8000 Fix 635 - Add country to grouping by mattroumaya · Pull Request #803 · Gilead-BioStats/gsm · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Fix 635 - Add country to grouping #803

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 5 commits into from
Oct 20, 2022
Merged

Fix 635 - Add country to grouping #803

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
3913052
add country option
mattroumaya Oct 11, 2022
e3e46fc
update tests
mattroumaya Oct 12, 2022
64bd000
ffwd
mattroumaya Oct 12, 2022
9316abc
Merge remote-tracking branch 'origin/dev' into fix-635
mattroumaya Oct 19, 2022
9abb8aa
Merge remote-tracking branch 'origin/dev' into fix-635
mattroumaya Oct 20, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion R/AE_Assess.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ AE_Assess <- function(dfInput,
stopifnot(
"strMethod is not 'poisson' or 'identity'" = strMethod %in% c("poisson", "identity"),
"strMethod must be length 1" = length(strMethod) == 1,
"strGroup must be one of: Site, Study, or CustomGroup" = strGroup %in% c("Site", "Study", "CustomGroup"),
"strGroup must be one of: Site, Study, Country, or CustomGroup" = strGroup %in% c("Site", "Study", "Country", "CustomGroup"),
"bQuiet must be logical" = is.logical(bQuiet)
)

Expand Down
1 change: 1 addition & 0 deletions R/AE_Map_Adam.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,7 @@ AE_Map_Adam <- function(
any_of(c(
SiteID = lMapping[["dfADSL"]][["strSiteCol"]],
StudyID = lMapping[["dfADSL"]][["strStudyCol"]],
CountryID = lMapping[["dfADSL"]][["strCountryCol"]],
CustomGroupID = lMapping[["dfADSL"]][["strCustomGroupCol"]]
)),
"Count",
Expand Down
1 change: 1 addition & 0 deletions R/AE_Map_Raw.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,7 @@ AE_Map_Raw <- function(
c(
SiteID = lMapping[["dfSUBJ"]][["strSiteCol"]],
StudyID = lMapping[["dfSUBJ"]][["strStudyCol"]],
CountryID = lMapping[["dfSUBJ"]][["strCountryCol"]],
CustomGroupID = lMapping[["dfSUBJ"]][["strCustomGroupCol"]]< EDBE /span>
)
),
Expand Down
2 changes: 1 addition & 1 deletion R/Consent_Assess.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ Consent_Assess <- function(
stopifnot(
"nThreshold must be numeric" = is.numeric(nThreshold),
"nThreshold must be length 1" = length(nThreshold) == 1,
"strGroup must be one of: Site, Study, or CustomGroup" = strGroup %in% c("Site", "Study", "CustomGroup"),
"strGroup must be one of: Site, Study, Country, or CustomGroup" = strGroup %in% c("Site", "Study", "Country", "CustomGroup"),
"bQuiet must be logical" = is.logical(bQuiet)
)

Expand Down
1 change: 1 addition & 0 deletions R/Consent_Map_Raw.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,7 @@ Consent_Map_Raw <- function(
c(
SiteID = lMapping[["dfSUBJ"]][["strSiteCol"]],
StudyID = lMapping[["dfSUBJ"]][["strStudyCol"]],
CountryID = lMapping[["dfSUBJ"]][["strCountryCol"]],
CustomGroupID = lMapping[["dfSUBJ"]][["strCustomGroupCol"]]
)
),
Expand Down
2 changes: 1 addition & 1 deletion R/Disp_Assess.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ Disp_Assess <- function(
stopifnot(
"strMethod is not 'fisher' or 'identity'" = strMethod %in% c("fisher", "identity"),
"strMethod must be length 1" = length(strMethod) == 1,
"strGroup must be one of: Site, Study, or CustomGroup" = strGroup %in% c("Site", "Study", "CustomGroup"),
"strGroup must be one of: Site, Study, Country, or CustomGroup" = strGroup %in% c("Site", "Study", "Country", "CustomGroup"),
"bQuiet must be logical" = is.logical(bQuiet)
)

Expand Down
1 change: 1 addition & 0 deletions R/Disp_Map_Raw.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,7 @@ Disp_Map_Raw <- function(
c(
SiteID = lMapping[["dfSUBJ"]][["strSiteCol"]],
StudyID = lMapping[["dfSUBJ"]][["strStudyCol"]],
CountryID = lMapping[["dfSUBJ"]][["strCountryCol"]],
CustomGroupID = lMapping[["dfSUBJ"]][["strCustomGroupCol"]]
)
)
Expand Down
2 changes: 1 addition & 1 deletion R/IE_Assess.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ IE_Assess <- function(
stopifnot(
"nThreshold must be numeric" = is.numeric(nThreshold),
"nThreshold must be length 1" = length(nThreshold) == 1,
"strGroup must be one of: Site, Study, or CustomGroup" = strGroup %in% c("Site", "Study", "CustomGroup"),
"strGroup must be one of: Site, Study, Country, or CustomGroup" = strGroup %in% c("Site", "Study", "Country", "CustomGroup"),
"bQuiet must be logical" = is.logical(bQuiet)
)

Expand Down
1 change: 1 addition & 0 deletions R/IE_Map_Raw.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,7 @@ IE_Map_Raw <- function(
c(
SiteID = lMapping[["dfSUBJ"]][["strSiteCol"]],
10000 StudyID = lMapping[["dfSUBJ"]][["strStudyCol"]],
CountryID = lMapping[["dfSUBJ"]][["strCountryCol"]],
CustomGroupID = lMapping[["dfSUBJ"]][["strCustomGroupCol"]]
)
)
Expand Down
2 changes: 1 addition & 1 deletion R/LB_Assess.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ LB_Assess <- function(
stopifnot(
"strMethod is not 'fisher' or 'identity'" = strMethod %in% c("fisher", "identity"),
"strMethod must be length 1" = length(strMethod) == 1,
"strGroup must be one of: Site, Study, or CustomGroup" = strGroup %in% c("Site", "Study", "CustomGroup"),
"strGroup must be one of: Site, Study, Country, or CustomGroup" = strGroup %in% c("Site", "Study", "Country", "CustomGroup"),
"bQuiet must be logical" = is.logical(bQuiet)
)

Expand Down
1 change: 1 addition & 0 deletions R/LB_Map_Raw.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,7 @@ LB_Map_Raw <- function(
c(
SiteID = lMapping[["dfSUBJ"]][["strSiteCol"]],
StudyID = lMapping[["dfSUBJ"]][["strStudyCol"]],
CountryID = lMapping[["dfSUBJ"]][["strCountryCol"]],
CustomGroupID = lMapping[["dfSUBJ"]][["strCustomGroupCol"]]
)
)
Expand Down
2 changes: 1 addition & 1 deletion R/PD_Assess.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ PD_Assess <- function(
stopifnot(
"strMethod is not 'poisson' or 'identity'" = strMethod %in% c("poisson", "identity"),
"strMethod must be length 1" = length(strMethod) == 1,
"strGroup must be one of: Site, Study, or CustomGroup" = strGroup %in% c("Site", "Study", "CustomGroup"),
"strGroup must be one of: Site, Study, Country, or CustomGroup" = strGroup %in% c("Site", "Study", "Country", "CustomGroup"),
"bQuiet must be logical" = is.logical(bQuiet)
)

Expand Down
1 change: 1 addition & 0 deletions R/PD_Map_Raw.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,7 @@ PD_Map_Raw <- function(
c(
SiteID = lMapping[["dfSUBJ"]][["strSiteCol"]],
StudyID = lMapping[["dfSUBJ"]][["strStudyCol"]],
CountryID = lMapping[["dfSUBJ"]][["strCountryCol"]],
CustomGroupID = lMapping[["dfSUBJ"]][["strCustomGroupCol"]]
)
),
Expand Down
1 change: 1 addition & 0 deletions inst/mappings/AE_Assess.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ dfInput:
strIDCol: "SubjectID"
strSiteCol: "SiteID"
strStudyCol: "StudyID"
strCountryCol: "CountryID"
strCustomGroupCol: "CustomGroupID"
strCountCol: "Count"
strExposureCol: "Exposure"
Expand Down
1 change: 1 addition & 0 deletions inst/mappings/Consent_Assess.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ dfInput:
strIDCol: "SubjectID"
strSiteC 4D32 ol: "SiteID"
strStudyCol: "StudyID"
strCountryCol: "CountryID"
strCustomGroupCol: "CustomGroupID"
strRandDateCol: "RandDate"
strCountCol: "Count"
Expand Down
1 change: 1 addition & 0 deletions inst/mappings/Disp_Assess.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ dfInput:
strIDCol: "SubjectID"
strSiteCol: "SiteID"
strStudyCol: "StudyID"
strCountryCol: "CountryID"
strCustomGroupCol: "CustomGroupID"
strCountCol: "Count"
strTotalCol: "Total"
1 change: 1 addition & 0 deletions inst/mappings/IE_Assess.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,6 @@ dfInput:
strIDCol: "SubjectID"
strSiteCol: "SiteID"
strStudyCol: "StudyID"
strCountryCol: "CountryID"
strCustomGroupCol: "CustomGroupID"
strCountCol: "Count"
1 change: 1 addition & 0 deletions inst/mappings/LB_Assess.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ dfInput:
strIDCol: "SubjectID"
strSiteCol: "SiteID"
strStudyCol: "StudyID"
strCountryCol: "CountryID"
strCustomGroupCol: "CustomGroupID"
strCountCol: "Count"
strTotalCol: "Total"
1 change: 1 addition & 0 deletions 1 inst/mappings/PD_Assess.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ dfInput:
strIDCol: "SubjectID"
strSiteCol: "SiteID"
strStudyCol: "StudyID"
strCountryCol: "CountryID"
strCustomGroupCol: "CustomGroupID"
strCountCol: "Count"
strExposureCol: "Exposure"
Expand Down
3 changes: 2 additions & 1 deletion inst/mappings/mapping_rawplus.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,8 @@ dfSUBJ:
strTimeOnStudyCol: timeonstudy
strTimeOnTreatmentCol: timeontreatment
strRandDateCol: rfpst_dt
strCustomGroupCol: country
strCustomGroupCol: invid
strCountryCol: country
dfAE:
strIDCol: subjid
strTreatmentEmergentCol: ae_te
Expand Down
19 changes: 17 additions & 2 deletions tests/testthat/_snaps/AE_Assess.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
---

Code
subsetGroupCols(customGroup)
subsetGroupCols(country)
Output
# A tibble: 3 x 1
GroupID
Expand All @@ -32,6 +32,18 @@
2 US
3 Japan

---

Code
subsetGroupCols(customGroup)
Output
# A tibble: 3 x 1
GroupID
<chr>
1 0X201
2 0X012
3 0X999

# incorrect inputs throw errors

strMethod is not 'poisson' or 'identity'
Expand Down Expand Up @@ -145,7 +157,7 @@


$lChecks$dfInput$dim
[1] 3 7
[1] 3 8


$lChecks$status
Expand All @@ -162,6 +174,9 @@
$lChecks$mapping$dfInput$strStudyCol
[1] "StudyID"

$lChecks$mapping$dfInput$strCountryCol
[1] "CountryID"

$lChecks$mapping$dfInput$strCustomGroupCol
[1] "CustomGroupID"

Expand Down
14 changes: 12 additions & 2 deletions tests/testthat/_snaps/AE_Map_Raw.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@
"names": {
"type": "character",
"attributes": {},
"value": ["strStudyCol", "strSiteCol", "strIDCol", "strTimeOnStudyCol", "strTimeOnTreatmentCol", "strRandDateCol", "strCustomGroupCol"]
"value": ["strStudyCol", "strSiteCol", "strIDCol", "strTimeOnStudyCol", "strTimeOnTreatmentCol", "strRandDateCol", "strCustomGroupCol", "strCountryCol"]
}
},
"value": [
Expand Down Expand Up @@ -156,6 +156,11 @@
"attributes": {},
"value": ["rfpst_dt"]
},
{
"type": "character",
"attributes": {},
"value": ["invid"]
},
{
"type": "character",
"attributes": {},
Expand Down Expand Up @@ -226,7 +231,7 @@
"names": {
"type": "character",
"attributes": {},
"value": ["strIDCol", "strSiteCol", "strStudyCol", "strCustomGroupCol", "strCountCol", "strExposureCol", "strRateCol"]
"value": ["strIDCol", "strSiteCol", "strStudyCol", "strCountryCol", "strCustomGroupCol", "strCountCol", "strExposureCol", "strRateCol"]
}
},
"value": [
Expand All @@ -245,6 +250,11 @@
"attributes": {},
"value": ["StudyID"]
},
{
"type": "character",
"attributes": {},
"value": ["CountryID"]
},
{
"type": "character",
"attributes": {},
Expand Down
14 changes: 13 additions & 1 deletion tests/testthat/_snaps/Consent_Assess.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
---

Code
subsetGroupCols(customGroup)
subsetGroupCols(country)
Output
# A tibble: 3 x 1
GroupID
Expand All @@ -32,6 +32,18 @@
2 China
3 Japan

---

Code
subsetGroupCols(customGroup)
Output
# A tibble: 3 x 1
GroupID
<chr>
1 0X012
2 0X201
3 0X999

# bQuiet works as intended

Code
Expand Down
14 changes: 12 additions & 2 deletions tests/testthat/_snaps/Consent_Map_Raw.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@
"names": {
"type": "character",
"attributes": {},
"value": ["strStudyCol", "strSiteCol", "strIDCol", "strTimeOnStudyCol", "strTimeOnTreatmentCol", "strRandDateCol", "strCustomGroupCol"]
"value": ["strStudyCol", "strSiteCol", "strIDCol", "strTimeOnStudyCol", "strTimeOnTreatmentCol", "strRandDateCol", "strCustomGroupCol", "strCountryCol"]
}
},
"value": [
Expand Down Expand Up @@ -151,6 +151,11 @@
"attributes": {},
"value": ["rfpst_dt"]
},
{
"type": "character",
"attributes": {},
"value": ["invid"]
},
{
"type": "character",
"attributes": {},
Expand Down Expand Up @@ -216,7 +221,7 @@
"names": {
"type": "character",
"attributes": {},
"value": ["strIDCol", "strSiteCol", "strStudyCol", "strCustomGroupCol", "strRandDateCol", "strCountCol"]
"value": ["strIDCol", "strSiteCol", "strStudyCol", "strCountryCol", "strCustomGroupCol", "strRandDateCol", "strCountCol"]
}
},
"value": [
Expand All @@ -235,6 +240,11 @@
"attributes": {},
"value": ["StudyID"]
},
{
"type": "character",
"attributes": {},
"value": ["CountryID"]
},
{
"type": "character",
"attributes": {},
Expand Down
14 changes: 13 additions & 1 deletion tests/testthat/_snaps/Disp_Assess.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
---

Code
subsetGroupCols(customGroup)
subsetGroupCols(country)
Output
# A tibble: 3 x 1
GroupID
Expand All @@ -22,6 +22,18 @@
2 Japan
3 US

---

Code
subsetGroupCols(customGroup)
Output
# A tibble: 3 x 1
GroupID
<chr>
1 0X201
2 0X012
3 0X999

# incorrect inputs throw errors

strMethod is not 'fisher' or 'identity'
Expand Down
14 changes: 12 additions & 2 deletions tests/testthat/_snaps/Disp_Map_Raw.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@
"names": {
"type": "character",
"attributes": {},
"value": ["strStudyCol", "strSiteCol", "strIDCol", "strTimeOnStudyCol", "strTimeOnTreatmentCol", "strRandDateCol", "strCustomGroupCol"]
"value": ["strStudyCol", "strSiteCol", "strIDCol", "strTimeOnStudyCol", "strTimeOnTreatmentCol", "strRandDateCol", "strCustomGroupCol", "strCountryCol"]
}
},
"value": [
Expand Down Expand Up @@ -146,6 +146,11 @@
"attributes": {},
"value": ["rfpst_dt"]
},
{
"type": "character",
"attributes": {},
"value": ["invid"]
},
{
"type": "character",
"attributes": {},
Expand Down Expand Up @@ -211,7 +216,7 @@
"names": {
"type": "character",
"attributes": {},
"value": ["strIDCol", "strSiteCol", "strStudyCol", "strCustomGroupCol", "strCountCol", "strTotalCol"]
"value": ["strIDCol", "strSiteCol", "strStudyCol", "strCountryCol", "strCustomGroupCol", "strCountCol", "strTotalCol"]
}
},
"value": [
Expand All @@ -230,6 +235,11 @@
"attributes": {},
"value": ["StudyID"]
},
{
"type": "character",
"attributes": {},
"value": ["CountryID"]
},
{
"type": "character",
"attributes": {},
Expand Down
Loading
0