| Version: | 0.2.0 |
| Date: | 2022-05-05 |
| Title: | Tools and Methods for Primatological Data Science |
| Author: | David Schruth [aut][cre], Marc Myers [ctb], Noel Rowe [aut] |
| Maintainer: | David Schruth <data@anthropoidea.org> |
| Depends: | R (≥ 1.8.0), caroline |
| Suggests: | RJDBC |
| Description: | Data from All the World's Primates relational SQL database and other tabular datasets are made available via drivers and connection functions. Additionally we provide several functions and examples to facilitate the merging and aggregation of these tabular inputs. |
| License: | Apache License version 1.1 | Apache License version 2.0 [expanded from: Apache License] |
| LazyLoad: | yes |
| NeedsCompilation: | no |
| Repository: | CRAN |
| Packaged: | 2022-05-05 18:18:45 UTC; mint |
| Date/Publication: | 2022-05-09 07:20:02 UTC |
Create a connection to the SQL DB
Description
Connect to the All the World's Primate Database
Usage
AWP.connect(drv=AWP.driver(), prefix='jdbc:jtds:sqlserver',
server="s09.everleap.com", port=1433,
db="DB_3918_atwpreview", user="DB_3918_atwpreview_user", pw="atwpreview_$_j")
Arguments
drv |
driver (output from AWP.driver() |
prefix |
prefix to the URL (before "://") |
server |
domain name for the database server |
port |
port name used by the server's database |
db |
database name |
user |
database user name |
pw |
database user password |
Value
a connection object for SQL
Examples
con <- AWP.connect(drv=AWP.driver())
Load the driver to access the All the World's Primate remote SQL database
Description
Load the driver to utilize the database sofware
Usage
AWP.driver(drv.name="net.sourceforge.jtds.jdbc.Driver",
drv.file=system.file("drivers","jtds-1.2.8.jar", package='primate'))
Arguments
drv.name |
The name of the driver |
drv.file |
The file name for the database driver |
Value
driver argument to AWP.connect
Examples
AWP.driver()
Get a SQL Table
Description
Retrieve a table from the All the World's Primates SQL database
Usage
AWP.get.SQL.table(con=AWP.connect(), tab.nm="tblGrovesMonkeys", clmns=c('all'),xpnd=FALSE)
Arguments
tab.nm |
table name (defaults to the main primate species list) |
con |
connection object |
clmns |
columns to return |
xpnd |
expand the lookup column codes into full text strings |
Value
a data.frame corresponding to SQL table
Examples
online.version <- AWP.get.SQL.table(tab.nm='LMType') #a small example table
Get a Lookup Table
Description
Get the lookup table from the All the World's Primates SQL database
Usage
AWP.get.lookup.table(con=AWP.connect(),tab.nm="TextType")
Arguments
con |
connection object |
tab.nm |
table name (for the parent table) |
Value
a data.frame corresponding to SQL table
Examples
AWP.get.lookup.table(con=AWP.connect(),tab.nm="TextType")
List the SQL tables
Description
List available tables from the All the World's Primates SQL database
Usage
AWP.list.SQL.tables(con=AWP.connect(), all=FALSE)
Arguments
con |
connection object from AWP.connect |
all |
list all tables available |
Value
a list (vector) of SQL table names
Examples
AWP.list.SQL.tables(con=AWP.connect(), all=FALSE)
Read a table from the All the World's primates example microarchive within this package
Description
Read an All the World's Primates table from the local package cache.
Usage
AWP.read.pkg.tab(tab.nm='dbo_tblGrovesMonkeys', id.clmn=NA)
Arguments
tab.nm |
table name |
id.clmn |
id column of table |
Value
data.frame corresponding to SQL table
Examples
primates.tab <- AWP.read.pkg.tab(tab.nm='dbo_tblGrovesMonkeys', id.clmn='MonkeyNumberGroves')
Run SQL querries
Description
Run arbitrary SQL querries on the All the World's Primate database
Usage
AWP.run.SQL(con=AWP.connect(), sql=NULL)
Arguments
con |
connection object |
sql |
SQL string |
Value
results of query
Examples
AWP.run.SQL(con=AWP.connect(), sql=NULL)
Add a genus species column
Description
Adds a genus_species column to the specified dataframe
Usage
add.gnsp.clmn(df,gn="Genus",sp="Species",rownames=FALSE,new.col=TRUE, gnsp.col = "gn_sp")
Arguments
df |
input data.frame |
gn |
column name for genus |
sp |
column name for species |
rownames |
use the new gn_sp column to assign data.frame rownames |
new.col |
TRUE if gn_sp column is to be retained, FALSE if it is to be removed |
gnsp.col |
the name of the new column to add, by default is "gn_sp" |
Value
modified data.frame (with genus species info concatenated and added)
Examples
primates.tab <- AWP.read.pkg.tab(tab.nm='dbo_tblGrovesMonkeys', id.clmn='MonkeyNumberGroves')
primates.tab <- add.gnsp.clmn(primates.tab,gn="Genus",sp="Species",rownames=FALSE,new.col=TRUE)
Re-group data.frame by Genus_species in either old or new dataframe
Description
Regroup based on the old or the new data frame using a direction parameter.
Usage
regroup.equivalent(df, gnsp.old, gnsp.new, clmns, agg='mean', direction='old2new')
Arguments
df |
a dataframe |
gnsp.old |
old nomenclature |
gnsp.new |
new nomenclature |
clmns |
the columns in the data.frame to re-group |
agg |
the aggregation type |
direction |
the aggregation priority |
Value
a regrouped data frame
Examples
primates.tab <- AWP.read.pkg.tab(tab.nm='dbo_tblGrovesMonkeys', id.clmn='MonkeyNumberGroves')
primates.tab <- add.gnsp.clmn(primates.tab,gn="Genus",sp="Species",rownames=FALSE,gnsp.col='gn_sp')
primates.tab <- add.gnsp.clmn(primates.tab,gn="Genus",sp="Species",rownames=FALSE,gnsp.col='gnspg')
pri.grpd <- regroup.gnsp(df=primates.tab,clmns=colnames(primates.tab), agg='max')
out <- regroup.equivalent(pri.grpd, gnsp.old=gn_sp, gnsp.new='gnspg',
clmns='MonkeyNumberGroves', agg='paste', direction='old2new')
Re-group data.frame by Genus_species
Description
Regroup a given data.frame by a column designated as unique genus_species combination. This function is essentially a wrapper for caroline:::groupBy()
Usage
regroup.gnsp(df,clmns,agg='mean',by='gn_sp')
Arguments
df |
a dataframe |
clmns |
columns |
agg |
type of aggregation to be used |
by |
the column name by which the data.frame should be re-grouped |
Value
returned value
Examples
primates.tab <- AWP.read.pkg.tab(tab.nm='dbo_tblGrovesMonkeys', id.clmn='MonkeyNumberGroves')
out <- regroup.gnsp(df=primates.tab,clmns=colnames(primates.tab), agg='paste')
Update the values of an AWP data.frame
Description
Update the values in an old dataframe with the values in a new dataframe. Useful for comparing a pre-existing or self-assembled dataset with AWP.
Usage
updatevals(x,y=NULL,v.old,v.new,verbose=TRUE,update=FALSE,
na.only=TRUE,all=TRUE,missing.only=TRUE)
Arguments
x |
first dataframe |
y |
second dataframe |
v.old |
variable old |
v.new |
variable new |
verbose |
get all the messages |
update |
update all the old with everything new |
na.only |
just update the missing values in the old dataframe |
all |
perform merge on all columns |
missing.only |
update only those that have missing values |
Value
values of one data frame are updated to reflect new data in another
Examples
pri.tab <- AWP.read.pkg.tab(tab.nm='Locomotion')
#pri.AWP <- AWP.get.SQL.table(tab.nm='Locomotion')
dim(pri.tab) #should may be fewer cols or rows locally ...
#dim(pri.AWP) # than there are available online.
apply(pri.tab, 2, function(x) sum(is.na(x))) # also more missing values
#apply(pri.AWP, 2, function(x) sum(is.na(x))) # locally than online
# update the "Comment" column locally with the same online
vars <- c('LocomotionID','Comment')
#tmp <- merge(x=pri.tab[,c(vars)] ,y=pri.AWP[,c(vars)], by='LocomotionID')
#out <- updatevals(x=tmp,y=NULL,v.old='Comment.x',v.new='Comment.y')