on: macOS-latest
14+
runs-on: ubuntu-latest
1515
env:
1616
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
1717
steps:

‎R/fn_get.R‎

Lines changed: 10 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -232,7 +232,7 @@ get_mdl_smrys <- function (ingredients_ls, mdl_nms_chr = NULL)
232232
#' @export
233233
#' @importFrom purrr map2_dfr map_chr map_lgl
234234
#' @importFrom ready4 get_from_lup_obj
235-
#' @importFrom dplyr filter mutate
235+
#' @importFrom dplyr filter mutate case_when
236236
#' @keywords internal
237237
get_mdls_lup <- function (ttu_dv_dss_tb = NULL, mdl_predrs_in_ds_chr = NULL,
238238
utility_type_chr = NULL, ttu_dv_nms_chr = "TTU", server_1L_chr = "dataverse.harvard.edu",
@@ -263,6 +263,8 @@ get_mdls_lup <- function (ttu_dv_dss_tb = NULL, mdl_predrs_in_ds_chr = NULL,
263263
character(0))
264264
})) %>% dplyr::mutate(ds_url = urls_chr)
265265
})
266+
mdls_lup <- mdls_lup %>% dplyr::mutate(source_chr = dplyr::case_when(is.na(source_chr) ~
267+
"Primary Analysis", T ~ source_chr))
266268
}
267269
else {
268270
mdls_lup <- NULL
@@ -280,8 +282,8 @@ get_mdls_lup <- function (ttu_dv_dss_tb = NULL, mdl_predrs_in_ds_chr = NULL,
280282
#' @return Model (a model)
281283
#' @rdname get_model
282284
#' @export
283-
#' @importFrom specific get_table_predn_mdl
284285
#' @importFrom ready4 get_from_lup_obj
286+
#' @importFrom specific get_table_predn_mdl
285287
#' @keywords internal
286288
get_model <- function (mdls_lup, mdl_nm_1L_chr, make_from_tbl_1L_lgl = T,
287289
mdl_meta_data_ls = NULL, server_1L_chr = "dataverse.harvard.edu",
@@ -292,10 +294,13 @@ get_model <- function (mdls_lup, mdl_nm_1L_chr, make_from_tbl_1L_lgl = T,
292294
mdl_meta_data_ls <- get_mdl_metadata(mdls_lup, mdl_nm_1L_chr = mdl_nm_1L_chr,
293295
server_1L_chr = server_1L_chr, key_1L_chr = key_1L_chr)
294296
}
297+
analysis_1L_chr <- ready4::get_from_lup_obj(mdls_lup,
298+
match_value_xx = mdl_nm_1L_chr, match_var_nm_1L_chr = "mdl_nms_chr",
299+
target_var_nm_1L_chr = "source_chr", evaluate_1L_lgl = F)
300+
if (analysis_1L_chr == "Primary Analysis")
301+
analysis_1L_chr <- NULL
295302
model_mdl <- specific::get_table_predn_mdl(mdl_nm_1L_chr,
296-
ingredients_ls = mdl_meta_data_ls, analysis_1L_chr = ready4::get_from_lup_obj(mdls_lup,
297-
match_value_xx = mdl_nm_1L_chr, match_var_nm_1L_chr = "mdl_nms_chr",
298-
target_var_nm_1L_chr = "source_chr", evaluate_1L_lgl = F))
303+
ingredients_ls = mdl_meta_data_ls, analysis_1L_chr = analysis_1L_chr)
299304
}
300305
else {
301306
model_mdl <- get_mdl_from_dv(mdl_nm_1L_chr, dv_ds_nm_1L_chr = get_mdl_ds_url(mdls_lup,

‎R/fn_make.R‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -356,6 +356,10 @@ make_predn_metadata_ls <- function (data_tb, cmprsn_groups_chr = NULL, cmprsn_va
356356
data_tb <- specific::rename_from_nmd_vec(data_tb, nmd_vec_chr = predr_vars_nms_chr,
357357
vec_nms_as_new_1L_lgl = T)
358358
}
359+
if (is.null(mdl_meta_data_ls)) {
360+
mdl_meta_data_ls <- get_mdl_metadata(mdls_lup, mdl_nm_1L_chr = mdl_nm_1L_chr,
361+
key_1L_chr = key_1L_chr, server_1L_chr = server_1L_chr)
362+
}
359363
predictors_lup <- get_predictors_lup(mdl_meta_data_ls = mdl_meta_data_ls,
360364
mdls_lup = mdls_lup, mdl_nm_1L_chr = mdl_nm_1L_chr, outp_is_abbrs_tb = F,
361365
server_1L_chr = server_1L_chr, key_1L_chr = key_1L_chr)

‎data-raw/fns/get.R‎

Lines changed: 18 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -71,11 +71,12 @@ get_mdl_ctlg_url <- function(mdls_lup,
7171
all_lbls_chr <- purrr::map_chr(ds_ls,~.x$label)
7272
include_lgl <- all_lbls_chr %>% purrr::map_lgl(~startsWith(.x,"AAA_TTU_MDL_CTG"))
7373
all_descs_chr <- purrr::map_chr(ds_ls,~.x$description)
74-
include_lgl <- include_lgl & (all_descs_chr %>% purrr::map_lgl(~stringr::str_detect(.x,
75-
ready4::get_from_lup_obj(mdls_lup,
76-
match_value_xx = mdl_nm_1L_chr,
77-
match_var_nm_1L_chr = "mdl_nms_chr",
78-
target_var_nm_1L_chr = "source_chr",
74+
include_lgl <- include_lgl & (all_descs_chr %>%
75+
purrr::map_lgl(~stringr::str_detect(.x,
76+
ready4::get_from_lup_obj(mdls_lup,
77+
match_value_xx = mdl_nm_1L_chr,
78+
match_var_nm_1L_chr = "mdl_nms_chr",
79+
target_var_nm_1L_chr = "source_chr",
7980
evaluate_1L_lgl = F))))
8081
idx_1L_int <- which(include_lgl)
8182
if(identical(idx_1L_int,integer(0))){
@@ -147,6 +148,9 @@ get_mdls_lup <- function(ttu_dv_dss_tb = NULL,
147148
character(0))})) %>%
148149
dplyr::mutate(ds_url = urls_chr)
149150
})
151+
mdls_lup <- mdls_lup %>%
152+
dplyr::mutate(source_chr = dplyr::case_when(is.na(source_chr) ~ "Primary Analysis",
153+
T ~ source_chr))
150154
}else{
151155
mdls_lup <- NULL
152156
}
@@ -199,13 +203,16 @@ get_model <- function(mdls_lup,
199203
server_1L_chr = server_1L_chr,
200204
key_1L_chr = key_1L_chr)
201205
}
206+
analysis_1L_chr <- ready4::get_from_lup_obj(mdls_lup,
207+
match_value_xx = mdl_nm_1L_chr,
208+
match_var_nm_1L_chr = "mdl_nms_chr",
209+
target_var_nm_1L_chr = "source_chr",
210+
evaluate_1L_lgl = F)
211+
if(analysis_1L_chr == "Primary Analysis")
212+
analysis_1L_chr <- NULL
202213
model_mdl <- specific::get_table_predn_mdl(mdl_nm_1L_chr,
203-
ingredients_ls = mdl_meta_data_ls,
204-
analysis_1L_chr = ready4::get_from_lup_obj(mdls_lup,
205-
match_value_xx = mdl_nm_1L_chr,
206-
match_var_nm_1L_chr = "mdl_nms_chr",
207-
target_var_nm_1L_chr = "source_chr",
208-
evaluate_1L_lgl = F))
214+
ingredients_ls = mdl_meta_data_ls,
215+
analysis_1L_chr = analysis_1L_chr)
209216
}else{
210217
model_mdl <- get_mdl_from_dv(mdl_nm_1L_chr,
211218
dv_ds_nm_1L_chr = get_mdl_ds_url(mdls_lup,

‎data-raw/fns/make.R‎

Lines changed: 11 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -274,11 +274,17 @@ make_predn_metadata_ls <- function(data_tb,
274274
utl_var_nm_1L_chr = "AQoL6D_HU",
275275
server_1L_chr = "dataverse.harvard.edu",
276276
key_1L_chr = NULL){
277-
if(!is.null(predr_vars_nms_chr)){
278-
data_tb <- specific::rename_from_nmd_vec(data_tb,
279-
nmd_vec_chr = predr_vars_nms_chr,
280-
vec_nms_as_new_1L_lgl = T)
281-
}
277+
if(!is.null(predr_vars_nms_chr)){
278+
data_tb <- specific::rename_from_nmd_vec(data_tb,
279+
nmd_vec_chr = predr_vars_nms_chr,
280+
vec_nms_as_new_1L_lgl = T)
281+
}
282+
if(is.null(mdl_meta_data_ls)){
283+
mdl_meta_data_ls <- get_mdl_metadata(mdls_lup,
284+
mdl_nm_1L_chr = mdl_nm_1L_chr,
285+
key_1L_chr = key_1L_chr,
286+
server_1L_chr = server_1L_chr)
287+
}
282288
predictors_lup <- get_predictors_lup(mdl_meta_data_ls = mdl_meta_data_ls,
283289
mdls_lup = mdls_lup,
284290
mdl_nm_1L_chr = mdl_nm_1L_chr,

‎data/mdls_lup.rda‎

-12 Bytes
Binary file not shown.

0 commit comments

Comments
 (0)