minor fixes

Author: matthewphamilton

CITATION.cff

@@ -1,12 +1,12 @@
 cff-version: 1.2.0
-message: "Matthew Hamilton and Caroline Gao  (2022). specific: Specify Candidate Models for Representing Mental Health Systems. Version 0.0.0.9073. Zenodo. https://doi.org/10.5281/zenodo.5768689"
+message: "Matthew Hamilton and Caroline Gao  (2022). specific: Specify Candidate Models for Representing Mental Health Systems. Version 0.0.0.9074. Zenodo. https://doi.org/10.5281/zenodo.5768689"
 authors:
   - family-names: "Hamilton"
     given-names: "Matthew"
   - family-names: "Gao"
     given-names: "Caroline"
 title: "specific: Specify Candidate Models for Representing Mental Health Systems"
-version: 0.0.0.9073
+version: 0.0.0.9074
 doi: 10.5281/zenodo.5768689
 date-released: 2022-02-15
 url: "https://ready4-dev.github.io/specific/"

DESCRIPTION

@@ -119,10 +119,15 @@ Collate:
     'pkg_specific.R'
     'specific-package.R'
 Suggests: 
-    scorz,
-    rmarkdown
-Remotes: 
+    scorz (>= 0.0.0.9048),
+    rmarkdown,
+    betareg,
+    cmdstanr (>= 0.4.0.9000),
+    rstan
+Remotes:  
     ready4-dev/ready4,
     ready4-dev/ready4show,
     ready4-dev/ready4use,
-    ready4-dev/youthvars
+    ready4-dev/youthvars,
+    stan-dev/cmdstanr,
+    ready4-dev/scorz

R/mthd_author.R

@@ -92,10 +92,12 @@ methods::setMethod("author", "SpecificSynopsis", function (x, reference_1L_int =
 {
     if (what_1L_chr == "Catalogue") {
         outp_smry_ls_ls <- manufacture(x@b_SpecificResults, what_1L_chr = "indexed_shareable")
-        if (is.na(reference_1L_int)) {
+        refs_int <- 1:length(outp_smry_ls_ls)
+        if (!is.na(reference_1L_int)) {
             outp_smry_ls_ls <- outp_smry_ls_ls[reference_1L_int]
+            refs_int <- reference_1L_int
         }
-        ctlg_nms_chr <- purrr::map2_chr(outp_smry_ls_ls, 1:length(outp_smry_ls_ls), 
+        ctlg_nms_chr <- purrr::map2_chr(outp_smry_ls_ls, refs_int, 
             ~{
                 fl_nm_1L_chr <- paste0("AAA_TTU_MDL_CTG", ifelse(.y == 
                   1, "", paste0("-", (.y - 1))))

R/mthd_depict.R

@@ -57,7 +57,7 @@ methods::setMethod("depict", "SpecificSynopsis", function (x, axis_text_sclg_1L_
             renew(old_nms_chr = timepoint_old_nms_chr, new_nms_chr = timepoint_new_nms_chr)
     }
     else {
-        correspondences_lup
+        correspondences_lup <- NULL
     }
     if (what_1L_chr == "composite_mdl") {
         plt <- make_cmpst_sctr_and_dnst_plt(outp_smry_ls, base_size_1L_dbl = base_size_1L_dbl, 

R/mthd_manufacture.R

@@ -18,10 +18,9 @@ methods::setMethod("manufacture", "SpecificResults", function (x, what_1L_chr =
         secondary_chr <- names(shareable_outp_ls)[startsWith(names(shareable_outp_ls), 
             "secondary_")]
         if (!identical(secondary_chr, character(0))) {
-            primary_ls <- shareable_outp_ls[names(shareable_outp_ls) != 
-                secondary_chr]
-            secondary_ls <- shareable_outp_ls[names(shareable_outp_ls) == 
-                secondary_chr]
+            primary_ls <- shareable_outp_ls[setdiff(names(shareable_outp_ls), 
+                secondary_chr)]
+            secondary_ls <- shareable_outp_ls[secondary_chr]
             object_xx <- append(list(primary_ls = primary_ls[(names(primary_ls))[!names(primary_ls) %>% 
                 duplicated()]]), secondary_ls %>% purrr::map(~.x[(.x %>% 
                 names())[!.x %>% names() %>% duplicated()]]))
@@ -187,7 +186,7 @@ methods::setMethod("manufacture", "SpecificSynopsis", function (x, depnt_var_nms
                 conclusion_1L_chr = x@conclusion_1L_chr, ethics_1L_chr = x@ethics_1L_chr, 
                 funding_1L_chr = x@funding_1L_chr, sample_desc_1L_chr = x@sample_desc_1L_chr, 
                 var_nm_change_lup = x@correspondences_r3)
-            if (what_1L_chr == "results_ls") {
+            if (what_1L_chr %in% c("abstract_args_ls", "results_ls")) {
                 object_xx <- make_results_ls(dv_ds_nm_and_url_chr = object_xx$path_params_ls$dv_ds_nm_and_url_chr, 
                   make_cmpst_plt_1L_lgl = make_cmpst_plt_1L_lgl, 
                   outp_smry_ls = x@b_SpecificResults@a_SpecificShareable@shareable_outp_ls, 

data-raw/s4_fns/author.R

@@ -112,11 +112,13 @@ author_SpecificSynopsis <- function(x,
   if(what_1L_chr == "Catalogue"){
     outp_smry_ls_ls <- manufacture(x@b_SpecificResults,
                                    what_1L_chr = "indexed_shareable")
-    if(is.na(reference_1L_int)){
+    refs_int <- 1:length(outp_smry_ls_ls)
+    if(!is.na(reference_1L_int)){
       outp_smry_ls_ls <- outp_smry_ls_ls[reference_1L_int]
+      refs_int <- reference_1L_int
     }
     ctlg_nms_chr <- purrr::map2_chr(outp_smry_ls_ls,
-                                    1:length(outp_smry_ls_ls),
+                                    refs_int,
                                     ~ {
                                       fl_nm_1L_chr <- paste0("AAA_TTU_MDL_CTG",
                                                              ifelse(.y==1,

data-raw/s4_fns/depict.R

@@ -72,7 +72,7 @@ depict_SpecificSynopsis <- function(x,
       renew(old_nms_chr = timepoint_old_nms_chr,
             new_nms_chr = timepoint_new_nms_chr)
   }else{
-    correspondences_lup
+    correspondences_lup <- NULL
   }
   if(what_1L_chr == "composite_mdl"){
     plt <- make_cmpst_sctr_and_dnst_plt(outp_smry_ls,

data-raw/s4_fns/manufacture.R

@@ -65,7 +65,7 @@ manufacture_SpecificSynopsis <- function(x,
                             #predr_ctgs_ls = NULL,
                             sample_desc_1L_chr = x@sample_desc_1L_chr,
                             var_nm_change_lup = x@correspondences_r3)
-      if(what_1L_chr == "results_ls"){
+      if(what_1L_chr %in% c("abstract_args_ls","results_ls")){
         object_xx <- make_results_ls(dv_ds_nm_and_url_chr = object_xx$path_params_ls$dv_ds_nm_and_url_chr,
                                      make_cmpst_plt_1L_lgl = make_cmpst_plt_1L_lgl,
                                      outp_smry_ls = x@b_SpecificResults@a_SpecificShareable@shareable_outp_ls,
@@ -182,8 +182,8 @@ manufacture_SpecificResults<- function(x,
                                      "a_SpecificShareable@shareable_outp_ls")
     secondary_chr <- names(shareable_outp_ls)[startsWith(names(shareable_outp_ls),"secondary_")]
     if(!identical(secondary_chr,character(0))){
-      primary_ls <- shareable_outp_ls[names(shareable_outp_ls)!=secondary_chr]
-      secondary_ls <- shareable_outp_ls[names(shareable_outp_ls)==secondary_chr]
+      primary_ls <- shareable_outp_ls[setdiff(names(shareable_outp_ls),secondary_chr)]
+      secondary_ls <- shareable_outp_ls[secondary_chr]
       object_xx <- append(list(primary_ls = primary_ls[(names(primary_ls))[!names(primary_ls) %>% duplicated()]]),
                            secondary_ls %>%
                              purrr::map(~.x[(.x %>% names())[!.x %>% names() %>% duplicated()]]))