NEWS

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SEERaBomb 2019.2 (2019-12-12)

• small bug fixes since 2019.1 version.

SEERaBomb 2019.1 (2019-05-07)

Notes

• The SEER9 registries now all start in 1975. This caused problems since I had assumed that 1973 would always be the starting year. If you want to use older SEER data that starts in 1973, please use a 2018 version of SEERaBomb.
• The three new registries (Idaho, Massachusetts and New York) do not seem to be present in the custom ASCII SEER data release.

SEERaBomb 2018.3

NEW FEATURES

• added mkMrtLocal() which makes mortality binaries from a local copy of the HMD data. This replaces mkMrt(). The R package demograhphy used by mkMrt() is thus no longer needed. Use this new function if mkMrt() gives you a password error, but you can get into HMD with your username and password (and thus know they work). Before running it download to your local drive (and unzip into your ~/data folder) at least one of the two full HMD data file trees (organized by country at the top, the other by statistics at the top).

SEERaBomb 2018.2

NEW FEATURES

• simulated survival simSurv().
• make life tables mkLT().

SEERaBomb 2018.1 (2018-05-11)

NEW FEATURES

• csd() now gets second cancer factor level order from seerSet$sec and moves years in t by 0.1 for each sec level to separate error bars in plots.
• mkAbomb now sorts cols into blocks: 1) grouping; 2) PY-weighted means; and 3) sums. DG ends the 1st and py starts the last. Cols ending in G are SEERaBomb group defaults. New t is time since bombing (yrs)
• incidAbomb takes a grouped A-bomb tibble with DG and py, and forms means, sums, and incidences.
• incidSEER converts canc and popsae into a data frame with py and cases, filtering years on cancers that had not yet started in SEER.
• mkSEER now automatically maps tAML 9920's into tMDS 9987's post 2009. All 9987 cases after 2009 are ones that were mapped over, so users can undo this if they wish, but I think its best to leave it. Values of 9999=missing in canc$surv are now set to missing in mkSEER().
• pickFields now sorts picks internally, so the user no longer needs to worry about pick ordering.

SEERaBomb 2017.3

NEW FEATURES

• desc field of getFields() is now var_label() in mkSEER() output (depends on R package labelled)
• added sas names to output of getFields and pickField
• shifted dependence from XLConnect to openxlsx to get rid of rJava dependence
• mapCODs maps COD integer codes to strings in CODS
• p2s generates times between primary/first and second cancers, at the individual level

Notes

• Fixed riskVsAge() so it no longer depends on trt being "rad" and "noRad"

SEERaBomb 2017.2 (2017-08-14)

NEW FEATURES

• mkDemographics is a new function that generates median age and OS tables in an Excel file

Notes

• There is now an ASCII version of the SEER data with radiatn and chemo as rightmost columns, so please ignore my Notes below. I assume users of SEERaBomb will get this "CUSTOM" dataset by filling out the data use agreement: radiatn and chemo are now default fields in pickFields.

SEERaBomb 2017.1 (2017-04-26)

Notes

• The field radiatn is no longer in the regular SEER release, so it has been removed from the pickFields default and mkSEER no longer calls mapTrts unless the field is there (if using data released in 2016). While one can get the radiation data by signing an extra DUA, it is only available through SEER*stat (one would have to export it from there) and SEER*stat only runs on Windows (and I'm on a mac). If you need this data acquisition route and are willing to replace getFields, pickFields, and mkSEER by a new function mkSEERcrt (crt for chemo radiation therapy data out of SEER*Stat), I'm happy to add you as an author to the SEERaBomb project on GitHub. Meanwhile, I will keep data released in 2016 in ~/data/SEER13 and will place the most recent data in ~/data/SEER. Thus, scripts that use radiatn now load data from ~/data/SEER13.

SEERaBomb 2016.3

NEW FEATURES

• riskVsAge is a new function that yields risks vs attained age after a first cancer
• esd (event since diagnosis) is an msd wrapper. It uses SEER incidences instead of mortalities to yield RR time courses for user defined second cancer data.

SEERaBomb 2016.2 (2016-11-11)

NEW FEATURES

• msd now takes a ybrks vector for showing calendar year trends

Notes

• mkExcel2 is now mkExcelCsd, and mkExcel is now mkExcelTsd, to emphasize that their inputs are the outputs of csd and tsd, respectively. mkExcelTsd and tsd are internal.

SEERaBomb 2016.1 (2016-04-25)

NEW FEATURES

• AML/MDS (leukemia 2016), CLL (leukemia research 2016), and CML (AAPSJ 2016) scripts were added to doc/papers

Notes

• Many fields were deleted or renamed in the SAS file of the 2016 SEER data release. Names used in my scipts that changed were reverted to originals in getFields() to avoid downstream problems. Numprims is no longer there, so use seqnum instead. A few fields were also added to the new SEER data release.

SEERaBomb 2015.3

NEW FEATURES

• The function msd (mortality since diagnosis) computes mortality RR since diagnosis of cancer.
• The function csd (cancer since diagnosis), now replaces tsd in computing 2nd cancer RR after a 1st cancer. An added feature of csd is that it handles different intervals of years and ages at diagnosis. This changed the internal list of lists structure of the output, which getDF (instead of mkDF) converts to a data.frame (DF) that ggplot2 can use, and which mkExcel2 (instead of mkExcel) uses to make an Excel file.

Notes

• tsd, mkExcel, and mkDF are now internal functions (in terms of help pages), i.e. they can still be used by old scripts
• mkSEER no longer makes age19 in canc and it no longer makes popsga. If you still want 19-age groups use mkSEERold.

SEERaBomb 2015.2 (2015-09-07)

NEW FEATURES

• The function tsd now takes a firstS argument, a verctor of first cancers of interest. This doesn't speed things up much but it makes the output of tst easier to read and the output of mkExcel much more focused.
• The latest National Vital Statistics Report data is now included as a data.frame.

SEERaBomb 2015.1 (2015-05-05)

NEW FEATURES

• simSeerSet simulates a seerSet class object for two cancer types, A and B.
• mkSEER (mkSEER2->mkSEER and mkSEER>-mkSEERold) uses stdUS 2000 to extend single age popsa to popsae. It also makes a trt column for radiation therapy by default.

Notes

• random crashes from the C++ code have been debugged. Variants of fillPYM in straight C and R used to debug it are now in the folder doc/extraFuncs

SEERaBomb 2014.4.2

NEW FEATURES

• added US 2000 populations as 19-, 86-, and 100-age group data.frames.
• created mkSEER2 to create pooled db files directly into e.g. ~\data\SEER\mrgd

SIGNIFICANT USER-LEVEL CHANGES

• mkHema87 was removed. Its functionality is now included in mkAbomb

Notes

• fixed pickFields() to make country and state of birth strings rather than integers

SEERaBomb 2014.4.1 (2014-04-18)

NEW FEATURES

• changed default seerHome directory to ~\data\SEER to no longer assume admin rights
• updated 2010 to 2011 in mkSEER and in several help pages to match April 15,2014 SEER release
• changed mkSEER SQL default to TRUE
• added pops single ages (popsa) to binary files and all.db

SEERaBomb 2014.3

NEW FEATURES

• added seetSet to make objects of class seerSet for the pipeline seerSet->mk2D->tsd.
• added mk2D that makes two-dimensional spline fits of incidence versus age and calendar year and plot2D to look at them.
• added tsd to compute RR over various time since diagnosis intervals and mkExcel to look at the results.
• added helper functions: getBinInfo, getPY, post1PYO, getE
• mapCancs is now called within mkSEER to make a cancer field in those files as well.

Notes

• Month is no longer in the package version number and year now reflects the SEER data release year rather than the SEERaBomb release year.
• published paper scripts now use the cancer field instead of histo2 (which is no longer included in pickfields by default) and plots now also use quartz() when on a mac. The old courses folder is now called examples; scripts therein were updated and some were removed.

SEERaBomb 2013.4.3 (2013-12-12)

NEW FEATURES

• added mkAbomb() to convert RERF file lsshempy.csv into a binary and SQLite database
• added mkHema87() to convert RERF file HEMA87.DAT into a binary with column names
• sq vs ad lung incidence and survival added to doc/courses
• JCO 2013 survival plots added to doc/papers/JCO2013
• activeMS is now doc/papers/radiatEnvironBiophys2013

SIGNIFICANT USER-LEVEL CHANGES

• old demos are now examples in doc/courses

Notes

• vignettes are not possible since SEER and Abomb data must be signed off on.

SEERaBomb 2013.4.1 (2013-04-27)

NEW FEATURES

• Now handles SEER data release of April 24, 2013
• Package version number now matches latest SEER release date.

SIGNIFICANT USER-LEVEL CHANGES

• No longer handles SEER data released in 2012.

Notes

• The SEER SAS file changed: fields are no longer a continuum. The implication is that getFields is now field name centric, since I can no longer count on all fields being in the SAS file.
• Survival is now already in months in SEER, so mapping it is no longer needed. Indeed, the SAS file no longer includes a field for survival with years and months as two character strings in a field of 4 chars, though this field does still remain in the SEER data files.

SEERaBomb 0.3.0

NEW FEATURES

• eod13 and eod2 are now set to strings in pickFields to avoid errors when picked