In leppott/CASTfxn: Functions for Causal Assessment Screening Tool (CAST)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "NEWS-"
)

cat(paste0("Last Update: ",Sys.time()))

Planned Updates

• None at this time.

Future Updates

• Convert site map to ggplot.

• input file data.SSTV.totabund for the function getStressorSpecificRegressions.

• StreamCat data. Boxplots with jitter points.

• getBioStressorResponses

  • Add stressor response plot from getCoOccur

Version History

Changes in Version 0.1.0.9235 (2019-9-05)

• getStressorList, Issue #82
  • Add "DirIncStress" to chem.info (raw data).
  • Use new parameter to decide on how to deal with probsHi and probsLo.
  • Previously looked only for "DO" or "pH".
• getCoOccur, Issue #82
  • Update example to use data.chem.info$DirIncStress to get col.Stressors.InvSc input.

Changes in Version 0.1.0.9234 (2019-9-05)

• getStressorList, Issue #81
  • File save, remove row names (line 372).

Changes in Version 0.1.0.9233 (2019-9-05)

• getCoOccur
  • Modify "pH" in defaults for col.Stressor.InvSc.

Changes in Version 0.1.0.9232 (2019-07-11)

• Shiny, map
  • Update map data for SMC.

Changes in Version 0.1.0.9231 (2019-07-11)

• Shiny, map, 2 versions, COMID and SiteID

Changes in Version 0.1.0.9230 (2019-06-26)

• Working on Shiny app. Incomplete. Issue #30.
  • Renamed CAST_v3 to CAST_AZ
  • Nearly complete.
  • Removed CAST_v1 and CAST_v2.
• getClusterInfo
  • Tweaks for Shiny App
  • Formatting.
  • boo_DEBUG for testings.

Changes in Version 0.1.0.9229 (2019-06-24)

• getClusterInfo, Issue #76
  • Add data.cluster as input parameter.

Changes in Version 0.1.0.9229 (2019-06-24)

• getClusterInfo, Issue #80
  • Add TargetSiteID as input parameter.

Changes in Version 0.1.0.9228 (2019-06-24)

• getBioStressorResponses, Issue #79
  • Suppress warnings for "predict".

Changes in Version 0.1.0.9227 (2019-06-24)

• Working on Shiny app. Incomplete. Issue #30.
• getSiteInfo, Issue #78
  • Update code to use function variable map_proj instead of example variable my.aea.

Changes in Version 0.1.0.9226 (2019-06-06)

• getBioStressorResponses, Issue #75
  • Modify lm() sections.
    • Convert NAN/Inf to NA
    • na.action inside of lm()

Changes in Version 0.1.0.9225 (2019-06-06)

• Update ShinyApp included in package, Issue #30
  • runShinyExample
    • Use CAST_v3
  • Add shinyjs to DESCRIPTION Imports
  • Still working
• Update console feedback to messages, Issue #73
  • So can trap in Shiny app and display to user.
  • getCluster.R
  • getBioStressorResponses
• Add output directory to Return section of help file.
  • getSiteInfo
  • getClusterInfo
  • getCoOccur
  • getVerifiedPredictions

Changes in Version 0.1.0.9224 (2019-05-31)

• Add testing, Issue #72.

Changes in Version 0.1.0.9223 (2019-05-31)

• runShinyExample, Issue 30
• Added additional Shiny Apps to the package.
  • CAST_MapSelection, was already in the package
  • CAST_v1, original design
  • CAST_v2, for testing of new app
• Added parameter to function to run the different Shiny apps.

Changes in Version 0.1.0.9222 (2019-05-20)

• getCoOccur
  • Modify scoring on box plot for DO and pH, Issue #70
  • Add new input variable for those with inverse scoring.
    • Use 25/50 instead of 50/75 as scoring threshold quantiles.
    • Scores are 1/0/-1 instead of -1/0/1
  • Modify scoring threshold quantiles on box plot.

Changes in Version 0.1.0.9221 (2019-05-20)

• getCoOccur
  • Modify scores for SR plot (plot2), Issue #71
  • Scores are in ascending order so Stressor Response plot matches Box plot.
  • Scores file output is now ordered by Param_Value instead of IBI.
• DESCRIPTION
  • Removed "StagedInstall: yes"

Changes in Version 0.1.0.9220 (2019-05-16)

• Changes for R 3.6.0 devtools, Issue #65
  • Readme
    • Rebuild.

Changes in Version 0.1.0.9219 (2019-05-16)

• Changes for R 3.6.0 devtools, Issue #65
  • Readme
    • Fix misspelling in installation example.

Changes in Version 0.1.0.9218 (2019-05-16)

• Changes for R 3.6.0 devtools, Issue #65
  • Readme
    • Moved install code inside of code box.
    • Added "help" section.
    • Updated badges, https://github.com/Naereen/badges

Changes in Version 0.1.0.9217 (2019-05-16)

• Changes for R 3.6.0 devtools, Issue #65
  • Need extra line for install from GitHub. Update readme.
    • Sys.setenv("TAR" = "internal")
• GitHub badges
  • Added Maintained to Readme.
  • https://github.com/Naereen/badges

Changes in Version 0.1.0.9216 (2019-05-16)

• Changes for R 3.6.0 staged install, Issue #65
  • Do not store package directory to any object. Always call with system.file.
    • getReport.R
    • getSiteInfo.R
• DESCRIPTION, Issue #69
  • Update for package changes that are no longer used in CASTfxn.
    • replyr, remove from Imports, package in maintenance mode
    • pryr, removed from Suggests, used prior to conversion to all ggplot2 plots.

Changes in Version 0.1.0.9215 (2019-05-16)

• getBioStressorResponse
  • Modify correlation file output, Issue #68
    • Update QC check for new "n" column.

Changes in Version 0.1.0.9214 (2019-05-15)

• getVerifiedPredictions
  • Add biocomm as input.
    • help file
    • example
    • function code
  • Score file modifications, Issue #68
    • Add "n".
    • Rename (include biocomm)
• getBioStressorResponse
  • Score file modifications, Issue #68
    • Correlations file, add "n".

Changes in Version 0.1.0.9213 (2019-05-14)

• getVerifiedPredictions
  • Update description Value.

Changes in Version 0.1.0.9212 (2019-05-13)

• getVerifiedPredictions, Issue #57
  • Add "n" to plot in caption.
  • Add scoring boundaries.
  • Add scores to the plot caption.
    • In ascending order to match plot (left to right).
  • Modify scores output file. Issue #61
  • Error/stop message for no "worse" bio sites for comparison.

Changes in Version 0.1.0.9211 (2019-05-10)

• getVerifiedPredictions, Issue #57
  • Add better bio, degraded = no points to the plot

Changes in Version 0.1.0.9210 (2019-05-09)

• getReport fails, Issue #67
  • Update for changes in BioStressorResponses scores output, Issue #58

Changes in Version 0.1.0.9209 (2019-05-06)

• Fixes after running "check" in RStudio.
  • Add package reference to functions that are not base package functions.
    • importFrom("grDevices", "pdf")
    • importFrom("graphics", "plot")
    • importFrom("stats", "lm", "predict", "var")
    • importFrom("utils", "flush.console", "read.delim")
  • examples lines wider than 100 characters
    • getBioMatches
    • getBioStressorResponses
    • getChemDataSubsets
    • getClusterInfo
    • getSSDplot
    • getSiteInfo
    • getStressorList
    • getVerifiedPredictions
  • Document data
    • data_CoOccur_AZ_Lo
• R v3.6.0., StagedInstall, Issue #65
  • DESCRIPTION
    • StagedInstall: yes

Changes in Version 0.1.0.9208 (2019-05-06)

• getBioStressorResponse, Issue #58.
  • 2nd Score.
  • Add scores to plot.
  • Rework output table.
• Add SiteID to all text file outputs, Issue #66
  • getBioStressorResponse
    • SRCKN001.61.SR.BMI.Scores.txt

Changes in Version 0.1.0.9207 (2019-05-02)

• getSSDplot
  • Add na.rm=TRUE to ggplot references to avoid warning messages, Issue #56.

Changes in Version 0.1.0.9206 (2019-05-02)

• R v3.6.0., StagedInstall, Issue #65
  • DESCRIPTION
    • StagedInstall: no
  • Use system.file(package="") without saving to a variable.
    • runShinyExample.R
    • getReport.R
    • getSiteInfo.R
• getSiteInfo
  • Update leaflet map RMD with SiteInfo subdirectory for static map. Issue #64

Changes in Version 0.1.0.9205 (2019-05-01)

• Shiny App, Issue #30.
  • Add COMID select with map.
• Sub-directories by function, Issue #64
  • Report and most functions.

Changes in Version 0.1.0.9204 (2019-04-26)

• getBioStressorResponses
  • Tweaks trying to find why fails for a user.
    • Formatting in code.
    • Algae example.
    • QC check on cor file header add "biocomm".

Changes in Version 0.1.0.9203 (2019-04-25)

• biocomm name on file scoring outputs, Issue #64.
  • getBioStressorResponses.
    • Add to table outputs.
  • getCoOccur
    • Add as input.
    • Add to txt output filenames.
    • Add to table outputs.
  • getStressorList
    • Add as input.
    • Add to txt output filenames.
    • Did not add to table outputs.
  • getReport
    • Modify RMD for new file names.
    • Add DT for tables.
• Add DT package to DESCRIPTION IMPORTS.

Changes in Version 0.1.0.9202 (2019-04-25)

• Remove function getRegPlotSet, Issue #63.

Changes in Version 0.1.0.9201 (2019-04-23)

• Remove unused inputs, Issue #60
  • getVerifiedPredictions
    • predint
    • varLegLoc
  • getBioStressorResponses
    • predint
    • varLegLoc

Changes in Version 0.1.0.9200 (2019-04-23)

• getVerifiedPredictions
  • Make inputs more generic, Issue #59
    • "bmi" to "bio".

Changes in Version 0.1.0.9199 (2019-04-23)

• getCoOccur
  • Example 2 (AZ) site to SRCKN001.61 to match other examples.

Changes in Version 0.1.0.9198 (2019-04-23)

• getBioStressorResponses
  • Scoring. No slope score to zero.

Changes in Version 0.1.0.9197 (2019-04-23)

• Declare "directory" as a required input.
  • getStressorList
  • getBioStressorResponses
  • getVerifiedPredictions
  • getClusterInfo
• getVerifiedPredictions
  • Rename function.
    • Earlier update only did file name.
• getBioMatches
  • Update names in output.

Changes in Version 0.1.0.9196 (2019-04-22)

• getBioMatches
  • Missing inputs:
    • data.stress.raw
    • data.bioMetrics
    • list.SiteSummary
    • data.SampSummary
    • data.chem.raw
  • Update documentation.
  • Update examples.
  • Update code; bio instead of bmi and alg.
• Update examples for changes to getBioMatches
  • CASTfxn_Vignette.RMD

Changes in Version 0.1.0.9195 (2019-04-22)

• Rename getStressorSpecificRegressions to getVerifiedPredictions
  • getStressorSpecificRegressions.R
  • CASTfxn_Vignette.RMD
  • Analysis.RMD
• CASTfxn_Vignette.RMD
  • Update examples for updates in functions.

Changes in Version 0.1.0.9194 (2019-04-22)

• Remove old deprecated functions.

Changes in Version 0.1.0.9193 (2019-04-18)

• getBioStressorResponses
  • Set minimum number of cluster samples 3 rather than 1.
    • predict and corr.test were failing with only 2 records.

Changes in Version 0.1.0.9192 (2019-04-18)

• getCoOccur
• Allow for special characters (e.g., %) in stressors.
• Error message for stressors not in input data.

Changes in Version 0.1.0.9191 (2019-04-17)

• getCoOccur
  • Attempt to remove warning messages from plot 1 (p1).
    • If skip geom_jitter the plot is missing parts so leave alone.

Changes in Version 0.1.0.9190 (2019-04-17)

• getBioStressorResponses
  • Update regression plot with 2nd regression line. Issue #55.

Changes in Version 0.1.0.9189 (2019-04-16)

• getCoOccur
  • Unwind removing Stressor plot. Keep for now. Issue #54.
  • Make edits to p2 to avoid warnings; Issue #56.

Changes in Version 0.1.0.9188 (2019-04-16)

• Add na.rm=TRUE to ggplot statements to avoid warnings; Issue #56.
  • getCoOccur

Changes in Version 0.1.0.9187 (2019-04-16)

• getCoOccur
  • Remove stressor plot (p2). Issue #54

Changes in Version 0.1.0.9186 (2019-04-15)

• getBioStressorResponses
  • Fix 'df.corr' object not found.
    • Previously renamed df.corr to df.corr_cl. Missed a reference.

Changes in Version 0.1.0.9185 (2019-04-15)

• getCoOccur
  • NA for stressor values.
    • Parameter was being skipped if no stressor values (i.e., all NA).
    • Output NA to scores file.
    • Message to console.

Changes in Version 0.1.0.9184 (2019-04-12)

• getBioStressorResponses
  • Minor edits to 0.1.0.9083 changes (r2).
  • Check for missing stressors.
    • Remove from stressor list.
    • Warning for those requested but missing from data.

Changes in Version 0.1.0.9183 (2019-04-12)

• getBioStressorResponses
  • Modify linear regression plot, Issue #55.
  • Incomplete. Still need 2nd regression for just the cluster.

Changes in Version 0.1.0.9182 (2019-04-12)

• Move the SR plot from getCoOccur to getBioStressorResponses, Issue #54.
  • Prepare code, did not make changes.

Changes in Version 0.1.0.9181 (2019-04-12)

• getBioStressorResponses
  • Update stop message for no response data.

Changes in Version 0.1.0.9180 (2019-04-12)

• make.names; undo edits for TargetSiteID in names for folders and files.
  • Some start with numbers and that is ok.
  • getBioStressorResponses
  • getClusterInfo
  • getCoOccur
  • getStressorList
  • getStressorSpecificRegressions
• getCoOccur
  • Boxplot not saving to TargetSiteID folder (line 414).

Changes in Version 0.1.0.9179 (2019-04-11)

• getBioStressorResponses
  • Line 262-267 QC check failed.
    • Move declaration into previous if/then by biocomm.
• Use make.names for ggsave exports of plots by variable.
  • getBioStressorResponses
  • getStressorSpecificRegressions
  • getCoOccur
  • getClusterInfo

Changes in Version 0.1.0.9178 (2019-03-22)

• getBioStressorResponses
  • End if no site response data (list.MatchBioData$site.a.rsp).

Changes in Version 0.1.0.9177 (2019-03-22)

• getCoOccur
  • End message for no data rather than error crash.
  • ID.plot to TargetSiteID
    • For consistency among functions.
  • dir.plots parameter not being used. Modify code to use it.
  • Example, remove "c" from col.ID.

Changes in Version 0.1.0.9176 (2019-03-21)

• Report_Results_summary
  • lines 155-175, SR.BMI.Scores. read statement corrected.

Changes in Version 0.1.0.9175 (2019-03-21)

• Report_Results_summary
  • lines 132-152, SR.BMI.Corrs. read statement corrected.

Changes in Version 0.1.0.9174 (2019-03-15)

• Report_Results_summary
  • Update show CoOccur for uneven box and SR plots.

Changes in Version 0.1.0.9173 (2019-03-15)

• Report_Results_summary
  • Show SSTV plots.
  • Update show CoOccur for no data.

Changes in Version 0.1.0.9172 (2019-03-15)

• Report_Results_summary
  • Show CoOccurrence plots.

Changes in Version 0.1.0.9171 (2019-03-13)

• getBioStressorResponses
  • Modify QC check for header for correlation plot data.
  • Resave file.
• Report_Results_summary
  • Make same modification as getBioStressorResponses.

Changes in Version 0.1.0.9171 (2019-03-13)

• getBioStressorResponses
• Add QC check for header for correlation plot data.

Changes in Version 0.1.0.9170 (2019-03-11)

• getStressorSpecificRegressions
  • Add ref.sites as a required input parameter.
• Add na.rm=TRUE to fun.aggregate=mean for dcast statements.
  • getBioStressorResponses.R
  • Report_Results_summary.rmd

Changes in Version 0.1.0.9169 (2019-03-11)

• Assign cluster in "algae" example.
• getBioStressorResponses
  • Update scores text file output for header row.
    • If case 1 didn't have results the file didn't have a header row.
    • And the report would fail.
• getReport
  • Report_Results_summary.rmd
    • Update dcast statement to include fun.aggregate = mean.

Changes in Version 0.1.0.9168 (2019-03-08)

• Modify QC procedures for plotting missing categories of data.
  • getStressorRef
  • getClusterInfo
  • getBioMatches
  • getBioStressorResponses

Changes in Version 0.1.0.9167 (2019-03-08)

• Assign data.cluster based on information in data_Sites.
  • Modify examples in each function.
    • getSiteInfo
    • getChemDataSubsets
    • getBioMatches
    • getBioStressorResponses
    • getClusterInfo
    • getStressorList
    • getStressorSpecificRegressions

Changes in Version 0.1.0.9166 (2019-03-07)

• getBioStressorResponses
  • Fix errors from testing.
    • Remove extra brackets for sections.
    • Add extra QC on correlation plot.
    • Output item message for ones skipped.

Changes in Version 0.1.0.9165 (2019-03-05)

• getStressorList
  • Fails when have no reference sites.
    • Change trigger for plotting ref sites.

Changes in Version 0.1.0.9164 (2019-03-05)

• getStressorSpecificRegressions.R
  • Revised plot output. Issue #50 and 44.
  • Old function R file renamed (prefixed with "z_") and marked with keyword "internal".
  • Remove stressor loop. Always sens and tol taxa.
• Data
  • Rebuild all data from raw data files using processing scripts.
  • Use dataset received 2019-02-27.
• getSSDplot
  • Update example to 'print' plots.
• getCoOccur
  • cluster to comparator.
    • Variables in function only.
• getBioStressorResponses
  • Ensure Alg version works, Issue #46
  • Update example to remove bad response variables, Issue #46
• DESCRIPTION
  • Move pryr package from imports to suggests. Issue #52.

Changes in Version 0.1.0.9163 (2019-02-26)

• getClusterInfo.R
  • Fix y-axis label the same for all plots, Issue #48.

Changes in Version 0.1.0.9162 (2019-02-19)

• getStressorSpecificRegressions.
  • ggplot graphics, Issue #41.
  • Started but unfinished.
  • Other changes proposed to this function.

Changes in Version 0.1.0.9161 (2019-02-18)

• Add geom_blank for ggplots where may not have a data group (e.g., cluster ref).
• Use same structure as in getBioStressorResponses.
  • getStressorList
  • getClusterInfo

Changes in Version 0.1.0.9160 (2019-02-15)

• getStressorList
  • Change "box" plots to ggplot. Issue #41.
  • Remove importFrom pryr "%<a-%".

Changes in Version 0.1.0.9159 (2019-02-15)

• getRegPlotSet
  • Mark functions as keyword internal so not in the help list

Changes in Version 0.1.0.9158 (2019-02-15)

• getBioStressorResponses
  • Remove importFrom pryr "%<a-%".
    • No longer needed with gglot graphics.

Changes in Version 0.1.0.9157 (2019-02-15)

• getClusterInfo
  • Updated plot title to match old graphic. Issue #41.

Changes in Version 0.1.0.9156 (2019-02-14)

• getClusterInfo
  • Convert to ggplot. Issue #41.

Changes in Version 0.1.0.9155 (2019-02-14)

• getBioStressorResponse
  • Fix plot error when missing a subset of data. Issue #43.

Changes in Version 0.1.0.9154 (2019-02-11)

• getBioStressorResponse
  • Fix PDF output after conversion to ggplot.

Changes in Version 0.1.0.9153 (2019-02-08)

• getBioStressorResponse
  • Add ref.sites as an input.
  • Update to ggplot, Issue #7
  • Edit code for clarity

Changes in Version 0.1.0.9152 (2019-02-07)

• getClusterInfo
  • Fixed siteClusters v. site.Clusters as a parameter.

Changes in Version 0.1.0.9151 (2019-02-07)

• getBioStressorResponses, Issue #7
  • Convert plot to ggplot
    • Test mode so not active.

Changes in Version 0.1.0.9150 (2019-02-06)

• getSiteInfo, Issue #32 and Issue #4
  • Add required objects to function input arguments.
  • Update example code
    • getBioMatches
    • getBioStressorResponses
    • getChemDataSubsets
    • getClusterInfo
    • getSiteInfo
    • getStressorList
    • getStressorSpecificRegressions
  • Remove required columns in data.cluster input. Issue #32.
    • W___AGRIC
    • W___URBAN
    • W___FOREST
  • leaflet map, Issue #42
    • Change addProviderTiles
    • Rename file and move inside Station folder.
  • ggplot map, Issue #14
    • Started but did not finish.
    • Left code in as comments.
    • Map takes 10 to 15 seconds with ggplot.

Changes in Version 0.1.0.9149 (2019-02-06)

• getStressorList
  • Error with NA reporting. Issue #38.
    • Added extra is.na in getChemDataSubsets.
• getChemDataSubsets
  • Fix error with NA reporting. Issue #38
  • Add in required parameters. Issue #4
• Update examples
  • getBioMatches
  • getBioStressorResponses
  • getChemDataSubsets
  • getClusterInfo
  • getStressorList
  • getStressorSpecificRegressions

Changes in Version 0.1.0.9148 (2019-02-05)

• Merget getBMIStressorRespones and getAlgStressorResponses into a single function, Issue #34
  • getBioStressorResponses
  • Deprecated BMI and Alg version with keyword internal.

Changes in Version 0.1.0.9147 (2019-02-05)

• Merge getBMIMatches and getAlgMatches into single function, Issue #33.
  • getBioMatches
  • Deprecated BMI and Alg version with keyword internal.

Changes in Version 0.1.0.9146 (2019-02-04)

• Remove clustertype, Issue #31
  • Function inputs.
    • getSiteInfo
    • getClugerInfo
    • getChemDataSubsets
  • Function examples.
    • getAlgmatches
    • getAlgStressorResponses
    • getBMImatches
    • getBMIStressorResponses
    • getChemDataSubsets
    • getClusterInfo
    • getSiteInfo
    • getSTressorList
    • getStressorSpecificRegressions
  • Vignettes
    • CASTfxn_Vignette
    • Analysis

Changes in Version 0.1.0.9145 (2019-02-04)

• Remove useLU, Issue #31
  • Function inputs.
    • getSiteInfo
    • getChemDataSubsets
    • getClusterInfo
    • getStressorList
  • Function examples.
    • getAlgmatches
    • getAlgStressorResponses
    • getBMIMatches
    • getMBIStressorResponses
    • getChemDataSubsets
    • getClusterInfo
    • getSiteInfo
    • getStressorList
    • getStressoSpecificRegressions
  • Vignettes
    • CASTfxn_Vignette
    • Analysis

Changes in Version 0.1.0.9144 (2019-02-01)

• Add shiny to DESCRIPTION

Changes in Version 0.1.0.9143 (2019-02-01)

• Add Shiny. Issue #30.
  • Added demo app (default, not CAST).
  • Added runShinyExample function to launch Shiny.
    • Includes links in help file to Shiny.io app online.

Changes in Version 0.1.0.9142 (2019-02-01)

• getCoOccur.R, Issue #25
  • Add individual plots as jpg.
    • Use ggsave instead of jpeg (as with other functions).

Changes in Version 0.1.0.9141 (2019-01-31)

• getCoOccur.R, Issue #25
  • Details
    • Use lowest biological condition score in box plots.
    • Bold section headers in details.
    • Changes to output (see below).
  • logistic regression
    • Ensure using Degraded Yes/No instead of Degraded/Reference.
  • Output
    • Save individuals JPG files as well as PDF.
  • Example
    • Modify example to be "Example 1, CA".
    • Add "Example 2, AZ hi".
  • Remove date from file names.
  • Use loweest biological score for a site.
    • Was mean.
  • Box plot.
    • Add scoring lines (as in SR plot).
    • Update text (make multiline).
  • Stressor Response (SR) Curve plot
    • Generate scores.
    • Save scores.
    • Add scores to plot.
• data
  • Modify data_CoOccur to be data_CoOccur_CA
  • Add data_CoOccur_AZ_Hi

Changes in Version 0.1.0.9140 (2019-01-24)

• getCoOccur.R, Issue #25
  • Add debugging.
  • Rework factor of Bio.Deg to ensure always in the same order.
  • Box plot
    • Remove y-axis elements (was confusing).
    • Remove x-axis quotes around parameter name.
    • Modify shape and color of jitter points for use in legend.
    • Update legend.
    • Update y-axis so scaling matches Curve plot when combined in output.
  • Curve plot
    • Update points and legend to match box plot.

Changes in Version 0.1.0.9139 (2019-01-18)

• Overall Report
  • getReport.R
  • inst/rmd/Report_Results_overall.rmd

Changes in Version 0.1.0.9138 (2019-01-17)

• getReport
  • Modified QC check for "summary" report.
• Report_Results_summary.rmd
  • Minor tweaks.
  • BMI.SR plots show all with p value < 0.05.

Changes in Version 0.1.0.9137 (2019-01-11)

• Update logtransf, Issue #23
  • getStressorSpecificResponses
    • Slightly different code. Use example from getStressorList.

Changes in Version 0.1.0.9136 (2019-01-10)

• Update logtransf, Issue #23
  • getAlgStressorResponses
  • getBMIStressorResponses

Changes in Version 0.1.0.9135 (2019-01-10)

• getStressorList
  • Add LogTransf to output. Issue #23

Changes in Version 0.1.0.9134 (2019-01-10)

• Misnumbered v0.1.0.9033 as 9032

Changes in Version 0.1.0.9133 (2019-01-10)

• getBMIStressorResponses
  • Ensure certain variables are not log transformed. Issue #24.
    • DO, pH, temperature, flow
  • Tweak plot output from changes made in previous update. Issue #23

Changes in Version 0.1.0.9132 (2019-01-10)

• getBMIStressorResponses
  • Fix duplicate output to console. Issue #23.

Changes in Version 0.1.0.9131 (2019-01-07)

• getSiteInfo
  • Map_Leaflet.rmd missing
  • inst/RMD was mistakenly in .gitignore

Changes in Version 0.1.0.9130 (2018-12-18)

• getSiteInfo
  • Add a leaflet map output as HTML (R Notebook).

Changes in Version 0.1.0.9129 (2018-12-18)

• getAlgStressorResponses
  • Add PDF of plots.

Changes in Version 0.1.0.9128 (2018-12-18)

• Update getReport template RMD for Algae corrplot.
  • \inst\rmd\Report_Results_summary.rmd

Changes in Version 0.1.0.9127 (2018-12-18)

• Update data documentation
  • data_AlgCounts
  • data_AlgMasterTaxa
  • data_AlgMetrics
• getAlgStressorResponses
• data_AlgMetrics
  • Alg.Metrics.SampID to Algae.Metrics.SampID

Changes in Version 0.1.0.9126 (2018-12-14)

• getAlgStressorResponses
  • Update with changes made to getBMIStressorResponses
• Update Algae Data
  • data_AlgMetrics
  • data_AlgMasterTaxa
  • data_Algcounts

Changes in Version 0.1.0.9125 (2018-12-14)

• Vignette Update
  • CASTfxn
    • Change name shown in help file.
  • Add vignette for "anlaysis".
    • Run all functions example.
• Correlation output file column names.
  • getBMIStressorResponses.R
  • getStressorSpecificRegressions.R
  • getAlgStressorResponses.R

Changes in Version 0.1.0.9124 (2018-12-13)

• getSSDplot
  • Add example to save created plot.
• getReport
  • Tweak summary report for names change of SSTV correlations file.

Changes in Version 0.1.0.9123 (2018-12-12)

• getStressorSpecificRegressions
  • Modify inputs.
  • Add master taxa list.
  • Replace SampleID with BMI.Metrics.SampID
  • Limit data with unique so only get one instance.
  • Add user feedback for progress.
• Add master taxa data file.
  • Process raw data.
  • Data description.

Changes in Version 0.1.0.9122 (2018-12-11)

• getBMIStressors
  • Update input variables.
  • Rename text output files to match other function outputs.
• Report_Results_summary.rmd
  • Update for change in text file outputs from getBMIStressors.

Changes in Version 0.1.0.9121 (2018-12-10)

• getBMIStressors
  • Fix error in df.CorrTable creation.

Changes in Version 0.1.0.9120 (2018-12-06)

• Modify plots to output a combined PDF as well as individual JPG files. Issue #19.
  • .SSTV.
    • getStressorSpecificRegressions
• getStressorSpecificRegressions
  • Change data.chem.info2 to data.chem.info.
  • Add required objects as function inputs.
• Fix duplicated first line in txt output for stressor responses. Issue #17
  • getBMIStressorResponses
  • getStressorSpecificRegressions
  • getAlgStressorResponses

Changes in Version 0.1.0.9119 (2018-12-06)

• Modify plots to output a combined PDF as well as individual JPG files. Issue #19.
  • .SR.BMI.
    • getBMIStressorResponse

Changes in Version 0.1.0.9119 (2018-12-06)

• Modify plots to output a combined PDF as well as individual JPG files. Issue #19.
  • .cluster.
    • getClusterInfo
  • .SR.BMI.
    • getBMIStressorResponse
  • .SR.Alg.
    • getAlgStressorResponse
  • .SSTV.
    • getStressorSpecificRegressions

Changes in Version 0.1.0.9118 (2018-12-06)

• Modify plots to output a combined PDF as well as individual JPG files. Issue #19.
  • .boxes.
    • getStressorList
• Added pryr package to aid in capture of plots for use in PDF output.

Changes in Version 0.1.0.9117 (2018-12-05)

• Report
  • Add CoOccurrence table.
  • Add ChemPctRank table.
  • Only "summary" report.
    • Stop message for "all" report.

Changes in Version 0.1.0.9116 (2018-12-05)

• getReport
  • Modify summary report to check if file exists
• getCoOccur
  • Modify user feedback to include overall item number; Issue #18
  • Modify file outputs to use "dot" delimiter to match other file outputs in package.
  • TSV to TXT for scores to match other data file outputs.

Changes in Version 0.1.0.9115 (2018-11-13)

• getReport
  • Function to output report.
  • All and Summary reports.
  • Report_Results.RMD to Report_Results_All.RMD
  • Add Report_Results_Summary.RMD
• DESCRIPTION
  • Add rmarkdown to IMPORTS

Changes in Version 0.1.0.9114 (2018-11-12)

• getBMIStressorResponses
  • Update jpg file name output. Issue #16.
    • Missing "dot" between SiteID and BMI.SR.

Changes in Version 0.1.0.9113 (2018-11-12)

• Report_Results.rmd
  • New results report.

Changes in Version 0.1.0.9112 (2018-10-17)

• data.R
  • Remove non-ASCII characters so the package will build properly.
  • Chemical names and units combinations were the culprit; n=334.

Changes in Version 0.1.0.9111 (2018-10-17)

• Elevation Vignette.

Changes in Version 0.1.0.9110 (2018-10-16)

• data.R
  • data_SSD_generator, correct typo. Issue #11.
  • Add more details to other data sets.

Changes in Version 0.1.0.9109 (2018-10-16)

• Add getElev function.

Changes in Version 0.1.0.9108 (2018-10-10)

• Vignette.
  • Fix errors.
• DESCRIPTION
  • Change R Depends from 2.1.0 to 2.10
  • Add Imports for sp and stringr
• Add utils:: for missing cases:
  • flush.console
  • write.table
• Non-standard names
  • getStressorList
    • boxes.water quality.x.jpg
    • Use make.names when build file names.
    • Don't need to adjust data.
  • Occurs in raw data; AZChemInfoFinal.tab
    • Category

Changes in Version 0.1.0.9107 (2018-10-10)

• getSiteInfo
  • Add user defined "Results" folder. Issue #13
  • Check for it and if not present create it.
  • Makes the function more generic. Issue #4

Changes in Version 0.1.0.9106 (2018-10-10)

• Merged Vignette branch (v0.1.0.9104) in previous committ (0.1.0.9105).
• Added project to TravisCI.
• ReadMe
  • Add badges.

Changes in Version 0.1.0.9104 (2018-08-02)

• getCoOccur
  • Update save directory code.

Changes in Version 0.1.0.9103 (2018-08-02)

• DESCRIPTION
  • Add authors in plain text
• CASTfxn.R
  • Revise with names of functions.
• Vignette
  • Add output descriptions.
• getStressorList
  • Add dot to filename of output after SiteID
  • SiteID.chem.pctrank.txt
• getClusterInfo
  • Added ".cluster." after SiteID to output plot names.

Changes in Version 0.1.0.9102 (2018-07-11)

• getBMIStressorResponses
  • More detailed console message.
• getStressorSpecificRegressions.
  • Modify QC check for horizontal and vertical lines.
  • Fix error with inset value for legend by using as.numeric.

Changes in Version 0.1.0.9101 (2018-07-10)

• getClusterInfo
  • Add QC print output to code.
  • Added QC check to ensure Y data for box plot is not all NA or is not non-numeric.

Changes in Version 0.1.0.9100 (2018-07-10)

• Use Ann's fork of CASTfxn as basis for fork in my repository.
• Jumping ahead to version "9100" to differentiate.
• Update NEWS
• getBMImatches
  • lines 85:86
  • Missing closing paren for print.
• getclusterInfo
  • lines 95:96
  • Missing a comma in paste.

• getStressorSpecificRegressions

  • lines 128:129
  • Missing closing paren for print.

• TargetSiteID

  • Used in functions but is not a parameter.
  • Assumed in the global environment.
  • QC checks fail.
  • Parameter in function call, example, and stop message if doesn't exist.
  • Add to the following functions:
  • getBMImatches (lines 85:86) [really just missing a parenthesis]
  • getClusterInfo (lines 95:96)
• Will need to follow up with examples in other functions.

Changes in Version 0.1.0.9044 (2017-06-22)

• Add dataset "data_Cluster_Lo".
  • Add to data-raw and to data.R
• Add "ElevCategory" (HI or LO) to each data file in data-raw.
  • data_303d
  • data_AlgMetrics
  • data_BMIMetrics
  • data_BMIRelAbund
  • data_BMIcounts
  • data_Chem
  • data_Cluster_Hi
  • data_Cluster_Lo
  • data_ReachMod
  • data_SampSummary
  • data_Sites
• Files not modified:
  • data_ChemInfo
  • data_CoOccur
  • data_GIS_Flow_HI
  • data_GIS_Flow_LO
  • data_GIS_AZ_Outline
  • data_SSD
  • data_SSD_generator
  • data_SSD_permethrin

Changes in Version 0.1.0.9043 (2017-06-21)

• getBMIStressorResponses
  • Review for scoring.
  • Change loop variable from r to q to avoid conflict with r and r2.

Changes in Version 0.1.0.9042 (2017-06-21)

• getCoOccur
  • Fix help file with too wide text.

Changes in Version 0.1.0.9041 (2017-06-21)

• getSSDplot examples.
  • Assign return plots to variables.
  • Additional example to demonstrate adding points to the plot.

Changes in Version 0.1.0.9040 (2017-06-21)

• Scoring output.
  • getCoOccur

Changes in Version 0.1.0.9039 (2017-06-20)

• Rename 2 functions with "get" to match others.
  • CoOccur
  • SSD
  • Update vignette.

Changes in Version 0.1.0.9038 (2017-06-20)

• Update examples. Issue #5.
  • getStressorSpecificRegressions
  • Use BMIRelAbund.rda for data.SSTV.totabund
  • Replace BenSampID with BMI.Metrics.SampID
  • Not finished. Not working.
• Add data file; BMIRelAbund.rda
  • Include in data-raw and Data.R
  • Data for data.SSTV.totabund in getStressorSpecificRegressions.

Changes in Version 0.1.0.9037 (2017-06-16)

• Update examples. Issue #5.
  • getAlgStressorReponses

Changes in Version 0.1.0.9036 (2017-06-16)

• Update examples. Issue #5.
  • getAlgMatches

Changes in Version 0.1.0.9035 (2017-06-16)

• Update examples. Issue #5.
  • getStressorSpecificRegressions
  • Need input file data.SSTV.totabund

Changes in Version 0.1.0.9034 (2017-06-15)

• Update examples. Issue #5.
  • getBMIStressorResponses

Changes in Version 0.1.0.9033 (2017-06-15)

• Update examples. Issue #5.
  • getBMImatches

Changes in Version 0.1.0.9032 (2017-06-15)

• Update examples. Issue #5.
  • getClusterInfo

Changes in Version 0.1.0.9031 (2017-06-15)

• Update examples. Issue #5.
  • getStressorList
• Add subdir check to functions that use "Results" subdire.
  • getSiteInfo
  • getChemDataSubsets
  • getStressorList
  • getClusterInfo
  • getAlgStressorResponses
  • getBMIStressorResponses
  • getStressorSpecificRegressions

Changes in Version 0.1.0.9030 (2017-06-15)

• Update examples. Issue #5.
  • getChemDataSubsets
• Update data.R.
  • data_Chem
  • data_ChemInfo (update data with GroupName)
  • data_Cluster_Hi

Changes in Version 0.1.0.9029 (2017-06-15)

• Add vignette.
  • Add package imager to Suggests in DESCRIPTION.
  • Basic outline.
  • getSiteInfo function.

Changes in Version 0.1.0.9028 (2017-06-14)

• GIS data.
  • Standardize projection for GIS layers.
  • getSiteInfo; modify plot and projection used for layers.
• getSiteInfo
  • modify "cluster" data column.
• Examples, change clustertype "H6" to "5"
  • getAlgMatches
  • getAlgStressorResponse
  • getBMIMatches
  • getBMIStressorResponses
  • getCheDataSubsests
  • getClsuterInfo
  • getSiteInfo
  • getStressorList
  • getStressorSpecificRegressions
• data_Sites
  • Modify reference to match code.

Changes in Version 0.1.0.9027 (2017-06-14)

• Add GIS data.
  • data.R
  • data_GIS_Flow_HI
  • data_GIS_Flow_LO
  • data_GIS_AZ_Outline
• Update getSiteInfo map.
  • Uncomment map code.
  • Change graphics::plot to sp::plot.
• Revised data_SampSummary.
• Revise SampIDs in other files to match format in SampSummary.
  • data_AlgMetrics
  • data_BMIcounts
  • data_BMIMetrics
  • data_Chem

Changes in Version 0.1.0.9026 (2017-06-12)

• Add data_BMIcounts.
  • Update data.R.
  • Update getStressorSpecificRegressions example.

Changes in Version 0.1.0.9025 (2017-06-12)

• Modify examples for TargetSite and getSiteInfo. Issue #5
  • getAlgmatches, getAlgStressorResponses, getBMImatches, getBMIStressorResponses , getClusterInfo, getStressorList, getStressorSpecificRegressions.
• Modify examples for file imports vs. included datasets. Issue #5
  • getAlgmatches, getBMImatches, getClusterInfo, getStressorSpecificRegressions

Changes in Version 0.1.0.9024 (2017-06-12)

• getChemDataSubset
  • default useLU to FALSE.
  • Error if no cluster information. Added "stop" condition.

Changes in Version 0.1.0.9023 (2017-06-11)

• Update example in getChemDataSubset. Issue #5.
  • Create data_ChemInfo
  • Create data_Chem
  • Remove "dontrun" in example.

Changes in Version 0.1.0.9022 (2017-06-11)

• Add AZ data to "data-raw" and "data". Issue #5.
• getSiteInfo.R
  • Add example datasets (include description in data.R)
  • Turn off mapping.
  • Turn off "donotrun" in example.

Changes in Version 0.1.0.9021 (2017-06-08)

• Add data requirements to "get" functions in the "details" section.
  • Include column names for required imports
• Add helper function getRegPlotSet.
• Add examples but mark as "dont' run". Issue #5.
• Add function getAlgMatches.
  • Include return value.

Changes in Version 0.1.0.9020 (2017-06-07)

• SSDplot
  • Add 3rd dataset so can QC against USEPA ssd generator Excel file.
  • Change proportion formula; rank-0.05 to rank-0.5 to match USEPA
  • Change "Species" to "Taxa" in 2 locations in the code.

Changes in Version 0.1.0.9019 (2017-06-07)

• Modify format of NEWS file. Issue #1.

Changes in Version 0.1.0.9018 (2017-06-06)

• Check issues addressed:
  • Depends R >= 2.1.0
  • no visible global function definition (multiple)
  • Add to Imports; graphics, grDevices, stats, utils
• Check issues not addressed:
  • data_CoOccur, non-ASCII characters in column names.
  • Undocumented object "cluster" in getChemDataSubsets
  • no visible binding for global variable (multiple)
• SSDplot
  • Add second dataset and example.
  • Modify text; font size and justification

Changes in Version 0.1.0.9017 (2017-06-06)

• Update functions for package dependencies, e.g., readOGR to rgdal::readOGR.
  • getSiteInfo; rgdal
  • getChemDataSubsets; reshape
  • getStressorList; dplyr

Changes in Version 0.1.0.9016 (2017-06-06)

• Rename SSD function to SSDplot due to conflict with stats::SSD.
• Update CASTfxn.R for function name change.

Changes in Version 0.1.0.9015 (2017-06-06)

• Fix StressorList return value. Issue #2.

Changes in Version 0.1.0.9014 (2017-06-06)

• Fix SSD function. Issue #3.

Changes in Version 0.1.0.9013 (2017-06-06)

• Add CASTfxn.R so the package has a help file.

Changes in Version 0.1.0.9012 (2017-06-06)

• Add function getStressorSpecificRegressions.

Changes in Version 0.1.0.9011 (2017-06-06)

• Add function getAlgStressorResponses.

Changes in Version 0.1.0.9010 (2017-06-06)

• Add function getBMIStressorResponses.

Changes in Version 0.1.0.9009 (2017-06-06)

• Add function getBMImatches.

Changes in Version 0.1.0.9008 (2017-06-06)

• Add function getStressorList.

Changes in Version 0.1.0.9007 (2017-06-06)

• Add function getClusterInfo.
• SSD.R
  • Remove "conf=0.95" from qnorm function.

Changes in Version 0.1.0.9006 (2017-06-06)

• Add function getChemDataSubsets.

Changes in Version 0.1.0.9005 (2017-06-06)

• Add function getSiteInfo.
• Add Imports to DESCRIPTION.
  • maps
  • maptools
  • raster
  • RColorBrewer
  • reshape
  • rgdal
  • rgeos
  • RgoogleMaps

Changes in Version 0.1.0.9004 (2017-06-06)

• CoOccur function.
  • Update example. Remove 2nd Stressors line.
  • Update details from Sue Norton presentation 2017-06-05.

Changes in Version 0.1.0.9003 (2017-06-05)

• SSD function, non-functional at this point
  • raw data
  • Process raw data script
  • data_SSD.rda in data folder
  • SSD function script
  • data.R, add description of data
• Remove hello function
• Add CoOccur function.
  • raw data
  • process raw data script
  • data_CoOccur in data folder
  • CoOccur script
  • data.R, add description of data

Changes in Version 0.1.0.9002 (2017-05-27)

• Knit README.RMD so README.md will display on GitHub.

Changes in Version 0.1.0.9001 (2017-05-27)

• Added basic package structure.
  • Folders (data, data-raw, inst/doc, inst/extdata, man, R, vignettes)
  • NEWS, README
• Update DESCRIPTION, NEWS, and README

Changes in Version 0.1.0 (2017-05-27)

• Initial commit on GitHub.

leppott/CASTfxn documentation built on Sept. 6, 2019, 11:04 p.m.